From 4d12c5455a18e14b77badca5e27743af47339947 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 17 Aug 2016 13:03:56 -0500
Subject: Fix NetCDF/HDF5 dependency resolution problems

---
 var/spack/repos/builtin/packages/netcdf/package.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index ab40c14340..9b4d80119c 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -50,10 +50,15 @@ class Netcdf(Package):
 
     # Required for NetCDF-4 support
     depends_on("zlib")
-    depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi')
-    depends_on('hdf5+mpi', when='@4.4.1:+mpi')
-    depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi')
-    depends_on('hdf5~mpi', when='@4.4.1:~mpi')
+    depends_on('hdf5')
+
+    # Variant forwarding
+    depends_on('hdf5+mpi',  when='+mpi')
+    depends_on('hdf5~mpi',  when='~mpi')
+
+    # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later
+    # https://github.com/Unidata/netcdf-c/issues/250
+    depends_on('hdf5@:1.8', when='@:4.4.0')
 
     def install(self, spec, prefix):
         # Environment variables
-- 
cgit v1.2.3-70-g09d2


From 28537ae7b75f7001fc3c11a530a752093d7bcdc0 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 18 Aug 2016 14:40:21 -0500
Subject: Workaround until variant forwarding works properly

---
 var/spack/repos/builtin/packages/hdf5/package.py   | 2 +-
 var/spack/repos/builtin/packages/netcdf/package.py | 9 +++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index aedaf18218..70cd168cc0 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -52,7 +52,7 @@ class Hdf5(Package):
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
 
-    variant('mpi', default=False, description='Enable MPI support')
+    variant('mpi', default=True, description='Enable MPI support')
     variant('szip', default=False, description='Enable szip support')
     variant('threadsafe', default=False,
             description='Enable thread-safe capabilities')
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 9b4d80119c..5dc686c907 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -52,15 +52,16 @@ class Netcdf(Package):
     depends_on("zlib")
     depends_on('hdf5')
 
-    # Variant forwarding
-    depends_on('hdf5+mpi',  when='+mpi')
-    depends_on('hdf5~mpi',  when='~mpi')
-
     # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later
     # https://github.com/Unidata/netcdf-c/issues/250
     depends_on('hdf5@:1.8', when='@:4.4.0')
 
     def install(self, spec, prefix):
+        # Workaround until variant forwarding works properly
+        if '+mpi' in spec and spec.satisfies('^hdf5~mpi'):
+            raise RuntimeError('Invalid spec. Package netcdf requires '
+                               'hdf5+mpi, but spec asked for hdf5~mpi.')
+
         # Environment variables
         CPPFLAGS = []
         LDFLAGS  = []
-- 
cgit v1.2.3-70-g09d2


From d39b666913eaed253dc008c91616fefebb599600 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 6 Sep 2016 11:21:26 +0200
Subject: plumed : avoid linking with libgslcblas

---
 var/spack/repos/builtin/packages/plumed/package.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index 79632abf38..60dfdf7405 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -66,6 +66,8 @@ class Plumed(Package):
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
 
+    depends_on('autoconf', type='build')
+
     # Dictionary mapping PLUMED versions to the patches it provides
     # interactively
     plumed_patches = {
@@ -98,6 +100,12 @@ class Plumed(Package):
         module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
 
     def install(self, spec, prefix):
+        # This part is needed to avoid linking with gsl cblas
+        # interface which will mask the cblas interface
+        # provided by optimized libraries due to linking order
+        filter_file('-lgslcblas', '', 'configure.ac')
+        autoreconf('-ivf')
+
         # From plumed docs :
         # Also consider that this is different with respect to what some other
         # configure script does in that variables such as MPICXX are
-- 
cgit v1.2.3-70-g09d2


From fc576a40d66ad6f83fd512ce053cc83e011a1e30 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 6 Sep 2016 15:07:11 +0200
Subject: modules : ('build',) type dependencies are not accounted when
 autoloading

fixes #1681
---
 lib/spack/spack/modules.py      |  3 ++-
 lib/spack/spack/test/modules.py | 22 ++++++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 70c3c35d8c..3db08a6e90 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -120,7 +120,7 @@ def dependencies(spec, request='all'):
         return []
 
     if request == 'direct':
-        return spec.dependencies()
+        return spec.dependencies(deptype=('link', 'run'))
 
     # FIXME : during module file creation nodes seem to be visited multiple
     # FIXME : times even if cover='nodes' is given. This work around permits
@@ -133,6 +133,7 @@ def dependencies(spec, request='all'):
              spec.traverse(order='post',
                            depth=True,
                            cover='nodes',
+                           deptype=('link', 'run'),
                            root=False),
              reverse=True)]
     return [xx for ii, xx in l if not (xx in seen or seen_add(xx))]
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index 5e280d8e43..55b771fc79 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -229,6 +229,28 @@ class TclTests(MockPackagesTest):
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
 
+        # dtbuild1 has
+        # - 1 ('run',) dependency
+        # - 1 ('build','link') dependency
+        # - 1 ('build',) dependency
+        # Just make sure the 'build' dependency is not there
+        spack.modules.CONFIGURATION = configuration_autoload_direct
+        spec = spack.spec.Spec('dtbuild1')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
+        # dtbuild1 has
+        # - 1 ('run',) dependency
+        # - 1 ('build','link') dependency
+        # - 1 ('build',) dependency
+        # Just make sure the 'build' dependency is not there
+        spack.modules.CONFIGURATION = configuration_autoload_all
+        spec = spack.spec.Spec('dtbuild1')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
     def test_prerequisites(self):
         spack.modules.CONFIGURATION = configuration_prerequisites_direct
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
-- 
cgit v1.2.3-70-g09d2


From f0192edf0da6c0a2f8045202b08e3449508a1be5 Mon Sep 17 00:00:00 2001
From: Kelly Thompson <KineticTheory@users.noreply.github.com>
Date: Tue, 6 Sep 2016 07:55:37 -0600
Subject: For OpenMPI v 2+, add a configure option to provide C++ bindings.
 (#1730)

+ Starting with version 2.0, OpenMPI no longer provides C++ bindings by default
  (libmpi_cxx.so). Add a configure option to instruct the build to also build
  and install libmpi_cxx.so.
+ This MPI feature is needed by at least one spack package (moab).
---
 var/spack/repos/builtin/packages/moab/package.py    | 2 +-
 var/spack/repos/builtin/packages/openmpi/package.py | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py
index 893a543e97..4dfc5432d2 100644
--- a/var/spack/repos/builtin/packages/moab/package.py
+++ b/var/spack/repos/builtin/packages/moab/package.py
@@ -37,7 +37,7 @@ class Moab(Package):
     homepage = "https://bitbucket.org/fathomteam/moab"
     url      = "http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.3.tar.gz"
 
-    version('4.9.1', 'bcb8bee3e58c076c7f31884db119088e')
+    version('4.9.1', '19cc2189fa266181ad9109b18d0b2ab8')
     version('4.9.0', '40695d0a159040683cfa05586ad4a7c2')
     version('4.8.2', '1dddd10f162fce3cfffaedc48f6f467d')
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index ca6bd473f1..67bf6f3713 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -165,6 +165,10 @@ class Openmpi(Package):
                        "--enable-shared",
                        "--enable-static"]
 
+        # for Open-MPI 2.0:, C++ bindings are disabled by default.
+        if self.spec.satisfies('@2.0:'):
+            config_args.extend(['--enable-mpi-cxx'])
+
         if getattr(self, 'config_extra', None) is not None:
             config_args.extend(self.config_extra)
 
-- 
cgit v1.2.3-70-g09d2


From 26d45bc106015b72685b5f957739997b0c09dbcd Mon Sep 17 00:00:00 2001
From: Jeffrey Salmond <js947@users.noreply.github.com>
Date: Tue, 6 Sep 2016 14:55:58 +0100
Subject: fontconfig: add --disable-docs to configure (#1729)

---
 var/spack/repos/builtin/packages/fontconfig/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index 0d7e47f228..bed27e6e02 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -36,7 +36,9 @@ class Fontconfig(Package):
     depends_on('libxml2')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix, "--enable-libxml2")
+        configure("--prefix=%s" % prefix,
+                  "--enable-libxml2",
+                  "--disable-docs")
 
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From ccfbfcc890a23e65987f6f7ba9e34c750152bcea Mon Sep 17 00:00:00 2001
From: "Robert D. French" <robert@robertdfrench.me>
Date: Tue, 6 Sep 2016 09:56:13 -0400
Subject: ITS XML Translation Tool (#1728)

---
 .../repos/builtin/packages/itstool/package.py      | 44 ++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/itstool/package.py

diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py
new file mode 100644
index 0000000000..b8b2b4459f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/itstool/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Itstool(Package):
+    """ITS Tool allows you to translate your XML documents with PO files, using
+       rules from the W3C Internationalization Tag Set (ITS) to determine what
+       to translate and how to separate it into PO file messages."""
+
+    homepage = "http://itstool.org/"
+    url      = "http://files.itstool.org/itstool/itstool-2.0.2.tar.bz2"
+
+    version('2.0.2', 'd472d877a7bc49899a73d442085b2f93')
+    version('2.0.1', '40935cfb08228488bd45575e5f001a34')
+    version('2.0.0', 'd8c702c3e8961db83d04182c2aa4730b')
+    version('1.2.0', 'c0925f6869e33af8e7fe56848c129152')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From f34dd94166ecf92b981908153a02bd583bdff164 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 6 Sep 2016 07:55:54 -0700
Subject: Add debug command for creating tarball of install DB.

---
 lib/spack/spack/cmd/debug.py | 84 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 lib/spack/spack/cmd/debug.py

diff --git a/lib/spack/spack/cmd/debug.py b/lib/spack/spack/cmd/debug.py
new file mode 100644
index 0000000000..958eb829b4
--- /dev/null
+++ b/lib/spack/spack/cmd/debug.py
@@ -0,0 +1,84 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+from datetime import datetime
+from glob import glob
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import working_dir
+
+import spack
+from spack.util.executable import which
+
+description = "Debugging commands for troubleshooting Spack."
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='debug_command')
+    sp.add_parser('create-db-tarball',
+                  help="Create a tarball of Spack's installation metadata.")
+
+
+def _debug_tarball_suffix():
+    now = datetime.now()
+    suffix = now.strftime('%Y-%m-%d-%H%M%S')
+
+    git = which('git')
+    if not git:
+        return 'nobranch-nogit-%s' % suffix
+
+    with working_dir(spack.spack_root):
+        if not os.path.isdir('.git'):
+            return 'nobranch.nogit.%s' % suffix
+
+        symbolic = git(
+            'rev-parse', '--abbrev-ref', '--short', 'HEAD', output=str).strip()
+        commit = git(
+            'rev-parse', '--short', 'HEAD', output=str).strip()
+
+        if symbolic == commit:
+            return "nobranch.%s.%s" % (commit, suffix)
+        else:
+            return "%s.%s.%s" % (symbolic, commit, suffix)
+
+
+def create_db_tarball(args):
+    tar = which('tar')
+    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
+    tarball_path = os.path.abspath(tarball_name)
+
+    with working_dir(spack.spack_root):
+        files = [spack.installed_db._index_path]
+        files += glob('%s/*/*/*/.spack/spec.yaml' % spack.install_path)
+        files = [os.path.relpath(f) for f in files]
+
+        tar('-czf', tarball_path, *files)
+
+    tty.msg('Created %s' % tarball_name)
+
+
+def debug(parser, args):
+    action = {'create-db-tarball': create_db_tarball}
+    action[args.debug_command](args)
-- 
cgit v1.2.3-70-g09d2


From 4b471ecc6e9b48e2083194d88023d9638fdf5f2d Mon Sep 17 00:00:00 2001
From: Ben Boeckel <mathstuf@gmail.com>
Date: Thu, 3 Mar 2016 10:10:26 -0500
Subject: qt: support detecting newer SDK paths

---
 var/spack/repos/builtin/packages/qt/package.py           |  2 ++
 .../repos/builtin/packages/qt/qt4-corewlan-new-osx.patch | 16 ++++++++++++++++
 2 files changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 436702fa4e..1a664e1287 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -53,6 +53,8 @@ class Qt(Package):
     # https://github.com/xboxdrv/xboxdrv/issues/188
     patch('btn_trigger_happy.patch', when='@5.7.0:')
 
+    patch('qt4-corewlan-new-osx.patch', when='@4')
+
     # Use system openssl for security.
     # depends_on("openssl")
 
diff --git a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
new file mode 100644
index 0000000000..370edf7fa5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
@@ -0,0 +1,16 @@
+diff -Nr -U5 qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro
+--- qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro	2014-04-10 14:37:12.000000000 -0400
++++ qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro	2015-12-02 12:21:34.608585392 -0500
+@@ -3,11 +3,11 @@
+ 
+ QT = core network
+ LIBS += -framework Foundation -framework SystemConfiguration
+ 
+ contains(QT_CONFIG, corewlan) {
+-    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, "/Developer/SDKs/MacOSX10\.[67]\.sdk") {
++    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[01])\.sdk") {
+          LIBS += -framework CoreWLAN -framework Security
+     }
+ }
+ 
+ HEADERS += qcorewlanengine.h \
-- 
cgit v1.2.3-70-g09d2


From 5ba1144515985889c72eb87fff9e98ec02fb865e Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:41:16 -0400
Subject: qt: create a dbus variant

---
 var/spack/repos/builtin/packages/qt/package.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 1a664e1287..8136208184 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -47,6 +47,7 @@ class Qt(Package):
     variant('krellpatch', default=False, description="Build with openspeedshop based patch.")
     variant('mesa',       default=False, description="Depend on mesa.")
     variant('gtk',        default=False, description="Build with gtkplus.")
+    variant('dbus',       default=False, description="Build with D-Bus support.")
 
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
@@ -61,7 +62,7 @@ class Qt(Package):
     depends_on("gtkplus", when='+gtk')
     depends_on("libxml2")
     depends_on("zlib")
-    depends_on("dbus", when='@4:')
+    depends_on("dbus", when='@4:+dbus')
     depends_on("libtiff")
     depends_on("libpng@1.2.56", when='@3')
     depends_on("libpng", when='@4:')
@@ -145,7 +146,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
-        return [
+        config_args = [
             '-prefix', self.prefix,
             '-v',
             '-opensource',
@@ -154,7 +155,6 @@ class Qt(Package):
             '-shared',
             '-confirm-license',
             '-openssl-linked',
-            '-dbus-linked',
             '-optimized-qmake',
             '-no-openvg',
             '-no-pch',
@@ -162,6 +162,13 @@ class Qt(Package):
             '-no-nis'
         ]
 
+        if '+dbus' in self.spec:
+            config_args.append('-dbus-linked')
+        else:
+            config_args.append('-no-dbus')
+
+        return config_args
+
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 
-- 
cgit v1.2.3-70-g09d2


From 4c566617f791e3081c8ed869af352323bcc145c7 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:41:35 -0400
Subject: qt: make libxcb a conditional dependency

OS X doesn't have X (usually).
---
 var/spack/repos/builtin/packages/qt/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 8136208184..d17aacd1d3 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 import os
+import sys
 
 
 class Qt(Package):
@@ -78,7 +79,7 @@ class Qt(Package):
 
     # OpenGL hardware acceleration
     depends_on("mesa", when='@4:+mesa')
-    depends_on("libxcb")
+    depends_on("libxcb", when=sys.platform != 'darwin')
 
     def url_for_version(self, version):
         # URL keeps getting more complicated with every release
-- 
cgit v1.2.3-70-g09d2


From a9bfd88248683a0791a009aeed6ef5d72b0a642c Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:41:59 -0400
Subject: qt: depend on OpenSSL

OS X doesn't come with an OpenSSL supported by Qt4.
---
 var/spack/repos/builtin/packages/qt/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index d17aacd1d3..4207b3527f 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -58,7 +58,7 @@ class Qt(Package):
     patch('qt4-corewlan-new-osx.patch', when='@4')
 
     # Use system openssl for security.
-    # depends_on("openssl")
+    depends_on("openssl")
 
     depends_on("gtkplus", when='+gtk')
     depends_on("libxml2")
-- 
cgit v1.2.3-70-g09d2


From 6075abfbdb25001615d5e2e256df5fb9f5ef9906 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:42:27 -0400
Subject: qt: depend on icu4c

---
 var/spack/repos/builtin/packages/qt/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 4207b3527f..e9cab85e81 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -75,7 +75,7 @@ class Qt(Package):
     # depends_on("flex", type='build')
     # depends_on("bison", type='build')
     # depends_on("ruby", type='build')
-    # depends_on("icu4c")
+    depends_on("icu4c")
 
     # OpenGL hardware acceleration
     depends_on("mesa", when='@4:+mesa')
-- 
cgit v1.2.3-70-g09d2


From aa9faceb0332e63c2dd83d90887e03ad6c2eb837 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:42:40 -0400
Subject: qt: disable phonon support

---
 var/spack/repos/builtin/packages/qt/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index e9cab85e81..80efc83c5a 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -156,6 +156,7 @@ class Qt(Package):
             '-shared',
             '-confirm-license',
             '-openssl-linked',
+            '-no-phonon',
             '-optimized-qmake',
             '-no-openvg',
             '-no-pch',
-- 
cgit v1.2.3-70-g09d2


From 71c357e485cf1d1bd7dc24a7da3b3ad042ca2ee1 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 11:58:52 -0400
Subject: qt: support building with 10.10+ SDKs

---
 var/spack/repos/builtin/packages/qt/package.py     |  1 +
 .../repos/builtin/packages/qt/qt4-el-capitan.patch | 31 ++++++++++++++++++++++
 2 files changed, 32 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 80efc83c5a..3f62c5c77f 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -56,6 +56,7 @@ class Qt(Package):
     patch('btn_trigger_happy.patch', when='@5.7.0:')
 
     patch('qt4-corewlan-new-osx.patch', when='@4')
+    patch('qt4-el-capitan.patch', when='@4')
 
     # Use system openssl for security.
     depends_on("openssl")
diff --git a/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch b/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch
new file mode 100644
index 0000000000..35f154d3b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-el-capitan.patch
@@ -0,0 +1,31 @@
+From 27aa46933bb32a88c310fe5918a49a3f34d65dfe Mon Sep 17 00:00:00 2001
+From: Mike McQuaid <mike@mikemcquaid.com>
+Date: Sun, 13 Sep 2015 11:55:59 +0100
+Subject: [PATCH] Fix El Capitan build.
+
+---
+ src/gui/painting/qpaintengine_mac.cpp | 8 +-------
+ 1 file changed, 1 insertion(+), 7 deletions(-)
+
+diff --git a/src/gui/painting/qpaintengine_mac.cpp b/src/gui/painting/qpaintengine_mac.cpp
+index 4aa0668..63b646d 100644
+--- a/src/gui/painting/qpaintengine_mac.cpp
++++ b/src/gui/painting/qpaintengine_mac.cpp
+@@ -340,13 +340,7 @@ CGColorSpaceRef QCoreGraphicsPaintEngine::macDisplayColorSpace(const QWidget *wi
+     }
+ 
+     // Get the color space from the display profile.
+-    CGColorSpaceRef colorSpace = 0;
+-    CMProfileRef displayProfile = 0;
+-    CMError err = CMGetProfileByAVID((CMDisplayIDType)displayID, &displayProfile);
+-    if (err == noErr) {
+-        colorSpace = CGColorSpaceCreateWithPlatformColorSpace(displayProfile);
+-        CMCloseProfile(displayProfile);
+-    }
++    CGColorSpaceRef colorSpace = CGDisplayCopyColorSpace(displayID);
+ 
+     // Fallback: use generic DeviceRGB
+     if (colorSpace == 0)
+-- 
+2.3.8 (Apple Git-58)
+
-- 
cgit v1.2.3-70-g09d2


From 3df1eeccb9b6e4c302db825b2fe6338462740fe8 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:53:21 -0400
Subject: qt: setup the sdk and platform arguments

---
 var/spack/repos/builtin/packages/qt/package.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 3f62c5c77f..8c918e4c0b 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -170,6 +170,24 @@ class Qt(Package):
         else:
             config_args.append('-no-dbus')
 
+        if sys.platform == 'darwin':
+            sdkpath = which('xcrun')('--show-sdk-path', output=str)
+            config_args.extend([
+                    '-sdk', sdkpath.strip(),
+                ])
+            use_clang_platform = False
+            if self.spec.compiler.name == 'clang' and \
+               str(self.spec.compiler.version).endwith('-apple'):
+                use_clang_platform = True
+            # No one uses gcc-4.2.1 anymore; this is clang.
+            if self.spec.compiler.name == 'gcc' and \
+               str(self.spec.compiler.version) == '4.2.1':
+                use_clang_platform = True
+            if use_clang_platform:
+                config_args.extend([
+                        '-platform', 'unsupported/macx-clang',
+                    ])
+
         return config_args
 
     # Don't disable all the database drivers, but should
@@ -190,7 +208,12 @@ class Qt(Package):
     def configure(self):
         configure('-fast',
                   '-no-webkit',
+<<<<<<< HEAD
                   '{0}-gtkstyle'.format('' if '+gtk' in self.spec else '-no'),
+||||||| parent of e72b834... qt: setup the sdk and platform arguments
+=======
+                  '-arch', str(self.spec.architecture.target),
+>>>>>>> e72b834... qt: setup the sdk and platform arguments
                   *self.common_config_args)
 
     @when('@5.0:5.6')
-- 
cgit v1.2.3-70-g09d2


From b810a113af9ce32b7e83d122187878cf1b014631 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 10:58:16 -0400
Subject: pixman: disable mmx

---
 var/spack/repos/builtin/packages/pixman/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 39041587f5..41aad0c90a 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -39,6 +39,7 @@ class Pixman(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
+                  "--disable-mmx",
                   "--disable-gtk")
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From a05a6456d5aa69fdc369b99134227a4958b9832e Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 11:00:58 -0400
Subject: glib: build on macos

---
 .../packages/glib/no-Werror=format-security.patch     | 16 ++++++++++++++++
 var/spack/repos/builtin/packages/glib/package.py      | 19 ++++++++++++++++++-
 2 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch

diff --git a/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch b/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch
new file mode 100644
index 0000000000..cfcfe424be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/no-Werror=format-security.patch
@@ -0,0 +1,16 @@
+--- a/configure.ac	2016-08-16 11:57:34.000000000 -0400
++++ b/configure.ac	2016-08-16 11:57:36.000000000 -0400
+@@ -3357,11 +3357,11 @@
+ 			      enable_compile_warnings=yes)
+ AS_IF([test "x$enable_compile_warnings" = xyes], [
+   CC_CHECK_FLAGS_APPEND([GLIB_WARN_CFLAGS], [CFLAGS], [\
+    -Wall -Wstrict-prototypes -Werror=declaration-after-statement \
+    -Werror=missing-prototypes -Werror=implicit-function-declaration \
+-   -Werror=pointer-arith -Werror=init-self -Werror=format-security \
+-   -Werror=format=2 -Werror=missing-include-dirs])
++   -Werror=pointer-arith -Werror=init-self \
++   -Werror=missing-include-dirs])
+ ])
+ AC_SUBST(GLIB_WARN_CFLAGS)
+ 
+ #
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 94ef95e7ab..3e687ccd95 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import os
 
 
 class Glib(Package):
@@ -38,14 +39,20 @@ class Glib(Package):
     version('2.48.1', '67bd3b75c9f6d5587b457dc01cdcd5bb')
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('pkg-config', type='build')
     depends_on('libffi')
     depends_on('zlib')
-    depends_on('pkg-config', type='build')
     depends_on('gettext')
     depends_on('pcre+utf', when='@2.48:')
 
     # The following patch is needed for gcc-6.1
     patch('g_date_strftime.patch', when='@2.42.1')
+    # Clang doesn't seem to acknowledge the pragma lines to disable the -Werror
+    # around a legitimate usage.
+    patch('no-Werror=format-security.patch')
 
     def url_for_version(self, version):
         """Handle glib's version-based custom URLs."""
@@ -53,6 +60,16 @@ class Glib(Package):
         return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version)
 
     def install(self, spec, prefix):
+        autoreconf = which("autoreconf")
+        autoreconf("--install", "--verbose", "--force",
+                   "-I", "config",
+                   "-I", os.path.join(spec['pkg-config'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['automake'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['libtool'].prefix,
+                                      "share", "aclocal"),
+                   )
         configure("--prefix=%s" % prefix)
         make()
         make("install", parallel=False)
-- 
cgit v1.2.3-70-g09d2


From 4687860885fc06ba8d911e99408b6a9f4221c64e Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Thu, 25 Aug 2016 15:57:29 -0400
Subject: qt: force the 10.9 SDK on macos

The 10.11 SDK fails to configure.
---
 var/spack/repos/builtin/packages/qt/package.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 8c918e4c0b..78bc4bed9c 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -171,7 +171,10 @@ class Qt(Package):
             config_args.append('-no-dbus')
 
         if sys.platform == 'darwin':
-            sdkpath = which('xcrun')('--show-sdk-path', output=str)
+            sdkpath = which('xcrun')('--show-sdk-path',
+                                     # XXX(macos): the 10.11 SDK fails to configure.
+                                     '--sdk', 'macosx10.9',
+                                     output=str)
             config_args.extend([
                     '-sdk', sdkpath.strip(),
                 ])
@@ -208,12 +211,8 @@ class Qt(Package):
     def configure(self):
         configure('-fast',
                   '-no-webkit',
-<<<<<<< HEAD
                   '{0}-gtkstyle'.format('' if '+gtk' in self.spec else '-no'),
-||||||| parent of e72b834... qt: setup the sdk and platform arguments
-=======
                   '-arch', str(self.spec.architecture.target),
->>>>>>> e72b834... qt: setup the sdk and platform arguments
                   *self.common_config_args)
 
     @when('@5.0:5.6')
-- 
cgit v1.2.3-70-g09d2


From 67462ca65a00a718e7713ecd6257de5309de4a14 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Mon, 29 Aug 2016 15:41:53 -0400
Subject: qt: fix pcre header conflict in javascriptcore

---
 var/spack/repos/builtin/packages/qt/package.py           |  1 +
 .../builtin/packages/qt/qt4-pcre-include-conflict.patch  | 16 ++++++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 78bc4bed9c..25c896074b 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -56,6 +56,7 @@ class Qt(Package):
     patch('btn_trigger_happy.patch', when='@5.7.0:')
 
     patch('qt4-corewlan-new-osx.patch', when='@4')
+    patch('qt4-pcre-include-conflict.patch', when='@4')
     patch('qt4-el-capitan.patch', when='@4')
 
     # Use system openssl for security.
diff --git a/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch b/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch
new file mode 100644
index 0000000000..854e564bfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-pcre-include-conflict.patch
@@ -0,0 +1,16 @@
+diff -U5 -Nru qt-everywhere-opensource-src-4.8.6/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h qt-everywhere-opensource-src-4.8.6.pcre/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h
+--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h	2014-04-10 14:37:12.000000000 -0400
++++ qt-everywhere-opensource-src-4.8.6.pcre/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h	2016-08-29 15:30:02.216546252 -0400
+@@ -32,11 +32,11 @@
+ 
+ #include "MacroAssembler.h"
+ #include "RegexPattern.h"
+ #include <UString.h>
+ 
+-#include <pcre.h>
++#include <pcre/pcre.h>
+ struct JSRegExp; // temporary, remove when fallback is removed.
+ 
+ #if CPU(X86) && !COMPILER(MSVC)
+ #define YARR_CALL __attribute__ ((regparm (3)))
+ #else
-- 
cgit v1.2.3-70-g09d2


From fca26c0b7916142471a2dda53ac1448a912eedda Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Mon, 29 Aug 2016 17:26:22 -0400
Subject: qt: make -no-phonon specific to qt4

---
 var/spack/repos/builtin/packages/qt/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 25c896074b..5fdd07c7a5 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -158,7 +158,6 @@ class Qt(Package):
             '-shared',
             '-confirm-license',
             '-openssl-linked',
-            '-no-phonon',
             '-optimized-qmake',
             '-no-openvg',
             '-no-pch',
@@ -166,6 +165,9 @@ class Qt(Package):
             '-no-nis'
         ]
 
+        if '@4' in self.spec:
+            config_args.append('-no-phonon')
+
         if '+dbus' in self.spec:
             config_args.append('-dbus-linked')
         else:
-- 
cgit v1.2.3-70-g09d2


From 112122bc28bea05e960691f4ee87acd53d15d509 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Tue, 30 Aug 2016 10:52:11 -0400
Subject: qt: progress on qt5.5 on osx

Qt5.5 searches for the SDK itself and just ignores environment variables
like CC and CXX, skipping the spack wrappers.
---
 var/spack/repos/builtin/packages/qt/package.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 5fdd07c7a5..3217b90215 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -173,7 +173,16 @@ class Qt(Package):
         else:
             config_args.append('-no-dbus')
 
-        if sys.platform == 'darwin':
+        if '@5:' in self.spec and sys.platform == 'darwin':
+            config_args.extend([
+                    '-no-xinput2',
+                    '-no-xcb-xlib',
+                    '-no-pulseaudio',
+                    '-no-alsa',
+                    '-no-gtkstyle',
+                ])
+
+        if '@4' in self.spec and sys.platform == 'darwin':
             sdkpath = which('xcrun')('--show-sdk-path',
                                      # XXX(macos): the 10.11 SDK fails to configure.
                                      '--sdk', 'macosx10.9',
@@ -222,7 +231,6 @@ class Qt(Package):
     def configure(self):
         configure('-no-eglfs',
                   '-no-directfb',
-                  '-qt-xcb',
                   '{0}-gtkstyle'.format('' if '+gtk' in self.spec else '-no'),
                   '-skip', 'qtwebkit',
                   *self.common_config_args)
-- 
cgit v1.2.3-70-g09d2


From 77611913c68bda147ec778215518abd5a09241e2 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Tue, 6 Sep 2016 16:02:25 -0400
Subject: qt: only pass -qt-xcb on non-OS X

---
 var/spack/repos/builtin/packages/qt/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 3217b90215..3032e81f78 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -237,12 +237,18 @@ class Qt(Package):
 
     @when('@5.7:')
     def configure(self):
+        args = self.common_config_args
+
+        if not sys.platform == 'darwin':
+            args.extend([
+                    '-qt-xcb',
+                ])
+
         configure('-no-eglfs',
                   '-no-directfb',
-                  '-qt-xcb',
                   '{0}-gtk'.format('' if '+gtk' in self.spec else '-no'),
                   '-skip', 'webengine',
-                  *self.common_config_args)
+                  *args)
 
     def install(self, spec, prefix):
         self.configure()
-- 
cgit v1.2.3-70-g09d2


From d55b17dd65a4b33d6ba548e1f18522b7b2681b6f Mon Sep 17 00:00:00 2001
From: Ian Lee <IanLee1521@gmail.com>
Date: Tue, 6 Sep 2016 14:52:44 -0700
Subject: Fixed broken link in README (#1733)

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0b6127c541..ec2da3934e 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://spack.readthedocs.io/latest/features.html)
+[Feature Overview](http://spack.readthedocs.io/en/latest/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
-- 
cgit v1.2.3-70-g09d2


From fd02a140c4b71a948fb478b810dce91ea0ab5ae8 Mon Sep 17 00:00:00 2001
From: scheibelp <scheibel1@llnl.gov>
Date: Wed, 7 Sep 2016 07:02:24 -0700
Subject: Fix fetching non-expanded resources from mirrors (#1310)

This closes #1308, where fetching a non-expanded resource from a mirror
will cause an error.

This also ensures that when a URL resource is fetched from a mirror,
that it will be named as though it were retrieved from the original
URL. This is particularly useful for non-expanded resources since it
ensures that the resource name is consistent for the installation
(this is less important for expanded resources because the build takes
place inside the expanded resource).
---
 lib/spack/spack/cmd/test.py       |  2 +-
 lib/spack/spack/fetch_strategy.py | 11 +++++------
 lib/spack/spack/stage.py          | 34 +++++++++++++++++++---------------
 3 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py
index bf7342f606..52c2a06778 100644
--- a/lib/spack/spack/cmd/test.py
+++ b/lib/spack/spack/cmd/test.py
@@ -56,7 +56,7 @@ class MockCache(object):
     def store(self, copyCmd, relativeDst):
         pass
 
-    def fetcher(self, targetPath, digest):
+    def fetcher(self, targetPath, digest, **kwargs):
         return MockCacheFetcher()
 
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index c69a23033c..4349e32d4f 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -170,12 +170,11 @@ class URLFetchStrategy(FetchStrategy):
             tty.msg("Already downloaded %s" % self.archive_file)
             return
 
-        possible_files = self.stage.expected_archive_files
         save_file = None
         partial_file = None
-        if possible_files:
-            save_file = self.stage.expected_archive_files[0]
-            partial_file = self.stage.expected_archive_files[0] + '.part'
+        if self.stage.save_filename:
+            save_file = self.stage.save_filename
+            partial_file = self.stage.save_filename + '.part'
 
         tty.msg("Trying to fetch from %s" % self.url)
 
@@ -858,9 +857,9 @@ class FsCache(object):
         mkdirp(os.path.dirname(dst))
         fetcher.archive(dst)
 
-    def fetcher(self, targetPath, digest):
+    def fetcher(self, targetPath, digest, **kwargs):
         url = "file://" + join_path(self.root, targetPath)
-        return CacheURLFetchStrategy(url, digest)
+        return CacheURLFetchStrategy(url, digest, **kwargs)
 
     def destroy(self):
         shutil.rmtree(self.root, ignore_errors=True)
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index c0705a89c8..b659cfb2fb 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -216,9 +216,9 @@ class Stage(object):
     def expected_archive_files(self):
         """Possible archive file paths."""
         paths = []
-        if isinstance(self.fetcher, fs.URLFetchStrategy):
+        if isinstance(self.default_fetcher, fs.URLFetchStrategy):
             paths.append(os.path.join(
-                self.path, os.path.basename(self.fetcher.url)))
+                self.path, os.path.basename(self.default_fetcher.url)))
 
         if self.mirror_path:
             paths.append(os.path.join(
@@ -226,19 +226,19 @@ class Stage(object):
 
         return paths
 
+    @property
+    def save_filename(self):
+        possible_filenames = self.expected_archive_files
+        if possible_filenames:
+            # This prefers using the URL associated with the default fetcher if
+            # available, so that the fetched resource name matches the remote
+            # name
+            return possible_filenames[0]
+
     @property
     def archive_file(self):
         """Path to the source archive within this stage directory."""
-        paths = []
-        if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(
-                self.path, os.path.basename(self.fetcher.url)))
-
-        if self.mirror_path:
-            paths.append(os.path.join(
-                self.path, os.path.basename(self.mirror_path)))
-
-        for path in paths:
+        for path in self.expected_archive_files:
             if os.path.exists(path):
                 return path
         else:
@@ -301,8 +301,10 @@ class Stage(object):
             # then use the same digest.  `spack mirror` ensures that
             # the checksum will be the same.
             digest = None
+            expand = True
             if isinstance(self.default_fetcher, fs.URLFetchStrategy):
                 digest = self.default_fetcher.digest
+                expand = self.default_fetcher.expand_archive
 
             # Have to skip the checksum for things archived from
             # repositories.  How can this be made safer?
@@ -310,9 +312,11 @@ class Stage(object):
 
             # Add URL strategies for all the mirrors with the digest
             for url in urls:
-                fetchers.insert(0, fs.URLFetchStrategy(url, digest))
-            fetchers.insert(0, spack.fetch_cache.fetcher(self.mirror_path,
-                                                         digest))
+                fetchers.insert(
+                    0, fs.URLFetchStrategy(url, digest, expand=expand))
+            fetchers.insert(
+                0, spack.fetch_cache.fetcher(
+                    self.mirror_path, digest, expand=expand))
 
             # Look for the archive in list_url
             package_name = os.path.dirname(self.mirror_path)
-- 
cgit v1.2.3-70-g09d2


From 0586b388df87f98194052ab9bfb9283ed569e962 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 8 Sep 2016 11:02:10 -0500
Subject: Add latest version of libpng, ncview depends on libpng (#1502)

* Add latest version of libpng

* ncview depends on libpng
---
 var/spack/repos/builtin/packages/libpng/package.py | 4 +++-
 var/spack/repos/builtin/packages/ncview/package.py | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index 1afe4911e6..c3a595d12d 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -30,6 +30,7 @@ class Libpng(Package):
     homepage = "http://www.libpng.org/pub/png/libpng.html"
     url      = "http://download.sourceforge.net/libpng/libpng-1.6.16.tar.gz"
 
+    version('1.6.24', '65213080dd30a9b16193d9b83adc1ee9')
     version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d')
     version('1.6.15', '829a256f3de9307731d4f52dc071916d')
     version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
@@ -37,9 +38,10 @@ class Libpng(Package):
     version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330')
     version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee')
 
-    depends_on('zlib')
+    depends_on('zlib@1.0.4:')  # 1.2.5 or later recommended
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
+        make("check")
         make("install")
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
index f61e6984b5..4abc09deb0 100644
--- a/var/spack/repos/builtin/packages/ncview/package.py
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -34,6 +34,7 @@ class Ncview(Package):
 
     depends_on("netcdf")
     depends_on("udunits2")
+    depends_on("libpng")
 
     # OS Dependencies
     # Ubuntu: apt-get install libxaw7-dev
-- 
cgit v1.2.3-70-g09d2


From 06d8a3ad239f17a2b766d0ec14dd743da7970461 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 8 Sep 2016 11:02:38 -0500
Subject: Add missing dependency for run-doc-tests (#1691)

---
 share/spack/qa/check_dependencies | 3 +++
 share/spack/qa/run-doc-tests      | 1 +
 2 files changed, 4 insertions(+)

diff --git a/share/spack/qa/check_dependencies b/share/spack/qa/check_dependencies
index 08fad9cdc9..cf3d204f48 100755
--- a/share/spack/qa/check_dependencies
+++ b/share/spack/qa/check_dependencies
@@ -27,6 +27,9 @@ for dep in "$@"; do
                 spack_package=py-flake8
                 pip_package=flake8
                 ;;
+            dot)
+                spack_package=graphviz
+                ;;
             git)
                 spack_package=git
                 ;;
diff --git a/share/spack/qa/run-doc-tests b/share/spack/qa/run-doc-tests
index 96b76a216e..67701167aa 100755
--- a/share/spack/qa/run-doc-tests
+++ b/share/spack/qa/run-doc-tests
@@ -20,6 +20,7 @@ DOC_DIR="$SPACK_ROOT/lib/spack/docs"
 deps=(
     sphinx-apidoc
     sphinx-build
+    dot
     git
     hg
     svn
-- 
cgit v1.2.3-70-g09d2


From a22f5d8d8691dd12309ebdb613c01341b55da1c3 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 8 Sep 2016 11:02:56 -0500
Subject: Don't overwrite PYTHONPATH in docs Makefile (#1693)

---
 lib/spack/docs/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/docs/Makefile b/lib/spack/docs/Makefile
index 95d26041b7..bdbdab7e8b 100644
--- a/lib/spack/docs/Makefile
+++ b/lib/spack/docs/Makefile
@@ -7,7 +7,7 @@ SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
 
-export PYTHONPATH = ../../spack
+export PYTHONPATH := ../../spack:$(PYTHONPATH)
 APIDOC_FILES  = spack*.rst
 
 # Internal variables.
-- 
cgit v1.2.3-70-g09d2


From ff7c0335ff7fc0b07a013724b39d5de87c51e8e3 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 8 Sep 2016 15:15:42 -0400
Subject: Declare fontconfig dependency on pkg-config (#1686)

---
 var/spack/repos/builtin/packages/fontconfig/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index bed27e6e02..311156378a 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -34,6 +34,7 @@ class Fontconfig(Package):
 
     depends_on('freetype')
     depends_on('libxml2')
+    depends_on('pkg-config', type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
-- 
cgit v1.2.3-70-g09d2


From e06a0271a4400f24016fa308e958fa5f114ba06d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 8 Sep 2016 16:27:47 -0400
Subject: New package h5hut (#1737)

* New package h5hut -- High-Performance I/O Library for Particle-based Simulations

* Set up MPI compilers

* Add version 1.8.12 to HDF5

* Correct Sphinx error
---
 var/spack/repos/builtin/packages/h5hut/package.py | 70 +++++++++++++++++++++++
 var/spack/repos/builtin/packages/hdf5/package.py  |  1 +
 2 files changed, 71 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/h5hut/package.py

diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py
new file mode 100644
index 0000000000..1501384493
--- /dev/null
+++ b/var/spack/repos/builtin/packages/h5hut/package.py
@@ -0,0 +1,70 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class H5hut(Package):
+    """H5hut (HDF5 Utility Toolkit)
+    High-Performance I/O Library for Particle-based Simulations
+    """
+
+    homepage = "https://amas.psi.ch/H5hut/"
+    url      = "https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/H5hut-1.99.13.tar.gz"
+
+    version("1.99.13", "2a07a449afe50534de006ac6954a421a")
+
+    variant("fortran", default=True, description="Enable Fortran support")
+    variant("mpi", default=False, description="Enable MPI support")
+
+    depends_on("autoconf @2.60:", type="build")
+    depends_on("automake", type="build")
+    depends_on("hdf5 +mpi", when="+mpi")
+    depends_on("hdf5 @1.8:")
+    # h5hut +mpi uses the obsolete function H5Pset_fapl_mpiposix:
+    depends_on("hdf5 @:1.8.12", when="+mpi")
+    depends_on("libtool", type="build")
+    depends_on("mpi", when="+mpi")
+
+    def install(self, spec, prefix):
+        autogen = Executable("./autogen.sh")
+        autogen()
+        configopts = ["--prefix={0}".format(prefix)]
+        if "+fortran" in spec:
+            if not self.compiler.fc:
+                raise RuntimeError(
+                    "Cannot build Fortran variant without a Fortran compiler")
+            configopts.append("--enable-fortran")
+        if "+mpi" in spec:
+            configopts.extend([
+                "--enable-parallel",
+                "CC=%s" % spec["mpi"].mpicc,
+                "CXX=%s" % spec["mpi"].mpicxx])
+            if "+fortran" in spec:
+                configopts.append("FC=%s" % spec["mpi"].mpifc)
+        configure(*configopts)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 70cd168cc0..5984e50f42 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -43,6 +43,7 @@ class Hdf5(Package):
     version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
     version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
+    version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
 
     variant('debug', default=False,
             description='Builds a debug version of the library')
-- 
cgit v1.2.3-70-g09d2


From 8249108cc6ef82b954ed5b5eabaff88be42ee2b8 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 9 Sep 2016 09:56:11 -0400
Subject: Qthreads: Switch back to using tarball to get released version
 (#1739)

* Qthreads: Switch back to using tarball for download

* Don't require autotools any more

* Re-enable autotools

* Remove autotools again

* Use .tar.bz tarball; remove outdated code
---
 var/spack/repos/builtin/packages/qthreads/ldflags.patch | 11 -----------
 var/spack/repos/builtin/packages/qthreads/package.py    | 17 ++---------------
 2 files changed, 2 insertions(+), 26 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/qthreads/ldflags.patch

diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
deleted file mode 100644
index 0c15eab386..0000000000
--- a/var/spack/repos/builtin/packages/qthreads/ldflags.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -40456,7 +40456,7 @@
-   hwloc_saved_LDFLAGS="$LDFLAGS"
-   if test "x$with_hwloc" != x; then
-   CPPFLAGS="-I$with_hwloc/include $CPPFLAGS"
--		 LDFLAGS="-L$with_hwloc/lib $CPPFLAGS"
-+		 LDFLAGS="-L$with_hwloc/lib $LDFLAGS"
- fi
-   
-   
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index 8d5cc87062..c68d8dba6c 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -38,28 +38,15 @@ class Qthreads(Package):
        attain either state."""
     homepage = "http://www.cs.sandia.gov/qthreads/"
 
-    # Google Code has stopped serving tarballs
-    # We assume the tarballs will soon be available on Github instead
-    # url = "https://qthreads.googlecode.com/files/qthread-1.10.tar.bz2"
-    # version('1.10', '5af8c8bbe88c2a6d45361643780d1671')
+    url = "https://github.com/Qthreads/qthreads/releases/download/1.10/qthread-1.10.tar.bz2"
+    version("1.10", "d1cf3cf3f30586921359f7840171e551")
 
-    # Temporarily install from a git branch
-    url = "https://github.com/Qthreads/qthreads"
-    version("1.10",
-            git="https://github.com/Qthreads/qthreads",
-            branch="release-1.10")
-
-    # patch("ldflags.patch")
     patch("restrict.patch")
     patch("trap.patch")
 
-    depends_on("autoconf", type="build")
-    depends_on("automake", type="build")
     depends_on("hwloc")
 
     def install(self, spec, prefix):
-        autogen = Executable("./autogen.sh")
-        autogen()
         configure("--prefix=%s" % prefix,
                   "--enable-guard-pages",
                   "--with-topology=hwloc",
-- 
cgit v1.2.3-70-g09d2


From 567d67fae2e2c014266c0df249ecd41d76b0cc6a Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 9 Sep 2016 15:57:49 -0400
Subject: Add libiconv dependency for git (#1468)

Also remove "--without-pcre" flag that git does not understand any more.
---
 var/spack/repos/builtin/packages/git/package.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index ed058e0a68..a687b2bb35 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -54,25 +54,27 @@ class Git(Package):
     # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
     # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
 
-    depends_on("openssl")
     depends_on("autoconf", type='build')
     depends_on("curl")
     depends_on("expat")
     depends_on("gettext")
-    depends_on("zlib")
+    depends_on("libiconv")
+    depends_on("openssl")
     depends_on("pcre")
     depends_on("perl")
+    depends_on("zlib")
 
     def install(self, spec, prefix):
         env['LDFLAGS'] = "-L%s" % spec['gettext'].prefix.lib + " -lintl"
         configure_args = [
             "--prefix=%s" % prefix,
-            "--with-libpcre=%s" % spec['pcre'].prefix,
-            "--with-openssl=%s" % spec['openssl'].prefix,
-            "--with-zlib=%s" % spec['zlib'].prefix,
             "--with-curl=%s" % spec['curl'].prefix,
             "--with-expat=%s" % spec['expat'].prefix,
+            "--with-iconv=%s" % spec['libiconv'].prefix,
+            "--with-libpcre=%s" % spec['pcre'].prefix,
+            "--with-openssl=%s" % spec['openssl'].prefix,
             "--with-perl=%s" % join_path(spec['perl'].prefix.bin, 'perl'),
+            "--with-zlib=%s" % spec['zlib'].prefix,
         ]
 
         which('autoreconf')('-i')
-- 
cgit v1.2.3-70-g09d2


From 1d09d1a4e2a71582acdc8fc4a0a2b7f621c11467 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 9 Sep 2016 16:50:37 -0400
Subject: Update netlib-lapack to 3.6.1 (#1597)

---
 var/spack/repos/builtin/packages/netlib-lapack/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 08c94a5c9b..93d64fb466 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -36,6 +36,7 @@ class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
+    version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
     version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
     version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
-- 
cgit v1.2.3-70-g09d2


From 4a1df7e0b22409d0cf9265fbc7952adb442212e2 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <elizabeth.fischer@columbia.edu>
Date: Wed, 14 Sep 2016 10:56:08 -0400
Subject: Resolved issues of py-pillow, py-scipy and binutils dependencies. 
 Resolves #1506

py-pillow: Remove version dependency on binutils@2.25.  In tests, it works just fine with binutils@2.26.

Fixed flake8 issues.
---
 var/spack/repos/builtin/packages/binutils/package.py  | 3 +--
 var/spack/repos/builtin/packages/py-pillow/package.py | 6 ++++--
 var/spack/repos/builtin/packages/py-scipy/package.py  | 3 ++-
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index e329e6fd7a..af4d87d5c2 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -31,9 +31,8 @@ class Binutils(Package):
     homepage = "http://www.gnu.org/software/binutils/"
     url      = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
 
-    # 2.26 is incompatible with py-pillow build for some reason.
     version('2.26', '64146a0faa3b411ba774f47d41de239f')
-    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True)
+    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
     version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
     version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 1d8b3faa6f..41b52de216 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -32,7 +32,8 @@ class PyPillow(Package):
     capabilities."""
 
     homepage = "https://python-pillow.org/"
-    url      = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
+    url = "https://pypi.python.org/packages/source" + \
+        "/P/Pillow/Pillow-3.0.0.tar.gz"
 
     # TODO: This version should be deleted once the next release comes out.
     # TODO: It fixes a bug that prevented us from linking to Tk/Tcl.
@@ -65,7 +66,8 @@ class PyPillow(Package):
 
     # Required dependencies
     extends('python')
-    depends_on('binutils', type='build')
+    # Known not to work with 2.23, 2.25
+    depends_on('binutils@2.26:', type='build')
     depends_on('py-setuptools', type='build')
 
     # Recommended dependencies
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index cab516e1df..58e08888ff 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -28,7 +28,7 @@ from spack import *
 class PyScipy(Package):
     """Scientific Library for Python."""
     homepage = "http://www.scipy.org/"
-    url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
+    url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
     version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
@@ -36,6 +36,7 @@ class PyScipy(Package):
 
     extends('python')
     depends_on('py-nose', type='build')
+    depends_on('binutils@2.26:', type='build')
     depends_on('py-numpy+blas+lapack', type=nolink)
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From 595ec7e0345c3b1831efbcd39f8b254e3a5fe396 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <elizabeth.fischer@columbia.edu>
Date: Wed, 14 Sep 2016 16:50:17 -0400
Subject: Bug fix capturing which packages work with which binutils.

---
 var/spack/repos/builtin/packages/py-pillow/package.py | 3 +--
 var/spack/repos/builtin/packages/py-scipy/package.py  | 1 +
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 41b52de216..c8e5a96f67 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -66,8 +66,7 @@ class PyPillow(Package):
 
     # Required dependencies
     extends('python')
-    # Known not to work with 2.23, 2.25
-    depends_on('binutils@2.26:', type='build')
+    depends_on('binutils', type='build')
     depends_on('py-setuptools', type='build')
 
     # Recommended dependencies
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 58e08888ff..83a69c5682 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -36,6 +36,7 @@ class PyScipy(Package):
 
     extends('python')
     depends_on('py-nose', type='build')
+    # Known not to work with 2.23, 2.25
     depends_on('binutils@2.26:', type='build')
     depends_on('py-numpy+blas+lapack', type=nolink)
 
-- 
cgit v1.2.3-70-g09d2


From a954d0976af30df460689fa817599f6c221b252a Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Wed, 14 Sep 2016 16:52:33 -0400
Subject: Put back full-length URL.

---
 var/spack/repos/builtin/packages/py-pillow/package.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index c8e5a96f67..211e3b4199 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -32,8 +32,7 @@ class PyPillow(Package):
     capabilities."""
 
     homepage = "https://python-pillow.org/"
-    url = "https://pypi.python.org/packages/source" + \
-        "/P/Pillow/Pillow-3.0.0.tar.gz"
+    url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
 
     # TODO: This version should be deleted once the next release comes out.
     # TODO: It fixes a bug that prevented us from linking to Tk/Tcl.
-- 
cgit v1.2.3-70-g09d2


From 2a823fbdfdf9d24d66d3b80ee579532e3eea4c74 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Wed, 14 Sep 2016 22:35:57 -0400
Subject: [RtM] Added py-proj/package.py  (RtM = Ready to Merge) (#717)

* Added py-proj package

* Added bug-fix patched version to the package.

* Removed dependency of py-proj on proj.

* py-proj: Added missing dependency

* py-proj: Removed versions from forked repos, now that necessary bug fixes have been merged into the main repo.

* Update package.py

Added a blank line that Travis wanted.

* 1. Added copyright
2. Used setup_py
3. Added type='build' for dependencies.
---
 .../repos/builtin/packages/py-proj/package.py      | 52 ++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-proj/package.py

diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py
new file mode 100644
index 0000000000..2835bfcca8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-proj/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by David Beckingsale, david@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class PyProj(Package):
+    """Python interface to the PROJ.4 Library."""
+    homepage = "http://jswhit.github.io/pyproj/"
+    url      = "https://github.com/jswhit/pyproj/tarball/v1.9.5.1rel"
+
+    # This is not a tagged release of pyproj.
+    # The changes in this "version" fix some bugs, especially with Python3 use.
+    version('1.9.5.1.1', 'd035e4bc704d136db79b43ab371b27d2',
+        url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f')
+
+    version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835')
+
+    extends('python')
+
+    depends_on('py-cython', type='build')
+    depends_on('py-setuptools', type='build')
+
+    # NOTE: py-proj does NOT depends_on('proj').
+    # The py-proj git repo actually includes the correct version of PROJ.4,
+    # which is built internally as part of the py-proj build.
+    # Adding depends_on('proj') will cause mysterious build errors.
+
+    def install(self, spec, prefix):
+        setup_py('install', '--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From 6117ef44e40358afe11e629309b344658cbe6cc3 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Wed, 14 Sep 2016 22:42:14 -0400
Subject: Make libstdc++-detection work on Darwin (#1778)

---
 lib/spack/spack/abi.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
index 064abb9782..7a6f9c3f40 100644
--- a/lib/spack/spack/abi.py
+++ b/lib/spack/spack/abi.py
@@ -54,10 +54,10 @@ class ABI(object):
         output = None
         if compiler.cxx:
             rungcc = Executable(compiler.cxx)
-            libname = "libstdc++.so"
+            libname = "libstdc++." + dso_suffix
         elif compiler.cc:
             rungcc = Executable(compiler.cc)
-            libname = "libgcc_s.so"
+            libname = "libgcc_s." + dso_suffix
         else:
             return None
         try:
-- 
cgit v1.2.3-70-g09d2


From 7fd44a983d5d33b7571468c8726ec5692db6871d Mon Sep 17 00:00:00 2001
From: Michael Kuhn <suraia@ikkoku.de>
Date: Thu, 15 Sep 2016 04:42:57 +0200
Subject: Update mvapich2 to 2.2 (#1775)

---
 var/spack/repos/builtin/packages/mvapich2/package.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index a123830185..06678bf08b 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -28,14 +28,12 @@ from spack import *
 class Mvapich2(Package):
     """MVAPICH2 is an MPI implementation for Infiniband networks."""
     homepage = "http://mvapich.cse.ohio-state.edu/"
-    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2rc2.tar.gz"
+    url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz"
 
-    version('2.2rc2', 'f9082ffc3b853ad1b908cf7f169aa878')
-    version('2.2b',   '5651e8b7a72d7c77ca68da48f3a5d108')
-    version('2.2a',   'b8ceb4fc5f5a97add9b3ff1b9cbe39d2')
-    version('2.1',    '0095ceecb19bbb7fb262131cb9c2cdd6')
-    version('2.0',    '9fbb68a4111a8b6338e476dc657388b4')
-    version('1.9',    '5dc58ed08fd3142c260b70fe297e127c')
+    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e')
+    version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6')
+    version('2.0', '9fbb68a4111a8b6338e476dc657388b4')
+    version('1.9', '5dc58ed08fd3142c260b70fe297e127c')
 
     patch('ad_lustre_rwcontig_open_source.patch', when='@1.9')
 
@@ -95,6 +93,7 @@ class Mvapich2(Package):
     ##########
 
     # FIXME : CUDA support is missing
+    depends_on('bison')
     depends_on('libpciaccess')
 
     def url_for_version(self, version):
-- 
cgit v1.2.3-70-g09d2


From 7043fff8078d0b7a62895302dabbe71904220edf Mon Sep 17 00:00:00 2001
From: Michael Kuhn <suraia@ikkoku.de>
Date: Thu, 15 Sep 2016 04:48:28 +0200
Subject: Fix location -p and -P (#1776)

---
 lib/spack/spack/cmd/location.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index b9c8b5c330..54f7185707 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -25,7 +25,6 @@
 import argparse
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
 
 import spack
 import spack.cmd
@@ -77,7 +76,7 @@ def location(parser, args):
         print spack.prefix
 
     elif args.packages:
-        print spack.repo.root
+        print spack.repo.first_repo().root
 
     elif args.stages:
         print spack.stage_path
@@ -99,7 +98,7 @@ def location(parser, args):
 
             if args.package_dir:
                 # This one just needs the spec name.
-                print join_path(spack.repo.root, spec.name)
+                print spack.repo.dirname_for_package_name(spec.name)
 
             else:
                 # These versions need concretized specs.
-- 
cgit v1.2.3-70-g09d2


From dfad4a0abc87e65ff9a6fa58aef2a34d7cc7eec8 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:12:40 -0400
Subject: Update binutils to 2.27 (#1598)

---
 var/spack/repos/builtin/packages/binutils/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index e329e6fd7a..2271c7cfcc 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -31,6 +31,7 @@ class Binutils(Package):
     homepage = "http://www.gnu.org/software/binutils/"
     url      = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
 
+    version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68')
     # 2.26 is incompatible with py-pillow build for some reason.
     version('2.26', '64146a0faa3b411ba774f47d41de239f')
     version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True)
-- 
cgit v1.2.3-70-g09d2


From 6848752feda35b444c18cdbe5170ef42953d33e0 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:12:52 -0400
Subject: Update cereal to 1.2.1 (#1599)

---
 var/spack/repos/builtin/packages/cereal/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index 716e0103d1..0ce6ec593c 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -39,6 +39,7 @@ class Cereal(Package):
     homepage = "http://uscilab.github.io/cereal/"
     url      = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
 
+    version('1.2.1', '64476ed74c19068ee543b53ad3992261')
     version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b')
     version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9')
     version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27')
-- 
cgit v1.2.3-70-g09d2


From ee2ddaa7cc8607475d9abdd2e55de05b01ef25f5 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:13:03 -0400
Subject: Update mbedtls to 2.3.0 (#1600)

---
 var/spack/repos/builtin/packages/mbedtls/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py
index e1a42c0d9a..493ea59f0b 100644
--- a/var/spack/repos/builtin/packages/mbedtls/package.py
+++ b/var/spack/repos/builtin/packages/mbedtls/package.py
@@ -35,6 +35,7 @@ class Mbedtls(Package):
     homepage = "https://tls.mbed.org"
     url      = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz"
 
+    version('2.3.0', '98158e1160a0825a3e8db38881a177a0')
     version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be')
     version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942')
     version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae')
-- 
cgit v1.2.3-70-g09d2


From ebde2a101eaef65c1ee5318b3b4c858121c6f837 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:13:14 -0400
Subject: Reorder versions in openssl (#1601)

---
 var/spack/repos/builtin/packages/openssl/package.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 8d9049a8f7..37442e1451 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -36,14 +36,14 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
     url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz"
 
-    version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
-    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
-    version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
-    version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
-    version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
-    version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
-    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
+    version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
+    version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
+    version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
+    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
+    version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
 
     depends_on("zlib")
     parallel = False
-- 
cgit v1.2.3-70-g09d2


From 2e490050f6dfb0f9e5253e83fcf640d605dd83f7 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:13:25 -0400
Subject: Update OpenBLAS to 0.2.19 (#1702)

---
 var/spack/repos/builtin/packages/openblas/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 37f7a7005d..23c7b02daf 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -32,6 +32,7 @@ class Openblas(Package):
     homepage = "http://www.openblas.net"
     url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
 
+    version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
     version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
-- 
cgit v1.2.3-70-g09d2


From bbdc429db3ba0bb0dfc3250871141d8228d93834 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:13:40 -0400
Subject: Update OpenMPI to 2.0.1 (#1721)

---
 var/spack/repos/builtin/packages/openmpi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 67bf6f3713..bb356aaccc 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -65,6 +65,7 @@ class Openmpi(Package):
     list_url = "http://www.open-mpi.org/software/ompi/"
     list_depth = 3
 
+    version('2.0.1', '6f78155bd7203039d2448390f3b51c96')
     version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
     version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
     version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
-- 
cgit v1.2.3-70-g09d2


From 48c87da07b1cf092eb0c200ef9a6c004206f7526 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:13:54 -0400
Subject: Update curl to 7.50.3 (#1747)

* Update curl to 7.50.2
* Update curl to 7.50.3
---
 var/spack/repos/builtin/packages/curl/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index 4954e435c0..a22ac52714 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -32,6 +32,8 @@ class Curl(Package):
     homepage = "http://curl.haxx.se"
     url      = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
 
+    version('7.50.3', 'bd177fd6deecce00cfa7b5916d831c5e')
+    version('7.50.2', '6e161179f7af4b9f8b6ea21420132719')
     version('7.50.1', '015f6a0217ca6f2c5442ca406476920b')
     version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
     version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
-- 
cgit v1.2.3-70-g09d2


From 682ac5194e977e10dec930c5efc52fe890f92013 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:14:06 -0400
Subject: Declare py-beautifulsoup4's dependency on py-setuptools (#1748)

---
 var/spack/repos/builtin/packages/py-beautifulsoup4/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
index 64368fe70d..d3a260bd7f 100644
--- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
@@ -37,5 +37,7 @@ class PyBeautifulsoup4(Package):
 
     extends('python')
 
+    depends_on('py-setuptools', type='build')
+
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix={0}'.format(prefix))
-- 
cgit v1.2.3-70-g09d2


From 140f1773cfa66bd74b4a859e46b509f43c6a9836 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:14:17 -0400
Subject: Update hwloc to 1.11.4 (#1752)

---
 var/spack/repos/builtin/packages/hwloc/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index c163628840..111c424b22 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -42,6 +42,7 @@ class Hwloc(Package):
     list_url = "http://www.open-mpi.org/software/hwloc/"
     list_depth = 3
 
+    version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d')
     version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f')
     version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23')
     version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc')
-- 
cgit v1.2.3-70-g09d2


From 8426b6559244a0062afa201ac7bffe04104724e1 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:14:37 -0400
Subject: Make cmake @2.8 build again (#1759)

---
 var/spack/repos/builtin/packages/cmake/package.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 0c16adcef7..83a68fda07 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -88,11 +88,13 @@ class Cmake(Package):
 
         options = [
             '--prefix={0}'.format(prefix),
-            '--parallel={0}'.format(make_jobs),
-            # jsoncpp requires CMake to build
-            # use CMake-provided library to avoid circular dependency
-            '--no-system-jsoncpp'
-        ]
+            '--parallel={0}'.format(make_jobs)]
+        if spec.satisfies("@3:"):
+            options.append(
+                # jsoncpp requires CMake to build
+                # use CMake-provided library to avoid circular dependency
+                '--no-system-jsoncpp'
+            )
 
         if '+ownlibs' in spec:
             # Build and link to the CMake-provided third-party libraries
-- 
cgit v1.2.3-70-g09d2


From 2a558e9d7adeaf4ee94120654b4f558262919333 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:14:55 -0400
Subject: Tighten HDF5 version requirements for Silo (#1760)

---
 var/spack/repos/builtin/packages/silo/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 5113c88bdf..691d53a9f1 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -41,7 +41,8 @@ class Silo(Package):
     variant('silex', default=False,
             description='Builds Silex, a GUI for viewing Silo files')
 
-    depends_on('hdf5')
+    # silo uses the obsolete function H5Pset_fapl_mpiposix:
+    depends_on("hdf5 @:1.8.12")
     depends_on('qt', when='+silex')
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From 70424b511eeed84f875393b2e8fee9c47993004d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:15:37 -0400
Subject: Work around cmake problems in VTK (#1761)

The cmake scripts can't handle the semicolons in gcc's version output. Filter them out before detecting the version.
---
 var/spack/repos/builtin/packages/vtk/gcc.patch  | 21 +++++++++++++++++++++
 var/spack/repos/builtin/packages/vtk/package.py |  2 ++
 2 files changed, 23 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/vtk/gcc.patch

diff --git a/var/spack/repos/builtin/packages/vtk/gcc.patch b/var/spack/repos/builtin/packages/vtk/gcc.patch
new file mode 100644
index 0000000000..37ba5ac45a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vtk/gcc.patch
@@ -0,0 +1,21 @@
+--- old/CMake/vtkCompilerExtras.cmake
++++ new/CMake/vtkCompilerExtras.cmake
+@@ -26,6 +26,8 @@
+   execute_process(COMMAND ${CMAKE_C_COMPILER} --version
+     OUTPUT_VARIABLE _gcc_version_info
+     ERROR_VARIABLE _gcc_version_info)
++
++  string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}")
+ 
+   string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]"
+     _gcc_version "${_gcc_version_info}")
+--- old/CMake/GenerateExportHeader.cmake
++++ new/CMake/GenerateExportHeader.cmake
+@@ -166,6 +166,7 @@
+     execute_process(COMMAND ${CMAKE_C_COMPILER} --version
+       OUTPUT_VARIABLE _gcc_version_info
+       ERROR_VARIABLE _gcc_version_info)
++    string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}")
+     string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]"
+       _gcc_version "${_gcc_version_info}")
+     # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 087c0e93eb..f7015904b0 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -40,6 +40,8 @@ class Vtk(Package):
 
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
+    patch("gcc.patch")
+
     depends_on('cmake', type='build')
     depends_on("qt")
 
-- 
cgit v1.2.3-70-g09d2


From bddb15ef4c42d249990c5e26a45d898e9b3982d0 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:15:58 -0400
Subject: Make VisIt build again (#1762)

- add new version 2.10.3
- explicitly require hdf5 variant ~mpi, since we don't know how to build with mpicc
- explicitly disable glew since it may not be installed
---
 var/spack/repos/builtin/packages/visit/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index d88caeb00a..5d2ab24cc5 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -31,13 +31,15 @@ class Visit(Package):
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
     url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
 
-    version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
+    version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b')
     version('2.10.2', '253de0837a9d69fb689befc98ea4d068')
+    version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
 
     depends_on("vtk@6.1.0~opengl2")
     depends_on("qt@4.8.6")
     depends_on("python")
     depends_on("silo+shared")
+    depends_on("hdf5~mpi")
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
@@ -46,6 +48,7 @@ class Visit(Package):
             feature_args.extend([
                 "-DVTK_MAJOR_VERSION=6",
                 "-DVTK_MINOR_VERSION=1",
+                "-DVISIT_USE_GLEW=OFF",
                 "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec[
                     'qt'].prefix.bin,
                 "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec[
-- 
cgit v1.2.3-70-g09d2


From bd6aac3102f0c107c3c5b65e0e04e342b4065e35 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 05:16:25 -0400
Subject: Update Julia to 0.4.7 (#1805)

---
 var/spack/repos/builtin/packages/julia/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 6ccaa11c90..93c8b1c4b3 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -39,7 +39,8 @@ class Julia(Package):
             git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
     version('release-0.4',
             git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
-    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
+    version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078', preferred=True)
+    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d')
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
     version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
 
-- 
cgit v1.2.3-70-g09d2


From efadc0e2997015545d656f587a5478c9fcc1c2ad Mon Sep 17 00:00:00 2001
From: Eric <muffgaga@gmx.de>
Date: Tue, 20 Sep 2016 11:18:26 +0200
Subject: Allow multi-user installations (#1804)

When re-using previously downloaded tarballs, spack copies from
`var/spack/stage/PACKAGE-VERSION-HASH/downloaded_file` to
`var/spack/cache/PACKAGE/downloaded_file`. This fails if the source is owned by
a different user (`shutil.copy` tries to retain all meta data including file
ownership). Change to a non-meta-data copy function (`shutil.copyfile`).
---
 lib/spack/spack/fetch_strategy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 4349e32d4f..21802c4556 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -306,7 +306,7 @@ class URLFetchStrategy(FetchStrategy):
         if not self.archive_file:
             raise NoArchiveFileError("Cannot call archive() before fetching.")
 
-        shutil.copy(self.archive_file, destination)
+        shutil.copyfile(self.archive_file, destination)
 
     @_needs_stage
     def check(self):
-- 
cgit v1.2.3-70-g09d2


From ea446c0f0ea0dc905ea66ad6a902cbb4713f920a Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Tue, 20 Sep 2016 11:26:25 +0200
Subject: lmod : added support for the creation of hierarchical lua module
 files (#1723)

Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features
---
 .gitignore                                       |   1 +
 lib/spack/spack/cmd/__init__.py                  |  10 +-
 lib/spack/spack/cmd/module.py                    |   2 +-
 lib/spack/spack/hooks/__init__.py                |  14 +-
 lib/spack/spack/hooks/lmodmodule.py              |  35 +++
 lib/spack/spack/modules.py                       | 239 ++++++++++++++-
 lib/spack/spack/schema/modules.py                |  15 +-
 lib/spack/spack/test/database.py                 |  14 +-
 lib/spack/spack/test/modules.py                  | 372 +++++++++++++++--------
 var/spack/repos/builtin/packages/llvm/package.py |   7 +-
 10 files changed, 560 insertions(+), 149 deletions(-)
 create mode 100644 lib/spack/spack/hooks/lmodmodule.py

diff --git a/.gitignore b/.gitignore
index b1215f0c7e..072bf30c07 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
+/share/spack/lmod
 /TAGS
 /htmlcov
 .coverage
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index f69f434afd..6b1561b7fc 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -69,17 +69,17 @@ def get_cmd_function_name(name):
 def get_module(name):
     """Imports the module for a particular command name and returns it."""
     module_name = "%s.%s" % (__name__, name)
-    module = __import__(
-        module_name, fromlist=[name, SETUP_PARSER, DESCRIPTION],
-        level=0)
+    module = __import__(module_name,
+                        fromlist=[name, SETUP_PARSER, DESCRIPTION],
+                        level=0)
 
     attr_setdefault(module, SETUP_PARSER, lambda *args: None)  # null-op
     attr_setdefault(module, DESCRIPTION, "")
 
     fn_name = get_cmd_function_name(name)
     if not hasattr(module, fn_name):
-        tty.die("Command module %s (%s) must define function '%s'."
-                % (module.__name__, module.__file__, fn_name))
+        tty.die("Command module %s (%s) must define function '%s'." %
+                (module.__name__, module.__file__, fn_name))
 
     return module
 
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 2d0b83fe00..c6fa84109e 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -29,10 +29,10 @@ import os
 import shutil
 import sys
 
+import llnl.util.filesystem as filesystem
 import llnl.util.tty as tty
 import spack.cmd
 import spack.cmd.common.arguments as arguments
-import llnl.util.filesystem as filesystem
 from spack.modules import module_types
 
 description = "Manipulate module files"
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index c7c84defa0..ff4ebc2e57 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -24,7 +24,7 @@
 ##############################################################################
 """This package contains modules with hooks for various stages in the
    Spack install process.  You can add modules here and they'll be
-   executaed by package at various times during the package lifecycle.
+   executed by package at various times during the package lifecycle.
 
    Each hook is just a function that takes a package as a parameter.
    Hooks are not executed in any particular order.
@@ -41,9 +41,10 @@
    features.
 """
 import imp
-from llnl.util.lang import memoized, list_modules
-from llnl.util.filesystem import join_path
+
 import spack
+from llnl.util.filesystem import join_path
+from llnl.util.lang import memoized, list_modules
 
 
 @memoized
@@ -70,12 +71,11 @@ class HookRunner(object):
                 if hasattr(hook, '__call__'):
                     hook(pkg)
 
-
 #
 # Define some functions that can be called to fire off hooks.
 #
-pre_install    = HookRunner('pre_install')
-post_install   = HookRunner('post_install')
+pre_install = HookRunner('pre_install')
+post_install = HookRunner('post_install')
 
-pre_uninstall  = HookRunner('pre_uninstall')
+pre_uninstall = HookRunner('pre_uninstall')
 post_uninstall = HookRunner('post_uninstall')
diff --git a/lib/spack/spack/hooks/lmodmodule.py b/lib/spack/spack/hooks/lmodmodule.py
new file mode 100644
index 0000000000..6b4318b1d0
--- /dev/null
+++ b/lib/spack/spack/hooks/lmodmodule.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import spack.modules
+
+
+def post_install(pkg):
+    dk = spack.modules.LmodModule(pkg.spec)
+    dk.write()
+
+
+def post_uninstall(pkg):
+    dk = spack.modules.LmodModule(pkg.spec)
+    dk.remove()
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 3db08a6e90..d75bfbac45 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -40,6 +40,7 @@ module file.
 """
 import copy
 import datetime
+import itertools
 import os
 import os.path
 import re
@@ -48,6 +49,7 @@ import textwrap
 
 import llnl.util.tty as tty
 import spack
+import spack.compilers  # Needed by LmodModules
 import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.build_environment import parent_class_modules
@@ -56,7 +58,8 @@ from spack.environment import *
 
 __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 
-# Registry of all types of modules.  Entries created by EnvModule's metaclass
+"""Registry of all types of modules.  Entries created by EnvModule's
+   metaclass."""
 module_types = {}
 
 CONFIGURATION = spack.config.get_config('modules')
@@ -633,3 +636,237 @@ class TclModule(EnvModule):
                         raise SystemExit('Module generation aborted.')
                 line = line.format(**naming_tokens)
             yield line
+
+# To construct an arbitrary hierarchy of module files:
+# 1. Parse the configuration file and check that all the items in
+#    hierarchical_scheme are indeed virtual packages
+#    This needs to be done only once at start-up
+# 2. Order the stack as `hierarchical_scheme + ['mpi, 'compiler']
+# 3. Check which of the services are provided by the package
+#    -> may be more than one
+# 4. Check which of the services are needed by the package
+#    -> this determines where to write the module file
+# 5. For each combination of services in which we have at least one provider
+#    here add the appropriate conditional MODULEPATH modifications
+
+
+class LmodModule(EnvModule):
+    name = 'lmod'
+    path = join_path(spack.share_path, "lmod")
+
+    environment_modifications_formats = {
+        PrependPath: 'prepend_path("{name}", "{value}")\n',
+        AppendPath: 'append_path("{name}", "{value}")\n',
+        RemovePath: 'remove_path("{name}", "{value}")\n',
+        SetEnv: 'setenv("{name}", "{value}")\n',
+        UnsetEnv: 'unsetenv("{name}")\n'
+    }
+
+    autoload_format = ('if not isloaded("{module_file}") then\n'
+                       '    LmodMessage("Autoloading {module_file}")\n'
+                       '    load("{module_file}")\n'
+                       'end\n\n')
+
+    prerequisite_format = 'prereq("{module_file}")\n'
+
+    family_format = 'family("{family}")\n'
+
+    path_part_with_hash = join_path('{token.name}', '{token.version}-{token.hash}')  # NOQA: ignore=E501
+    path_part_without_hash = join_path('{token.name}', '{token.version}')
+
+    # TODO : Check that extra tokens specified in configuration file
+    # TODO : are actually virtual dependencies
+    configuration = CONFIGURATION.get('lmod', {})
+    hierarchy_tokens = configuration.get('hierarchical_scheme', [])
+    hierarchy_tokens = hierarchy_tokens + ['mpi', 'compiler']
+
+    def __init__(self, spec=None):
+        super(LmodModule, self).__init__(spec)
+        # Sets the root directory for this architecture
+        self.modules_root = join_path(LmodModule.path, self.spec.architecture)
+        # Retrieve core compilers
+        self.core_compilers = self.configuration.get('core_compilers', [])
+        # Keep track of the requirements that this package has in terms
+        # of virtual packages
+        # that participate in the hierarchical structure
+        self.requires = {'compiler': self.spec.compiler}
+        # For each virtual dependency in the hierarchy
+        for x in self.hierarchy_tokens:
+            if x in self.spec and not self.spec.package.provides(
+                    x):  # if I depend on it
+                self.requires[x] = self.spec[x]  # record the actual provider
+        # Check what are the services I need (this will determine where the
+        # module file will be written)
+        self.substitutions = {}
+        self.substitutions.update(self.requires)
+        # TODO : complete substitutions
+        # Check what service I provide to others
+        self.provides = {}
+        # If it is in the list of supported compilers family -> compiler
+        if self.spec.name in spack.compilers.supported_compilers():
+            self.provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
+        # Special case for llvm
+        if self.spec.name == 'llvm':
+            self.provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
+            self.provides['compiler'].name = 'clang'
+
+        for x in self.hierarchy_tokens:
+            if self.spec.package.provides(x):
+                self.provides[x] = self.spec[x]
+
+    def _hierarchy_token_combinations(self):
+        """
+        Yields all the relevant combinations that could appear in the hierarchy
+        """
+        for ii in range(len(self.hierarchy_tokens) + 1):
+            for item in itertools.combinations(self.hierarchy_tokens, ii):
+                if 'compiler' in item:
+                    yield item
+
+    def _hierarchy_to_be_provided(self):
+        """
+        Filters a list of hierarchy tokens and yields only the one that we
+        need to provide
+        """
+        for item in self._hierarchy_token_combinations():
+            if any(x in self.provides for x in item):
+                yield item
+
+    def token_to_path(self, name, value):
+        # If we are dealing with a core compiler, return 'Core'
+        if name == 'compiler' and str(value) in self.core_compilers:
+            return 'Core'
+        # CompilerSpec does not have an hash
+        if name == 'compiler':
+            return self.path_part_without_hash.format(token=value)
+        # For virtual providers add a small part of the hash
+        # to distinguish among different variants in a directory hierarchy
+        value.hash = value.dag_hash(length=6)
+        return self.path_part_with_hash.format(token=value)
+
+    @property
+    def file_name(self):
+        parts = [self.token_to_path(x, self.requires[x])
+                 for x in self.hierarchy_tokens if x in self.requires]
+        hierarchy_name = join_path(*parts)
+        fullname = join_path(self.modules_root, hierarchy_name,
+                             self.use_name + '.lua')
+        return fullname
+
+    @property
+    def use_name(self):
+        return self.token_to_path('', self.spec)
+
+    def modulepath_modifications(self):
+        # What is available is what we require plus what we provide
+        entry = ''
+        available = {}
+        available.update(self.requires)
+        available.update(self.provides)
+        available_parts = [self.token_to_path(x, available[x])
+                           for x in self.hierarchy_tokens if x in available]
+        # Missing parts
+        missing = [x for x in self.hierarchy_tokens if x not in available]
+        # Direct path we provide on top of compilers
+        modulepath = join_path(self.modules_root, *available_parts)
+        env = EnvironmentModifications()
+        env.prepend_path('MODULEPATH', modulepath)
+        for line in self.process_environment_command(env):
+            entry += line
+
+        def local_variable(x):
+            lower, upper = x.lower(), x.upper()
+            fmt = 'local {lower}_name = os.getenv("LMOD_{upper}_NAME")\n'
+            fmt += 'local {lower}_version = os.getenv("LMOD_{upper}_VERSION")\n'  # NOQA: ignore=501
+            return fmt.format(lower=lower, upper=upper)
+
+        def set_variables_for_service(env, x):
+            upper = x.upper()
+            s = self.provides[x]
+            name, version = os.path.split(self.token_to_path(x, s))
+
+            env.set('LMOD_{upper}_NAME'.format(upper=upper), name)
+            env.set('LMOD_{upper}_VERSION'.format(upper=upper), version)
+
+        def conditional_modulepath_modifications(item):
+            entry = 'if '
+            needed = []
+            for x in self.hierarchy_tokens:
+                if x in missing:
+                    needed.append('{x}_name '.format(x=x))
+            entry += 'and '.join(needed) + 'then\n'
+            entry += '  local t = pathJoin("{root}"'.format(
+                root=self.modules_root)
+            for x in item:
+                if x in missing:
+                    entry += ', {lower}_name, {lower}_version'.format(
+                        lower=x.lower())
+                else:
+                    entry += ', "{x}"'.format(
+                        x=self.token_to_path(x, available[x]))
+            entry += ')\n'
+            entry += '  prepend_path("MODULEPATH", t)\n'
+            entry += 'end\n\n'
+            return entry
+
+        if 'compiler' not in self.provides:
+            # Retrieve variables
+            entry += '\n'
+            for x in missing:
+                entry += local_variable(x)
+            entry += '\n'
+            # Conditional modifications
+            conditionals = [x
+                            for x in self._hierarchy_to_be_provided()
+                            if any(t in missing for t in x)]
+            for item in conditionals:
+                entry += conditional_modulepath_modifications(item)
+
+            # Set environment variables for the services we provide
+            env = EnvironmentModifications()
+            for x in self.provides:
+                set_variables_for_service(env, x)
+            for line in self.process_environment_command(env):
+                entry += line
+
+        return entry
+
+    @property
+    def header(self):
+        timestamp = datetime.datetime.now()
+        # Header as in
+        # https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/advanced-user-guide/more-about-writing-module-files
+        header = "-- -*- lua -*-\n"
+        header += '-- Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp  # NOQA: ignore=E501
+        header += '--\n'
+        header += '-- %s\n' % self.spec.short_spec
+        header += '--\n'
+
+        # Short description -> whatis()
+        if self.short_description:
+            header += "whatis([[Name : {name}]])\n".format(name=self.spec.name)
+            header += "whatis([[Version : {version}]])\n".format(
+                version=self.spec.version)
+
+        # Long description -> help()
+        if self.long_description:
+            doc = re.sub(r'"', '\"', self.long_description)
+            header += "help([[{documentation}]])\n".format(documentation=doc)
+
+        # Certain things need to be done only if we provide a service
+        if self.provides:
+            # Add family directives
+            header += '\n'
+            for x in self.provides:
+                header += self.family_format.format(family=x)
+            header += '\n'
+            header += '-- MODULEPATH modifications\n'
+            header += '\n'
+            # Modify MODULEPATH
+            header += self.modulepath_modifications()
+            # Set environment variables for services we provide
+            header += '\n'
+            header += '-- END MODULEPATH modifications\n'
+            header += '\n'
+
+        return header
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index f8066919f1..bdc70c9ef1 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -139,7 +139,20 @@ schema = {
                     'default': [],
                     'items': {
                         'type': 'string',
-                        'enum': ['tcl', 'dotkit']}},
+                        'enum': ['tcl', 'dotkit', 'lmod']}},
+                'lmod': {
+                    'allOf': [
+                        # Base configuration
+                        {'$ref': '#/definitions/module_type_configuration'},
+                        {
+                            'core_compilers': {
+                                '$ref': '#/definitions/array_of_strings'
+                            },
+                            'hierarchical_scheme': {
+                                '$ref': '#/definitions/array_of_strings'
+                            }
+                        }  # Specific lmod extensions
+                    ]},
                 'tcl': {
                     'allOf': [
                         # Base configuration
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 22b1f17890..b114bbacb8 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -26,8 +26,8 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
-import os.path
 import multiprocessing
+import os.path
 
 import spack
 from llnl.util.filesystem import join_path
@@ -88,16 +88,16 @@ class DatabaseTest(MockDatabase):
         # query specs with multiple configurations
         mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
         callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
-        mpi_specs      = [s for s in all_specs if s.satisfies('mpi')]
+        mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs  = [s for s in all_specs if s.satisfies('dyninst')]
+        dyninst_specs = [s for s in all_specs if s.satisfies('dyninst')]
         libdwarf_specs = [s for s in all_specs if s.satisfies('libdwarf')]
-        libelf_specs   = [s for s in all_specs if s.satisfies('libelf')]
+        libelf_specs = [s for s in all_specs if s.satisfies('libelf')]
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
@@ -163,16 +163,16 @@ class DatabaseTest(MockDatabase):
         # query specs with multiple configurations
         mpileaks_specs = self.installed_db.query('mpileaks')
         callpath_specs = self.installed_db.query('callpath')
-        mpi_specs      = self.installed_db.query('mpi')
+        mpi_specs = self.installed_db.query('mpi')
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs  = self.installed_db.query('dyninst')
+        dyninst_specs = self.installed_db.query('dyninst')
         libdwarf_specs = self.installed_db.query('libdwarf')
-        libelf_specs   = self.installed_db.query('libelf')
+        libelf_specs = self.installed_db.query('libelf')
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index 55b771fc79..88f67090f1 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -49,105 +49,10 @@ def mock_open(filename, mode):
         handle.close()
 
 
-configuration_autoload_direct = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'autoload': 'direct'
-        }
-    }
-}
-
-configuration_autoload_all = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'autoload': 'all'
-        }
-    }
-}
-
-configuration_prerequisites_direct = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'prerequisites': 'direct'
-        }
-    }
-}
-
-configuration_prerequisites_all = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'prerequisites': 'all'
-        }
-    }
-}
-
-configuration_alter_environment = {
-    'enable': ['tcl'],
-    'tcl': {
-        'all': {
-            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']},
-            'environment': {
-                'set': {'{name}_ROOT': '{prefix}'}
-            }
-        },
-        'platform=test target=x86_64': {
-            'environment': {
-                'set': {'FOO': 'foo'},
-                'unset': ['BAR']
-            }
-        },
-        'platform=test target=x86_32': {
-            'load': ['foo/bar']
-        }
-    }
-}
-
-configuration_blacklist = {
-    'enable': ['tcl'],
-    'tcl': {
-        'whitelist': ['zmpi'],
-        'blacklist': ['callpath', 'mpi'],
-        'all': {
-            'autoload': 'direct'
-        }
-    }
-}
-
-configuration_conflicts = {
-    'enable': ['tcl'],
-    'tcl': {
-        'naming_scheme': '{name}/{version}-{compiler.name}',
-        'all': {
-            'conflict': ['{name}', 'intel/14.0.1']
-        }
-    }
-}
-
-configuration_wrong_conflicts = {
-    'enable': ['tcl'],
-    'tcl': {
-        'naming_scheme': '{name}/{version}-{compiler.name}',
-        'all': {
-            'conflict': ['{name}/{compiler.name}']
-        }
-    }
-}
-
-configuration_suffix = {
-    'enable': ['tcl'],
-    'tcl': {
-        'mpileaks': {
-            'suffixes': {
-                '+debug': 'foo',
-                '~debug': 'bar'
-            }
-        }
-    }
-}
+# Spec strings that will be used throughout the tests
+mpich_spec_string = 'mpich@3.0.4'
+mpileaks_spec_string = 'mpileaks'
+libdwarf_spec_string = 'libdwarf arch=x64-linux'
 
 
 class HelperFunctionsTests(MockPackagesTest):
@@ -187,44 +92,156 @@ class HelperFunctionsTests(MockPackagesTest):
         self.assertTrue('CPATH' in names)
 
 
-class TclTests(MockPackagesTest):
+class ModuleFileGeneratorTests(MockPackagesTest):
+    """
+    Base class to test module file generators. Relies on child having defined
+    a 'factory' attribute to create an instance of the generator to be tested.
+    """
 
     def setUp(self):
-        super(TclTests, self).setUp()
-        self.configuration_obj = spack.modules.CONFIGURATION
+        super(ModuleFileGeneratorTests, self).setUp()
+        self.configuration_instance = spack.modules.CONFIGURATION
+        self.module_types_instance = spack.modules.module_types
         spack.modules.open = mock_open
         # Make sure that a non-mocked configuration will trigger an error
         spack.modules.CONFIGURATION = None
+        spack.modules.module_types = {self.factory.name: self.factory}
 
     def tearDown(self):
         del spack.modules.open
-        spack.modules.CONFIGURATION = self.configuration_obj
-        super(TclTests, self).tearDown()
+        spack.modules.module_types = self.module_types_instance
+        spack.modules.CONFIGURATION = self.configuration_instance
+        super(ModuleFileGeneratorTests, self).tearDown()
 
     def get_modulefile_content(self, spec):
         spec.concretize()
-        generator = spack.modules.TclModule(spec)
+        generator = self.factory(spec)
         generator.write()
         content = FILE_REGISTRY[generator.file_name].split('\n')
         return content
 
+
+class TclTests(ModuleFileGeneratorTests):
+
+    factory = spack.modules.TclModule
+
+    configuration_autoload_direct = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    configuration_autoload_all = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'autoload': 'all'
+            }
+        }
+    }
+
+    configuration_prerequisites_direct = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'prerequisites': 'direct'
+            }
+        }
+    }
+
+    configuration_prerequisites_all = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'prerequisites': 'all'
+            }
+        }
+    }
+
+    configuration_alter_environment = {
+        'enable': ['tcl'],
+        'tcl': {
+            'all': {
+                'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']},
+                'environment': {
+                    'set': {'{name}_ROOT': '{prefix}'}
+                }
+            },
+            'platform=test target=x86_64': {
+                'environment': {
+                    'set': {'FOO': 'foo'},
+                    'unset': ['BAR']
+                }
+            },
+            'platform=test target=x86_32': {
+                'load': ['foo/bar']
+            }
+        }
+    }
+
+    configuration_blacklist = {
+        'enable': ['tcl'],
+        'tcl': {
+            'whitelist': ['zmpi'],
+            'blacklist': ['callpath', 'mpi'],
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    configuration_conflicts = {
+        'enable': ['tcl'],
+        'tcl': {
+            'naming_scheme': '{name}/{version}-{compiler.name}',
+            'all': {
+                'conflict': ['{name}', 'intel/14.0.1']
+            }
+        }
+    }
+
+    configuration_wrong_conflicts = {
+        'enable': ['tcl'],
+        'tcl': {
+            'naming_scheme': '{name}/{version}-{compiler.name}',
+            'all': {
+                'conflict': ['{name}/{compiler.name}']
+            }
+        }
+    }
+
+    configuration_suffix = {
+        'enable': ['tcl'],
+        'tcl': {
+            'mpileaks': {
+                'suffixes': {
+                    '+debug': 'foo',
+                    '~debug': 'bar'
+                }
+            }
+        }
+    }
+
     def test_simple_case(self):
-        spack.modules.CONFIGURATION = configuration_autoload_direct
-        spec = spack.spec.Spec('mpich@3.0.4')
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpich_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertTrue('module-whatis "mpich @3.0.4"' in content)
         self.assertRaises(TypeError, spack.modules.dependencies,
                           spec, 'non-existing-tag')
 
     def test_autoload(self):
-        spack.modules.CONFIGURATION = configuration_autoload_direct
-        spec = spack.spec.Spec('mpileaks')
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpileaks_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
 
-        spack.modules.CONFIGURATION = configuration_autoload_all
-        spec = spack.spec.Spec('mpileaks')
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
+        spec = spack.spec.Spec(mpileaks_spec_string)
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
         self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
@@ -252,18 +269,18 @@ class TclTests(MockPackagesTest):
         self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
 
     def test_prerequisites(self):
-        spack.modules.CONFIGURATION = configuration_prerequisites_direct
+        spack.modules.CONFIGURATION = self.configuration_prerequisites_direct
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'prereq' in x]), 2)
 
-        spack.modules.CONFIGURATION = configuration_prerequisites_all
+        spack.modules.CONFIGURATION = self.configuration_prerequisites_all
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'prereq' in x]), 5)
 
     def test_alter_environment(self):
-        spack.modules.CONFIGURATION = configuration_alter_environment
+        spack.modules.CONFIGURATION = self.configuration_alter_environment
         spec = spack.spec.Spec('mpileaks platform=test target=x86_64')
         content = self.get_modulefile_content(spec)
         self.assertEqual(
@@ -293,7 +310,7 @@ class TclTests(MockPackagesTest):
             len([x for x in content if 'setenv LIBDWARF_ROOT' in x]), 1)
 
     def test_blacklist(self):
-        spack.modules.CONFIGURATION = configuration_blacklist
+        spack.modules.CONFIGURATION = self.configuration_blacklist
         spec = spack.spec.Spec('mpileaks ^zmpi')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
@@ -307,7 +324,7 @@ class TclTests(MockPackagesTest):
         self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
 
     def test_conflicts(self):
-        spack.modules.CONFIGURATION = configuration_conflicts
+        spack.modules.CONFIGURATION = self.configuration_conflicts
         spec = spack.spec.Spec('mpileaks')
         content = self.get_modulefile_content(spec)
         self.assertEqual(
@@ -317,11 +334,11 @@ class TclTests(MockPackagesTest):
         self.assertEqual(
             len([x for x in content if x == 'conflict intel/14.0.1']), 1)
 
-        spack.modules.CONFIGURATION = configuration_wrong_conflicts
+        spack.modules.CONFIGURATION = self.configuration_wrong_conflicts
         self.assertRaises(SystemExit, self.get_modulefile_content, spec)
 
     def test_suffixes(self):
-        spack.modules.CONFIGURATION = configuration_suffix
+        spack.modules.CONFIGURATION = self.configuration_suffix
         spec = spack.spec.Spec('mpileaks+debug arch=x86-linux')
         spec.concretize()
         generator = spack.modules.TclModule(spec)
@@ -333,18 +350,123 @@ class TclTests(MockPackagesTest):
         self.assertTrue('bar' in generator.use_name)
 
 
-configuration_dotkit = {
-    'enable': ['dotkit'],
-    'dotkit': {
-        'all': {
-            'prerequisites': 'direct'
+class LmodTests(ModuleFileGeneratorTests):
+    factory = spack.modules.LmodModule
+
+    configuration_autoload_direct = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'autoload': 'direct'
+            }
         }
     }
-}
+
+    configuration_autoload_all = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'autoload': 'all'
+            }
+        }
+    }
+
+    configuration_alter_environment = {
+        'enable': ['lmod'],
+        'lmod': {
+            'all': {
+                'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
+            },
+            'platform=test target=x86_64': {
+                'environment': {
+                    'set': {'FOO': 'foo'},
+                    'unset': ['BAR']
+                }
+            },
+            'platform=test target=x86_32': {
+                'load': ['foo/bar']
+            }
+        }
+    }
+
+    configuration_blacklist = {
+        'enable': ['lmod'],
+        'lmod': {
+            'blacklist': ['callpath'],
+            'all': {
+                'autoload': 'direct'
+            }
+        }
+    }
+
+    def test_simple_case(self):
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpich_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertTrue('-- -*- lua -*-' in content)
+        self.assertTrue('whatis([[Name : mpich]])' in content)
+        self.assertTrue('whatis([[Version : 3.0.4]])' in content)
+
+    def test_autoload(self):
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 2)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 2)
+
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 5)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 5)
+
+    def test_alter_environment(self):
+        spack.modules.CONFIGURATION = self.configuration_alter_environment
+        spec = spack.spec.Spec('mpileaks platform=test target=x86_64')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend_path("CMAKE_PREFIX_PATH"')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv("FOO", "foo")' in x]), 1)
+        self.assertEqual(
+            len([x for x in content if 'unsetenv("BAR")' in x]), 1)
+
+        spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32')
+        content = self.get_modulefile_content(spec)
+        print('\n'.join(content))
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path("CMAKE_PREFIX_PATH"')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv("FOO", "foo")' in x]), 0)
+        self.assertEqual(
+            len([x for x in content if 'unsetenv("BAR")' in x]), 0)
+
+    def test_blacklist(self):
+        spack.modules.CONFIGURATION = self.configuration_blacklist
+        spec = spack.spec.Spec(mpileaks_spec_string)
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(
+            len([x for x in content if 'if not isloaded(' in x]), 1)
+        self.assertEqual(len([x for x in content if 'load(' in x]), 1)
 
 
 class DotkitTests(MockPackagesTest):
 
+    configuration_dotkit = {
+        'enable': ['dotkit'],
+        'dotkit': {
+            'all': {
+                'prerequisites': 'direct'
+            }
+        }
+    }
+
     def setUp(self):
         super(DotkitTests, self).setUp()
         self.configuration_obj = spack.modules.CONFIGURATION
@@ -365,7 +487,7 @@ class DotkitTests(MockPackagesTest):
         return content
 
     def test_dotkit(self):
-        spack.modules.CONFIGURATION = configuration_dotkit
+        spack.modules.CONFIGURATION = self.configuration_dotkit
         spec = spack.spec.Spec('mpileaks arch=x86-linux')
         content = self.get_modulefile_content(spec)
         self.assertTrue('#c spack' in content)
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 61ea8daac4..7582faeb92 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -22,9 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-from spack import *
 import os
 
+from spack import *
+
 
 class Llvm(Package):
     """The LLVM Project is a collection of modular and reusable compiler and
@@ -37,9 +38,11 @@ class Llvm(Package):
     homepage = 'http://llvm.org/'
     url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
+    family = 'compiler'  # Used by lmod
+
     # currently required by mesa package
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005',
-            url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')
+            url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')  # currently required by mesa package
 
     variant('debug', default=False,
             description="Build a debug version of LLVM, this increases "
-- 
cgit v1.2.3-70-g09d2


From d71f8dcab5b6e760df0b145e1cc08d89cd596d5f Mon Sep 17 00:00:00 2001
From: Tom Merrick <thomas.merrick@tamucc.edu>
Date: Tue, 20 Sep 2016 04:27:19 -0500
Subject: samtools could not find the ncurses library (#1785)

---
 var/spack/repos/builtin/packages/samtools/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index 6b0b224785..b82a7e55d6 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -42,7 +42,8 @@ class Samtools(Package):
 
     def install(self, spec, prefix):
         if self.spec.version >= Version('1.3.1'):
-            configure('--prefix={0}'.format(prefix), '--with-ncurses')
+            configure('--prefix={0}'.format(prefix), '--with-ncurses',
+                      'CURSES_LIB=-lncurses')
             make()
             make('install')
         else:
-- 
cgit v1.2.3-70-g09d2


From c9fe2cd469f3f4e5e6cdb9905401da42ff214223 Mon Sep 17 00:00:00 2001
From: Eric <muffgaga@gmx.de>
Date: Tue, 20 Sep 2016 11:27:35 +0200
Subject: Fix format string (in class RemoveFailedError) (#1803)

---
 lib/spack/spack/directory_layout.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 73286483ef..8ef7d3c480 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -423,7 +423,7 @@ class RemoveFailedError(DirectoryLayoutError):
     def __init__(self, installed_spec, prefix, error):
         super(RemoveFailedError, self).__init__(
             'Could not remove prefix %s for %s : %s'
-            % prefix, installed_spec.short_spec, error)
+            % (prefix, installed_spec.short_spec, error))
         self.cause = error
 
 
-- 
cgit v1.2.3-70-g09d2


From e73a7c80bf98e7b95647a7dd6322a0aa9609c2b0 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 20 Sep 2016 02:46:13 -0700
Subject: Update Package : Zoltan (#1793)

* Refactored and reorganized the 'zoltan' install script.

* Fixed a few bugs with the '+mpi' and '+fortan' variants of 'zoltan'.

* Reintroduced and improved the '+shared' variant for the 'zoltan' package.

* Improved compatibility with different MPI providers for 'zoltan'.
---
 var/spack/repos/builtin/packages/zoltan/package.py | 115 +++++++++++++--------
 1 file changed, 71 insertions(+), 44 deletions(-)

diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index 0094395968..8d4dd321b0 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -22,10 +22,11 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
+from spack import *
 import re
 import os
 import glob
-from spack import *
 
 
 class Zoltan(Package):
@@ -47,23 +48,28 @@ class Zoltan(Package):
     version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9')
     version('3.3', '5eb8f00bda634b25ceefa0122bd18d65')
 
-    variant('debug', default=False,
-            description='Builds a debug version of the library')
-    variant('shared', default=True,
-            description='Builds a shared version of the library')
+    variant('debug', default=False, description='Builds a debug version of the library.')
+    variant('shared', default=True, description='Builds a shared version of the library.')
 
-    variant('fortran', default=True, description='Enable Fortran support')
-    variant('mpi', default=False, description='Enable MPI support')
+    variant('fortran', default=True, description='Enable Fortran support.')
+    variant('mpi', default=True, description='Enable MPI support.')
 
     depends_on('mpi', when='+mpi')
 
+    def url_for_version(self, version):
+        return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version)
+
     def install(self, spec, prefix):
-        config_args = [
-            '--enable-f90interface'
-            if '+fortan' in spec else '--disable-f90interface',
+        # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers
+        # because of some complicated generic type problem.
+        if spec.satisfies('@:3.6+fortran+mpi'):
+            raise RuntimeError(('Cannot build Zoltan v{0} with +fortran and '
+                                '+mpi; please disable one of these features '
+                                'or upgrade versions.').format(self.version))
 
-            '--enable-mpi'
-            if '+mpi' in spec else '--disable-mpi',
+        config_args = [
+            self.get_config_flag('f90interface', 'fortran'),
+            self.get_config_flag('mpi', 'mpi'),
         ]
         config_cflags = [
             '-O0' if '+debug' in spec else '-O3',
@@ -71,49 +77,70 @@ class Zoltan(Package):
         ]
 
         if '+shared' in spec:
-            config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_args.append('RANLIB=echo')
+            config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_cflags.append('-fPIC')
+            if spec.satisfies('%gcc'):
+                config_args.append('--with-libs={0}'.format('-lgfortran'))
 
         if '+mpi' in spec:
-            config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin)
-            config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin)
-            config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
-            config_args.append('--with-mpi-compilers=%s' %
-                               spec['mpi'].prefix.bin)
+            config_args.append('CC={0}'.format(spec['mpi'].mpicc))
+            config_args.append('CXX={0}'.format(spec['mpi'].mpicxx))
+            config_args.append('FC={0}'.format(spec['mpi'].mpifc))
+
+            mpi_libs = ' -l'.join(self.get_mpi_libs())
+            config_args.append('--with-mpi={0}'.format(spec['mpi'].prefix))
+            config_args.append('--with-mpi-libs=-l{0}'.format(mpi_libs))
 
         # NOTE: Early versions of Zoltan come packaged with a few embedded
         # library packages (e.g. ParMETIS, Scotch), which messes with Spack's
         # ability to descend directly into the package's source directory.
+        source_directory = self.stage.source_path
         if spec.satisfies('@:3.6'):
-            cd('Zoltan_v%s' % self.version)
-
-        mkdirp('build')
-        cd('build')
-
-        config_zoltan = Executable('../configure')
-        config_zoltan(
-            '--prefix=%s' % pwd(),
-            '--with-cflags=%s' % ' '.join(config_cflags),
-            '--with-cxxflags=%s' % ' '.join(config_cflags),
-            *config_args)
-
-        make()
-        make('install')
+            zoltan_directory = 'Zoltan_v{0}'.format(self.version)
+            source_directory = join_path(source_directory, zoltan_directory)
+
+        build_directory = join_path(source_directory, 'build')
+        with working_dir(build_directory, create=True):
+            config = Executable(join_path(source_directory, 'configure'))
+            config(
+                '--prefix={0}'.format(prefix),
+                '--with-cflags={0}'.format(' '.join(config_cflags)),
+                '--with-cxxflags={0}'.format(' '.join(config_cflags)),
+                '--with-fcflags={0}'.format(' '.join(config_cflags)),
+                *config_args
+            )
+
+            # NOTE: Earlier versions of Zoltan cannot be built in parallel
+            # because they contain nested Makefile dependency bugs.
+            make(parallel=not spec.satisfies('@:3.6+fortran'))
+            make('install')
 
         # NOTE: Unfortunately, Zoltan doesn't provide any configuration
         # options for the extension of the output library files, so this
         # script must change these extensions as a post-processing step.
         if '+shared' in spec:
-            for libpath in glob.glob('lib/*.a'):
-                libdir, libname = (os.path.dirname(libpath),
-                                   os.path.basename(libpath))
-                move(libpath, os.path.join(
-                    libdir, re.sub(r'\.a$', '.so', libname)))
-
-        mkdirp(prefix)
-        move('include', prefix)
-        move('lib', prefix)
-
-    def url_for_version(self, version):
-        return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version)
+            for lib_path in glob.glob(join_path(prefix, 'lib', '*.a')):
+                lib_static_name = os.path.basename(lib_path)
+                lib_shared_name = re.sub(r'\.a$', '.{0}'.format(dso_suffix),
+                                         lib_static_name)
+                move(lib_path, join_path(prefix, 'lib', lib_shared_name))
+
+    def get_config_flag(self, flag_name, flag_variant):
+        flag_pre = 'en' if '+{0}'.format(flag_variant) in self.spec else 'dis'
+        return '--{0}able-{1}'.format(flag_pre, flag_name)
+
+    # NOTE: Zoltan assumes that it's linking against an MPI library that can
+    # be found with '-lmpi,' which isn't the case for many MPI packages.  This
+    # function finds the names of the actual libraries for Zoltan's MPI dep.
+    def get_mpi_libs(self):
+        mpi_libs = set()
+
+        for lib_path in glob.glob(join_path(self.spec['mpi'].prefix.lib, '*')):
+            mpi_lib_match = re.match(
+                r'^(lib)((\w*)mpi(\w*))\.((a)|({0}))$'.format(dso_suffix),
+                os.path.basename(lib_path))
+            if mpi_lib_match:
+                mpi_libs.add(mpi_lib_match.group(2))
+
+        return list(mpi_libs)
-- 
cgit v1.2.3-70-g09d2


From 20fcd3f1dd31aa36bd535ba187de98af259ea260 Mon Sep 17 00:00:00 2001
From: Bruno Turcksin <bruno.turcksin@gmail.com>
Date: Tue, 20 Sep 2016 05:46:30 -0400
Subject: Add Python support to gdb. (#1790)

---
 var/spack/repos/builtin/packages/gdb/package.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index a14e166ed4..f90e4e7ff0 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -41,9 +41,18 @@ class Gdb(Package):
     version('7.9', '8f8ced422fe462a00e0135a643544f17')
     version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
+    variant('python', default=True, description='Compile with Python support')
+
+    # Required dependency
     depends_on('texinfo', type='build')
 
+    # Optional dependency
+    depends_on('python', when='+python')
+
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
+        options = ['--prefix=%s' % prefix]
+        if '+python' in spec:
+            options.extend(['--with-python'])
+        configure(*options)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 1565a643bd467196cb9d42ab244488bdeaebd0ff Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 20 Sep 2016 11:46:57 +0200
Subject: dealii: add 8.4.2 (#1782)

---
 var/spack/repos/builtin/packages/dealii/package.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 939d8fc013..9e8c639128 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -32,6 +32,7 @@ class Dealii(Package):
     homepage = "https://www.dealii.org"
     url      = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
 
+    version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7')
     version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d')
     version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
     version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
@@ -67,11 +68,11 @@ class Dealii(Package):
     # Boost 1.58 is blacklisted, see
     # https://github.com/dealii/dealii/issues/1591
     # Require at least 1.59
-    # +python won't affect @:8.4.1
+    # +python won't affect @:8.4.2
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
-               when='@:8.4.1~mpi')
+               when='@:8.4.2~mpi')
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi",
-               when='@:8.4.1+mpi')
+               when='@:8.4.2+mpi')
     # since @8.5.0: (and @develop) python bindings are introduced:
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
                when='@8.5.0:~mpi~python')
@@ -102,8 +103,8 @@ class Dealii(Package):
     depends_on("netcdf-cxx",       when='+netcdf+mpi')
     depends_on("oce",              when='+oce')
     depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi",        when='@8.5.0:+petsc+mpi')
-    depends_on("slepc",            when='@8.5.0:+slepc+petsc+mpi')
+    depends_on("petsc+mpi",        when='@8.4.2:+petsc+mpi')
+    depends_on("slepc",            when='@8.4.2:+slepc+petsc+mpi')
     depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi')
     depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi')
     depends_on("trilinos",         when='+trilinos+mpi')
-- 
cgit v1.2.3-70-g09d2


From 5c11fe88df32d5ed01ad85341a829979aad90a9a Mon Sep 17 00:00:00 2001
From: "Robert D. French" <robert@robertdfrench.me>
Date: Tue, 20 Sep 2016 05:47:10 -0400
Subject: Add UberFTP utility (#1780)

---
 .../repos/builtin/packages/uberftp/package.py      | 44 ++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/uberftp/package.py

diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py
new file mode 100644
index 0000000000..b1b7dada6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/uberftp/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Uberftp(Package):
+    """UberFTP is an interactive (text-based) client for GridFTP"""
+
+    homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php"
+    url      = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz"
+
+    version('2_8', 'bc7a159955a9c4b9f5f42f3d2b8fc830')
+    version('2_7', 'faaea2d6e1958c1105cfc9147824e03c')
+    version('2_6', '784210976f259f9d19c0798c19778d34')
+
+    depends_on('globus_toolkit')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From 2cbae1d691ade03dac23b949d8233d3680961906 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 20 Sep 2016 02:48:31 -0700
Subject: Update Package: Metis (#1783)

* Fixed a bug that was causing post-install METIS tests to fail.

* Improved the patching procedure used in the 'metis' install script.

* Enabled patch skipping for the 'metis' and 'parmetis' packages.

* Fixed some minor style issues in the 'parmetis' package.

* Improved the 'metis' test fix and added 'run_tests' support.
---
 var/spack/repos/builtin/packages/metis/package.py  | 157 +++++++++++----------
 .../repos/builtin/packages/parmetis/package.py     |  18 +--
 2 files changed, 91 insertions(+), 84 deletions(-)

diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 9f8ed5c9e8..ca48a47817 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -43,16 +43,12 @@ class Metis(Package):
     version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
     version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
-    variant('shared', default=True,
-            description='Enables the build of shared libraries')
-    variant('debug', default=False,
-            description='Builds the library in debug mode')
-    variant('gdb', default=False, description='Enables gdb support')
+    variant('shared', default=True, description='Enables the build of shared libraries.')
+    variant('debug', default=False, description='Builds the library in debug mode.')
+    variant('gdb', default=False, description='Enables gdb support.')
 
-    variant('idx64', default=False,
-            description='Use int64_t as default index type')
-    variant('real64', default=False,
-            description='Use double precision floating point types')
+    variant('idx64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
+    variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.')
 
     depends_on('cmake@2.8:', when='@5:', type='build')
 
@@ -62,13 +58,38 @@ class Metis(Package):
         verdir = 'OLD/' if version < Version('4.0.3') else ''
         return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)
 
+    @when('@:4')
+    def patch(self):
+        pass
+
+    @when('@5:')
+    def patch(self):
+        source_path = self.stage.source_path
+        metis_header = FileFilter(join_path(source_path, 'include', 'metis.h'))
+
+        metis_header.filter(
+            r'(\b)(IDXTYPEWIDTH )(\d+)(\b)',
+            r'\1\2{0}\4'.format('64' if '+idx64' in self.spec else '32'),
+        )
+        metis_header.filter(
+            r'(\b)(REALTYPEWIDTH )(\d+)(\b)',
+            r'\1\2{0}\4'.format('64' if '+real64' in self.spec else '32'),
+        )
+
+        # Make clang 7.3 happy.
+        # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
+        # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
+        # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
+        if self.spec.satisfies('%clang@7.3.0'):
+            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
+                        join_path(source_path, 'GKlib', 'error.c'))
+
     @when('@:4')
     def install(self, spec, prefix):
         # Process library spec and options
-        unsupp_vars = [v for v in ('+gdb', '+idx64', '+real64') if v in spec]
-        if unsupp_vars:
-            msg = 'Given variants %s are unsupported by METIS 4!' % unsupp_vars
-            raise InstallError(msg)
+        if any('+{0}'.format(v) in spec for v in ['gdb', 'idx64', 'real64']):
+            raise InstallError('METIS@:4 does not support the following '
+                               'variants: gdb, idx64, real64.')
 
         options = ['COPTIONS=-fPIC']
         if '+debug' in spec:
@@ -118,49 +139,48 @@ class Metis(Package):
                  join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
                  '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
 
-        test_bin = lambda testname: join_path(prefix.bin, testname)
-        test_graph = lambda graphname: join_path(prefix.share, graphname)
-
-        graph = test_graph('4elt.graph')
-        os.system('%s %s' % (test_bin('mtest'), graph))
-        os.system('%s %s 40' % (test_bin('kmetis'), graph))
-        os.system('%s %s' % (test_bin('onmetis'), graph))
-        graph = test_graph('test.mgraph')
-        os.system('%s %s 2' % (test_bin('pmetis'), graph))
-        os.system('%s %s 2' % (test_bin('kmetis'), graph))
-        os.system('%s %s 5' % (test_bin('kmetis'), graph))
-        graph = test_graph('metis.mesh')
-        os.system('%s %s 10' % (test_bin('partnmesh'), graph))
-        os.system('%s %s 10' % (test_bin('partdmesh'), graph))
-        os.system('%s %s' % (test_bin('mesh2dual'), graph))
-
-        # FIXME: The following code should replace the testing code in the
-        # block above since it causes installs to fail when one or more of the
-        # Metis tests fail, but it currently doesn't work because the 'mtest',
-        # 'onmetis', and 'partnmesh' tests return error codes that trigger
-        # false positives for failure.
-        """
-        Executable(test_bin('mtest'))(test_graph('4elt.graph'))
-        Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
-        Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
-
-        Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
-        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
-        Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
-
-        Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
-        Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
-        Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
-        """
+        if self.run_tests:
+            test_bin = lambda testname: join_path(prefix.bin, testname)
+            test_graph = lambda graphname: join_path(prefix.share, graphname)
+
+            graph = test_graph('4elt.graph')
+            os.system('%s %s' % (test_bin('mtest'), graph))
+            os.system('%s %s 40' % (test_bin('kmetis'), graph))
+            os.system('%s %s' % (test_bin('onmetis'), graph))
+            graph = test_graph('test.mgraph')
+            os.system('%s %s 2' % (test_bin('pmetis'), graph))
+            os.system('%s %s 2' % (test_bin('kmetis'), graph))
+            os.system('%s %s 5' % (test_bin('kmetis'), graph))
+            graph = test_graph('metis.mesh')
+            os.system('%s %s 10' % (test_bin('partnmesh'), graph))
+            os.system('%s %s 10' % (test_bin('partdmesh'), graph))
+            os.system('%s %s' % (test_bin('mesh2dual'), graph))
+
+            # FIXME: The following code should replace the testing code in the
+            # block above since it causes installs to fail when one or more of
+            # the Metis tests fail, but it currently doesn't work because the
+            # 'mtest', 'onmetis', and 'partnmesh' tests return error codes that
+            # trigger false positives for failure.
+            """
+            Executable(test_bin('mtest'))(test_graph('4elt.graph'))
+            Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
+            Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
+
+            Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
+            Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
+            Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
+
+            Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
+            Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
+            Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
+            """
 
     @when('@5:')
     def install(self, spec, prefix):
-        options = []
-        options.extend(std_cmake_args)
-
-        build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
+        build_directory = join_path(source_directory, 'build')
 
+        options = std_cmake_args[:]
         options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
@@ -172,26 +192,24 @@ class Metis(Package):
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        metis_header = join_path(source_directory, 'include', 'metis.h')
-        if '+idx64' in spec:
-            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-        if '+real64' in spec:
-            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
-
-        # Make clang 7.3 happy.
-        # Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
-        # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
-        # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
-        if spec.satisfies('%clang@7.3.0'):
-            filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
-                        join_path(source_directory, 'GKlib', 'error.c'))
-
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make('install')
 
-            # now run some tests:
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include, 'GKlib')
+            mkdirp(GKlib_dist)
+            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
+            for hfile in hfiles:
+                install(hfile, GKlib_dist)
+
+        if self.run_tests:
+            # FIXME: On some systems, the installed binaries for METIS cannot
+            # be executed without first being read.
+            ls = which('ls')
+            ls('-a', '-l', prefix.bin)
+
             for f in ['4elt', 'copter2', 'mdual']:
                 graph = join_path(source_directory, 'graphs', '%s.graph' % f)
                 Executable(join_path(prefix.bin, 'graphchk'))(graph)
@@ -202,10 +220,3 @@ class Metis(Package):
             Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
             graph = join_path(source_directory, 'graphs', 'metis.mesh')
             Executable(join_path(prefix.bin, 'mpmetis'))(graph, '2')
-
-            # install GKlib headers, which will be needed for ParMETIS
-            GKlib_dist = join_path(prefix.include, 'GKlib')
-            mkdirp(GKlib_dist)
-            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
-            for hfile in hfiles:
-                install(hfile, GKlib_dist)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 8afae91af1..74e00cc9e0 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -38,11 +38,9 @@ class Parmetis(Package):
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
-    variant('shared', default=True,
-            description='Enables the build of shared libraries')
-    variant('debug', default=False,
-            description='Builds the library in debug mode')
-    variant('gdb', default=False, description='Enables gdb support')
+    variant('shared', default=True, description='Enables the build of shared libraries.')
+    variant('debug', default=False, description='Builds the library in debug mode.')
+    variant('gdb', default=False, description='Enables gdb support.')
 
     depends_on('cmake@2.8:', type='build')
     depends_on('mpi')
@@ -50,9 +48,9 @@ class Parmetis(Package):
 
     patch('enable_external_metis.patch')
     # bug fixes from PETSc developers
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/  # NOQA: E501
     patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/  # NOQA: E501
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
     def url_for_version(self, version):
@@ -60,12 +58,10 @@ class Parmetis(Package):
         return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)
 
     def install(self, spec, prefix):
-        options = []
-        options.extend(std_cmake_args)
-
-        build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
+        build_directory = join_path(source_directory, 'build')
 
+        options = std_cmake_args[:]
         options.extend([
             '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
             '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
-- 
cgit v1.2.3-70-g09d2


From eb8a0ef75ee2d4b66418f39a336c4f0a829b5670 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Tue, 20 Sep 2016 16:47:13 +0200
Subject: fix : failing unit tests due to missing `self` (#1806)

---
 lib/spack/spack/test/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index 88f67090f1..c4cf2865bb 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -251,7 +251,7 @@ class TclTests(ModuleFileGeneratorTests):
         # - 1 ('build','link') dependency
         # - 1 ('build',) dependency
         # Just make sure the 'build' dependency is not there
-        spack.modules.CONFIGURATION = configuration_autoload_direct
+        spack.modules.CONFIGURATION = self.configuration_autoload_direct
         spec = spack.spec.Spec('dtbuild1')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
@@ -262,7 +262,7 @@ class TclTests(ModuleFileGeneratorTests):
         # - 1 ('build','link') dependency
         # - 1 ('build',) dependency
         # Just make sure the 'build' dependency is not there
-        spack.modules.CONFIGURATION = configuration_autoload_all
+        spack.modules.CONFIGURATION = self.configuration_autoload_all
         spec = spack.spec.Spec('dtbuild1')
         content = self.get_modulefile_content(spec)
         self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
-- 
cgit v1.2.3-70-g09d2


From f180d748be3041ec105d46f3e9a44a6137e21ec0 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 20 Sep 2016 10:01:55 -0500
Subject: Remove lingering boilerplate FIXMEs (#1756)

---
 var/spack/repos/builtin/packages/bpp-suite/package.py        | 1 -
 var/spack/repos/builtin/packages/icu/package.py              | 4 ++--
 var/spack/repos/builtin/packages/libuuid/package.py          | 3 +--
 var/spack/repos/builtin/packages/py-py2neo/package.py        | 7 ++++---
 var/spack/repos/builtin/packages/xorg-util-macros/package.py | 2 +-
 5 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py
index ef7f25a7ce..d15030622e 100644
--- a/var/spack/repos/builtin/packages/bpp-suite/package.py
+++ b/var/spack/repos/builtin/packages/bpp-suite/package.py
@@ -34,7 +34,6 @@ class BppSuite(Package):
 
     version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4')
 
-    # FIXME: Add dependencies if required.
     depends_on('cmake', type='build')
     depends_on('texinfo', type='build')
     depends_on('bpp-core')
diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/icu/package.py
index b8d366b905..bf24067879 100644
--- a/var/spack/repos/builtin/packages/icu/package.py
+++ b/var/spack/repos/builtin/packages/icu/package.py
@@ -31,8 +31,8 @@ class Icu(Package):
        Globalization support for software applications. ICU is widely
        portable and gives applications the same results on all
        platforms."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
+
+    homepage = "http://site.icu-project.org/"
     url      = "http://download.icu-project.org/files/icu4c/54.1/icu4c-54_1-src.tgz"
 
     version('54.1', 'e844caed8f2ca24c088505b0d6271bc0')
diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py
index 553f0dddb8..b8f6b1cc3a 100644
--- a/var/spack/repos/builtin/packages/libuuid/package.py
+++ b/var/spack/repos/builtin/packages/libuuid/package.py
@@ -27,7 +27,7 @@ from spack import *
 
 class Libuuid(Package):
     """Portable uuid C library"""
-    # FIXME: add a proper url for your package's homepage here.
+
     homepage = "http://sourceforge.net/projects/libuuid/"
     url      = "http://downloads.sourceforge.net/project/libuuid/libuuid-1.0.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Flibuuid%2F&ts=1433881396&use_mirror=iweb"
 
@@ -36,6 +36,5 @@ class Libuuid(Package):
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py
index a79c2e477b..97632493af 100644
--- a/var/spack/repos/builtin/packages/py-py2neo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2neo/package.py
@@ -27,9 +27,10 @@ from spack import Package
 
 
 class PyPy2neo(Package):
-    """FIXME: put a proper description of your package here."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
+    """Py2neo is a client library and toolkit for working with Neo4j from
+    within Python applications and from the command line."""
+
+    homepage = "http://py2neo.org/"
     url      = "https://github.com/nigelsmall/py2neo/archive/py2neo-2.0.8.tar.gz"
 
     version('2.0.8', 'e3ec5172a9e006515ef4155688a05a55')
diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
index cd50d46826..3cfc4c2408 100644
--- a/var/spack/repos/builtin/packages/xorg-util-macros/package.py
+++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
@@ -28,7 +28,7 @@ from spack import *
 class XorgUtilMacros(Package):
     """The m4 macros used by all of the Xorg packages."""
 
-    homepage = "http://www.example.com"
+    homepage = "https://cgit.freedesktop.org/xorg/util/macros/"
     url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2"
 
     version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1')
-- 
cgit v1.2.3-70-g09d2


From 00bac8f2941ebbbe86fe56808ad2791454ba7d38 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 13:05:57 -0400
Subject: PETSc: Explicitly point to cpp when configuring (#1807)

I encountered an HPC system where PETSc's configure stage does not find a valid `cpp` (C preprocessor). Explicitly pointing to Spack's `cpp` wrapper resolves the problem.
---
 var/spack/repos/builtin/packages/petsc/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 73091bb182..1f1b9adffd 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -90,6 +90,8 @@ class Petsc(Package):
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
             compiler_opts = [
+                '--with-cpp=cpp',
+                '--with-cxxcpp=cpp',
                 '--with-cc=%s' % os.environ['CC'],
                 '--with-cxx=%s' % (os.environ['CXX']
                                    if self.compiler.cxx is not None else '0'),
@@ -111,6 +113,8 @@ class Petsc(Package):
                 raise RuntimeError('\n'.join(errors))
         else:
             compiler_opts = [
+                '--with-cpp=cpp',
+                '--with-cxxcpp=cpp',
                 '--with-mpi=1',
                 '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
             ]
-- 
cgit v1.2.3-70-g09d2


From 7f9e89eb53c0e093c5efbb8b270e0b3815c90570 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 20 Sep 2016 10:08:25 -0700
Subject: Update Package: Git-LFS (#1769)

* Fixed a few small bugs in the 'git-lfs' install script.

* Fixed a bug in the '(go|go-bootstrap)@1.4.2+test' install scripts.

* Fixing a minor style issue in the 'git-lfs' install script.
---
 .../repos/builtin/packages/git-lfs/package.py      | 23 ++++++---
 .../repos/builtin/packages/go-bootstrap/package.py | 56 +++++++++++++++++----
 var/spack/repos/builtin/packages/go/package.py     | 57 +++++++++++++++++-----
 3 files changed, 109 insertions(+), 27 deletions(-)

diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py
index a080660721..25e440ff6d 100644
--- a/var/spack/repos/builtin/packages/git-lfs/package.py
+++ b/var/spack/repos/builtin/packages/git-lfs/package.py
@@ -26,17 +26,28 @@ from spack import *
 
 
 class GitLfs(Package):
-    """Tool for managing large files with Git."""
+    """Git LFS is a system for managing and versioning large files in
+       association with a Git repository.  Instead of storing the large files
+       within the Git repository as blobs, Git LFS stores special "pointer
+       files" in the repository, while storing the actual file contents on a
+       Git LFS server."""
 
     homepage = "https://git-lfs.github.com"
-    url      = "https://github.com/github/git-lfs/archive/v1.4.1.tar.gz"
+    git_url  = "https://github.com/github/git-lfs.git"
 
-    version('1.4.1', 'c62a314d96d3a30af4d98fa3305ad317')
+    version('1.4.1', git=git_url, tag='v1.4.1')
+    version('1.3.1', git=git_url, tag='v1.3.1')
+
+    # TODO: Implement this by following the instructions at this location:
+    # https://github.com/github/git-lfs/blob/master/CONTRIBUTING.md#building
+    # variant('test', default=True, description='Build and run tests as part of the build.')  # NOQA: E501
 
     depends_on('go@1.5:', type='build')
     depends_on('git@1.8.2:', type='run')
 
     def install(self, spec, prefix):
-        bootstrap = Executable('./scripts/bootstrap')
-        bootstrap()
-        install('bin/git-lfs', prefix.bin)
+        bootstrap_script = Executable(join_path('script', 'bootstrap'))
+        bootstrap_script()
+
+        mkdirp(prefix.bin)
+        install(join_path('bin', 'git-lfs'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py
index b0e2109fd3..d48c7c9756 100644
--- a/var/spack/repos/builtin/packages/go-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 import os
 import shutil
 import glob
@@ -17,25 +41,37 @@ class GoBootstrap(Package):
 
     extendable = True
 
-    # temporary fix until tags are pulled correctly
+    # NOTE: Go@1.4.2 is the only supported bootstrapping compiler because all
+    # later versions require a Go compiler to build.
+    # See: https://golang.org/doc/install/source
     version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2')
 
-    variant('test',
-            default=True,
-            description="Run tests as part of build, a good idea but quite"
-            " time consuming")
+    variant('test', default=True, description='Build and run tests as part of the build.')
 
     provides('golang@:1.4.2')
 
-    depends_on('git')
+    depends_on('git', type='alldeps')
+
+    # NOTE: Older versions of Go attempt to download external files that have
+    # since been moved while running the test suite.  This patch modifies the
+    # test files so that these tests don't cause false failures.
+    # See: https://github.com/golang/go/issues/15694
+    @when('@:1.4.3')
+    def patch(self):
+        test_suite_file = FileFilter(join_path('src', 'run.bash'))
+        test_suite_file.filter(
+            r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$',
+            r'# \1\2\3',
+        )
+
+    @when('@1.5.0:')
+    def patch(self):
+        pass
 
     def install(self, spec, prefix):
         bash = which('bash')
         with working_dir('src'):
-            if '+test' in spec:
-                bash('all.bash')
-            else:
-                bash('make.bash')
+            bash('{0}.bash'.format('all' if '+test' in spec else 'make'))
 
         try:
             os.makedirs(prefix)
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 259498c145..5fa3017ab5 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 import os
 import shutil
 import glob
@@ -12,28 +36,39 @@ class Go(Package):
 
     extendable = True
 
-    version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4')
     version('1.6.2', git='https://go.googlesource.com/go', tag='go1.6.2')
+    version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4')
+    version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2')
 
-    variant('test',
-            default=True,
-            description="Run tests as part of build, a good idea but quite"
-            " time consuming")
+    variant('test', default=True, description='Build and run tests as part of the build.')
 
     provides('golang')
 
-    # to-do, make non-c self-hosting compilers feasible without backflips
+    depends_on('git', type='alldeps')
+    # TODO: Make non-c self-hosting compilers feasible without backflips
     # should be a dep on external go compiler
     depends_on('go-bootstrap', type='build')
-    depends_on('git', type='alldeps')
+
+    # NOTE: Older versions of Go attempt to download external files that have
+    # since been moved while running the test suite.  This patch modifies the
+    # test files so that these tests don't cause false failures.
+    # See: https://github.com/golang/go/issues/15694
+    @when('@:1.4.3')
+    def patch(self):
+        test_suite_file = FileFilter(join_path('src', 'run.bash'))
+        test_suite_file.filter(
+            r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$',
+            r'# \1\2\3',
+        )
+
+    @when('@1.5.0:')
+    def patch(self):
+        pass
 
     def install(self, spec, prefix):
         bash = which('bash')
         with working_dir('src'):
-            if '+test' in spec:
-                bash('all.bash')
-            else:
-                bash('make.bash')
+            bash('{0}.bash'.format('all' if '+test' in spec else 'make'))
 
         try:
             os.makedirs(prefix)
-- 
cgit v1.2.3-70-g09d2


From db483e77e4c7071d8ad390859bc470a26686b6c6 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 20 Sep 2016 12:17:51 -0500
Subject: Remove url_for_version as it breaks spack info (#1503)

---
 var/spack/repos/builtin/packages/openssl/package.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 37442e1451..40c8b1b9f1 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -48,12 +48,6 @@ class Openssl(Package):
     depends_on("zlib")
     parallel = False
 
-    def url_for_version(self, version):
-        if '@system' in self.spec:
-            return '@system (reserved version for system openssl)'
-        else:
-            return super(Openssl, self).url_for_version(self.version)
-
     def handle_fetch_error(self, error):
         tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has "
                  "been updated, and the version in your instance of Spack is "
-- 
cgit v1.2.3-70-g09d2


From ef1f44142497160e09fa0cb4a36a42737dbd42c8 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 20 Sep 2016 15:40:58 -0400
Subject: Julia: Add version 0.5.0 (#1809)

---
 var/spack/repos/builtin/packages/julia/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 93c8b1c4b3..c7c701175e 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -37,9 +37,10 @@ class Julia(Package):
             git='https://github.com/JuliaLang/julia.git', branch='master')
     version('release-0.5',
             git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
+    version('0.5.0', 'b61385671ba74767ab452363c43131fb', preferred=True)
     version('release-0.4',
             git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
-    version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078', preferred=True)
+    version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078')
     version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d')
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
     version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
@@ -163,7 +164,7 @@ class Julia(Package):
         # Configure Julia
         with open(join_path(prefix, "etc", "julia", "juliarc.jl"),
                   "a") as juliarc:
-            if "@master" in spec or "@release-0.5" in spec:
+            if "@master" in spec or "@release-0.5" in spec or "@0.5:" in spec:
                 # This is required for versions @0.5:
                 juliarc.write(
                     '# Point package manager to working certificates\n')
-- 
cgit v1.2.3-70-g09d2


From 25ee9456f535eee7aadc7ea1f24b8064569328a7 Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@llnl.gov>
Date: Tue, 20 Sep 2016 16:09:31 -0700
Subject: added STAT release 3.0.0

---
 var/spack/repos/builtin/packages/stat/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index 8c4663c524..eae4971ace 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -34,8 +34,8 @@ class Stat(Package):
     version('2.2.0', '26bd69dd57a15afdd5d0ebdb0b7fb6fc')
     version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
     version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
-    version('3.0.0b', '8851912ba40e31cf7be6dde3be8e702c',
-            url='https://github.com/LLNL/STAT/files/427762/STAT-3.0.0b.tar.gz')
+    version('3.0.0', 'a97cb235c266371c4a26329112de48a2',
+            url='https://github.com/LLNL/STAT/releases/download/v3.0.0/STAT-3.0.0.tar.gz')
 
     # TODO: dysect requires Dyninst patch for version 3.0.0b
     variant('dysect', default=False, description="enable DySectAPI")
-- 
cgit v1.2.3-70-g09d2


From 27801c354be7e05bca1b3fd68468db1d2728376b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 21 Sep 2016 02:25:23 +0200
Subject: fix MacOs class for Sierra (#1811)

---
 lib/spack/spack/operating_systems/mac_os.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py
index 3e5ab9b2e9..dafb5c1d41 100644
--- a/lib/spack/spack/operating_systems/mac_os.py
+++ b/lib/spack/spack/operating_systems/mac_os.py
@@ -22,7 +22,7 @@ class MacOs(OperatingSystem):
                         "10.11": "elcapitan",
                         "10.12": "sierra"}
 
-        mac_ver = py_platform.mac_ver()[0][:-2]
+        mac_ver = '.'.join(py_platform.mac_ver()[0].split('.')[:2])
         name = mac_releases.get(mac_ver, "macos")
         super(MacOs, self).__init__(name, mac_ver)
 
-- 
cgit v1.2.3-70-g09d2


From e6dc448f1843078f922d9ff018cc4bd0c9a19967 Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Wed, 31 Aug 2016 12:13:08 -0500
Subject: Compiling python with gnu c++ on macos fails with toolboxglue
 enabled.

---
 var/spack/repos/builtin/packages/python/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 57783b0542..e95bb4ba24 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -110,6 +110,8 @@ class Python(Package):
             'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
             'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
         ]
+        if spec.satisfies("platform=darwin") and ('%gcc' in spec):
+            config_args.append('--disable-toolbox-glue')
 
         if '+ucs4' in spec:
             if spec.satisfies('@:2.7'):
-- 
cgit v1.2.3-70-g09d2


From 746495896cff3f1c43ef306afac3fd3e63695d62 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <skosukhin@gmail.com>
Date: Wed, 21 Sep 2016 09:25:14 +0200
Subject: Qt library: added variant to enable/disable compilation of examples
 (#1763)

---
 var/spack/repos/builtin/packages/qt/package.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 436702fa4e..0534c43a7c 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -47,6 +47,7 @@ class Qt(Package):
     variant('krellpatch', default=False, description="Build with openspeedshop based patch.")
     variant('mesa',       default=False, description="Depend on mesa.")
     variant('gtk',        default=False, description="Build with gtkplus.")
+    variant('examples',   default=False, description="Build examples.")
 
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
@@ -143,7 +144,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
-        return [
+        common_arg_list = [
             '-prefix', self.prefix,
             '-v',
             '-opensource',
@@ -160,6 +161,11 @@ class Qt(Package):
             '-no-nis'
         ]
 
+        if '~examples' in self.spec:
+            common_arg_list.extend(['-nomake', 'examples'])
+
+        return common_arg_list
+
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 
-- 
cgit v1.2.3-70-g09d2


From 3c7ea3000a948cd2fd336881ffc4c4fd8981603b Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Wed, 21 Sep 2016 03:37:46 -0400
Subject: Wrap yt package (#1751)

yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
---
 var/spack/repos/builtin/packages/py-yt/package.py | 78 +++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-yt/package.py

diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py
new file mode 100644
index 0000000000..646bd4db2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-yt/package.py
@@ -0,0 +1,78 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class PyYt(Package):
+    """Volumetric Data Analysis
+
+       yt is a python package for analyzing and visualizing
+       volumetric, multi-resolution data from astrophysical
+       simulations, radio telescopes, and a burgeoning
+       interdisciplinary community.
+    """
+    homepage = "http://yt-project.org"
+    url = "https://bitbucket.org/yt_analysis/yt"
+
+    version("3.3.1", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.3.1", commit="9bc3d0e9b750c923d44d73c447df64fc431f5838")
+    version("3.2.3", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.2.3", commit="83d2c1e9313e7d83eb5b96888451ff2646fd8ff3")
+    version("3.1.0", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.1.0", commit="fd7cdc4836188a3badf81adb477bcc1b9632e485")
+    version("3.0.2", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-3.0.2", commit="511887af4c995a78fe606e58ce8162c88380ecdc")
+    version("2.6.3", hg="https://bitbucket.org/yt_analysis/yt",
+            tag="yt-2.6.3", commit="816186f16396a16853810ac9ebcde5057d8d5b1a")
+    version("development", hg="https://bitbucket.org/yt_analysis/yt",
+            branch="yt")
+
+    variant("astropy", default=True, description="enable astropy support")
+    variant("h5py", default=True, description="enable h5py support")
+    variant("scipy", default=True, description="enable scipy support")
+
+    extends("python")
+
+    depends_on("py-astropy", type="nolink", when="+astropy")
+    depends_on("py-cython", type="nolink")
+    depends_on("py-h5py", type="nolink", when="+h5py")
+    depends_on("py-ipython", type="nolink")
+    depends_on("py-matplotlib", type="nolink")
+    depends_on("py-numpy", type="nolink")
+    depends_on("py-scipy", type="nolink", when="+scipy")
+    depends_on("py-setuptools", type="build")
+    depends_on("py-sympy", type="nolink")
+    depends_on("python @2.7:2.999,3.4:")
+
+    def install(self, spec, prefix):
+        setup_py("install", "--prefix=%s" % prefix)
+        self.check_install(spec, prefix)
+
+    def check_install(self, spec, prefix):
+        # The Python interpreter path can be too long for this
+        # yt = Executable(join_path(prefix.bin, "yt"))
+        # yt("--help")
+        python(join_path(prefix.bin, "yt"), "--help")
-- 
cgit v1.2.3-70-g09d2


From 1cc48bf7d78f592097f795a62546effd5f04d38d Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Wed, 21 Sep 2016 09:51:49 +0200
Subject: grackle : added package (#1725)

Modifications :

* grackle : added package
* grackle : added version 2.2
---
 .../builtin/packages/grackle/Make.mach.template    | 71 +++++++++++++++++
 .../repos/builtin/packages/grackle/package.py      | 89 ++++++++++++++++++++++
 2 files changed, 160 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/grackle/Make.mach.template
 create mode 100644 var/spack/repos/builtin/packages/grackle/package.py

diff --git a/var/spack/repos/builtin/packages/grackle/Make.mach.template b/var/spack/repos/builtin/packages/grackle/Make.mach.template
new file mode 100644
index 0000000000..83abaa26d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grackle/Make.mach.template
@@ -0,0 +1,71 @@
+MACH_TEXT  = Generic Linux
+MACH_VALID = 1
+MACH_FILE  = Make.mach.@ARCHITECTURE
+
+#-----------------------------------------------------------------------
+# Install paths (local variables)
+#-----------------------------------------------------------------------
+
+LOCAL_HDF5_INSTALL = @HDF5_ROOT
+
+#-----------------------------------------------------------------------
+# Compiler settings
+#-----------------------------------------------------------------------
+
+MACH_CC_NOMPI  = @CC # C compiler
+MACH_CXX_NOMPI = @CXX # C++ compiler
+MACH_FC_NOMPI  = @F77 # Fortran 77
+MACH_F90_NOMPI = @FC # Fortran 90
+MACH_LD_NOMPI  = @FC # Linker
+@LINK_VARIABLES_DEFINITION
+
+#-----------------------------------------------------------------------
+# Machine-dependent defines
+#-----------------------------------------------------------------------
+
+MACH_DEFINES   = -DLINUX -DH5_USE_16_API -fPIC
+
+#-----------------------------------------------------------------------
+# Compiler flag settings
+#-----------------------------------------------------------------------
+
+MACH_CPPFLAGS = -P -traditional
+MACH_CFLAGS   = 
+MACH_CXXFLAGS = 
+MACH_FFLAGS   = -fno-second-underscore -ffixed-line-length-132
+MACH_F90FLAGS = -fno-second-underscore
+MACH_LDFLAGS  = @STDCXX_LIB
+
+#-----------------------------------------------------------------------
+# Optimization flags
+#-----------------------------------------------------------------------
+
+MACH_OPT_WARN        = -Wall -g
+MACH_OPT_DEBUG       = -g
+MACH_OPT_HIGH        = -O2
+MACH_OPT_AGGRESSIVE  = -O3 -g
+
+#-----------------------------------------------------------------------
+# Includes
+#-----------------------------------------------------------------------
+
+LOCAL_INCLUDES_HDF5   = -I@HDF5_ROOT/include # HDF5 includes
+
+MACH_INCLUDES         = $(LOCAL_INCLUDES_HDF5)
+
+#-----------------------------------------------------------------------
+# Libraries
+#-----------------------------------------------------------------------
+
+LOCAL_LIBS_HDF5   = -L@HDF5_ROOT/lib -lhdf5 # HDF5 libraries
+LOCAL_LIBS_MACH   =  # Machine-dependent libraries
+
+MACH_LIBS         = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH)
+
+#-----------------------------------------------------------------------
+# Installation
+#-----------------------------------------------------------------------
+
+MACH_INSTALL_PREFIX = @PREFIX
+MACH_INSTALL_LIB_DIR =
+MACH_INSTALL_INCLUDE_DIR =
diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py
new file mode 100644
index 0000000000..7e3777158f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grackle/package.py
@@ -0,0 +1,89 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os.path
+import shutil
+import inspect
+
+from spack import *
+
+
+class Grackle(Package):
+    """Grackle is a chemistry and radiative cooling library for astrophysical
+    simulations with interfaces for C, C++, and Fortran codes. It is a
+    generalized and trimmed down version of the chemistry network of the Enzo
+    simulation code
+    """
+    homepage = 'http://grackle.readthedocs.io/en/grackle-2.2/'
+    url = 'https://bitbucket.org/grackle/grackle/get/grackle-2.0.1.tar.bz2'
+
+    version('2.2', 'ec49ed1db5a42db21f478285150c2ba3')
+    version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d')
+
+    depends_on('libtool', when='@2.2')
+
+    depends_on('mpi')
+    depends_on('hdf5+mpi')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        template_name = '{0.architecture}-{0.compiler.name}'
+        grackle_architecture = template_name.format(spec)
+        link_variables = 'MACH_AR = ar' if spec.version < Version(2.2) else 'MACH_LIBTOOL = libtool'  # NOQA: ignore=E501
+        substitutions = {
+            '@ARCHITECTURE': grackle_architecture,
+            '@CC': spec['mpi'].mpicc,
+            '@CXX': spec['mpi'].mpicxx,
+            '@FC': spec['mpi'].mpifc,
+            '@F77': spec['mpi'].mpif77,
+            '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs),
+            '@HDF5_ROOT': spec['hdf5'].prefix,
+            '@PREFIX': prefix,
+            '@LINK_VARIABLES_DEFINITION': link_variables
+        }
+
+        template = join_path(
+            os.path.dirname(inspect.getmodule(self).__file__),
+            'Make.mach.template'
+        )
+        makefile = join_path(
+            self.stage.source_path,
+            'src',
+            'clib',
+            'Make.mach.{0}'.format(grackle_architecture)
+        )
+        shutil.copy(template, makefile)
+        for key, value in substitutions.items():
+            filter_file(key, value, makefile)
+
+        configure()
+        with working_dir('src/clib'):
+            make('clean')
+            make('machine-{0}'.format(grackle_architecture))
+            make('opt-high')
+            make('show-config')
+            make()
+            mkdirp(prefix.lib)
+            make('install')
-- 
cgit v1.2.3-70-g09d2


From 02307cf7ceabdf16d02f1afd0f38c50bd7501080 Mon Sep 17 00:00:00 2001
From: Alfredo Adolfo Gimenez <alfredo.gimenez@gmail.com>
Date: Wed, 21 Sep 2016 00:52:09 -0700
Subject: Set JAVA_HOME on module load and on dependent installs. (#1716)

* Set JAVA_HOME on module load and on dependent installs.

* Include environment setup from dependencies in dependee module (#1714)
---
 lib/spack/spack/modules.py                      | 1 +
 var/spack/repos/builtin/packages/jdk/package.py | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d75bfbac45..aa3ad5843f 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -392,6 +392,7 @@ class EnvModule(object):
             for mod in modules:
                 set_module_variables_for_package(package, mod)
             set_module_variables_for_package(package, package.module)
+            package.setup_environment(spack_env, env)
             package.setup_dependent_package(self.pkg.module, self.spec)
             package.setup_dependent_environment(spack_env, env, self.spec)
 
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 63bf6514cb..bab0920434 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -68,3 +68,9 @@ class Jdk(Package):
 
     def install(self, spec, prefix):
         distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('JAVA_HOME', self.spec.prefix)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('JAVA_HOME', self.spec.prefix)
-- 
cgit v1.2.3-70-g09d2


From 3254d2f8f9d3b26f9afbfa73d6fb66dffafdaadd Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Wed, 21 Sep 2016 09:53:06 +0200
Subject: cp2k : added dependencies (#1724)

* wannier90 : added package (#24)

* wannier90 : added package

* cp2k : added dependency on wannier90

* elpa : updated package, added cp2k dependency (#26)

Conflicts:
	var/spack/repos/builtin/packages/elpa/package.py
---
 var/spack/repos/builtin/packages/cp2k/package.py   |  21 +++-
 var/spack/repos/builtin/packages/elpa/package.py   |  19 +++-
 .../repos/builtin/packages/wannier90/make.sys      |   7 ++
 .../repos/builtin/packages/wannier90/package.py    | 117 +++++++++++++++++++++
 4 files changed, 157 insertions(+), 7 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/wannier90/make.sys
 create mode 100644 var/spack/repos/builtin/packages/wannier90/package.py

diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 052c7a971c..785de08d34 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -53,13 +53,13 @@ class Cp2k(Package):
     depends_on('plumed+shared+mpi', when='+plumed+mpi')
     depends_on('plumed+shared~mpi', when='+plumed~mpi')
     depends_on('pexsi', when='+mpi')
+    depends_on('wannier90', when='+mpi')
+    depends_on('elpa', when='+mpi')
 
     # TODO : add dependency on libint
     # TODO : add dependency on libsmm, libxsmm
-    # TODO : add dependency on elpa
     # TODO : add dependency on CUDA
     # TODO : add dependency on QUIP
-    # TODO : add dependency on libwannier90
 
     parallel = False
 
@@ -109,7 +109,8 @@ class Cp2k(Package):
                 # Add required macro
                 cppflags.extend(['-D__PLUMED2'])
                 libs.extend([
-                    join_path(self.spec['plumed'].prefix.lib, 'libplumed.so')
+                    join_path(self.spec['plumed'].prefix.lib,
+                              'libplumed.{0}'.format(dso_suffix))
                 ])
 
             mkf.write('CC = {0.compiler.cc}\n'.format(self))
@@ -143,15 +144,26 @@ class Cp2k(Package):
             if '+mpi' in self.spec:
                 cppflags.extend([
                     '-D__parallel',
+                    '-D__WANNIER90',
+                    '-D__ELPA3',
                     '-D__SCALAPACK'
                 ])
                 fcflags.extend([
+                    '-I' + join_path(
+                        spec['elpa'].prefix,
+                        'include',
+                        'elpa-{0}'.format(str(spec['elpa'].version)),
+                        'modules'
+                    ),
                     '-I' + join_path(spec['pexsi'].prefix, 'fortran')
                 ])
                 ldflags.extend([
                     '-L' + spec['scalapack'].prefix.lib
                 ])
                 libs.extend([
+                    join_path(spec['elpa'].prefix.lib,
+                              'libelpa.{0}'.format(dso_suffix)),
+                    join_path(spec['wannier90'].prefix.lib, 'libwannier.a'),
                     join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
                     join_path(spec['superlu-dist'].prefix.lib,
                               'libsuperlu_dist.a'),
@@ -173,7 +185,8 @@ class Cp2k(Package):
                 '-L' + spec['blas'].prefix.lib
             ])
             libs.extend([
-                join_path(spec['fftw'].prefix.lib, 'libfftw3.so'),
+                join_path(spec['fftw'].prefix.lib,
+                          'libfftw3.{0}'.format(dso_suffix)),
                 spec['lapack'].lapack_shared_lib,
                 spec['blas'].blas_shared_lib
             ])
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index f28d63f6c3..ae3f26b3ec 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -34,8 +34,16 @@ class Elpa(Package):
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
-    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6',
-            url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz')
+    version(
+        '2016.05.003',
+        '88a9f3f3bfb63e16509dd1be089dcf2c',
+        url='http://elpa.mpcdf.mpg.de/html/Releases/2016.05.003/elpa-2016.05.003.tar.gz'
+    )
+    version(
+        '2015.11.001',
+        'de0f35b7ee7c971fd0dca35c900b87e6',
+        url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
+    )
 
     variant('openmp', default=False, description='Activates OpenMP support')
 
@@ -46,7 +54,12 @@ class Elpa(Package):
 
     def install(self, spec, prefix):
 
-        options = ["--prefix=%s" % prefix]
+        options = [
+            'CC={0}'.format(self.spec['mpi'].mpicc),
+            'FC={0}'.format(self.spec['mpi'].mpifc),
+            'CXX={0}'.format(self.spec['mpi'].mpicxx),
+            '--prefix={0}'.format(self.prefix)
+        ]
 
         if '+openmp' in spec:
             options.append("--enable-openmp")
diff --git a/var/spack/repos/builtin/packages/wannier90/make.sys b/var/spack/repos/builtin/packages/wannier90/make.sys
new file mode 100644
index 0000000000..f96fa23fb2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wannier90/make.sys
@@ -0,0 +1,7 @@
+F90 = @F90
+COMMS=mpi
+MPIF90=@MPIF90
+FCOPTS=-O2 -fpic
+LDOPTS=-O2 -fpic
+
+LIBS = @LIBS
diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py
new file mode 100644
index 0000000000..189e568cdc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wannier90/package.py
@@ -0,0 +1,117 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import inspect
+import os.path
+import shutil
+
+from spack import *
+
+
+class Wannier90(Package):
+    """Wannier90 calculates maximally-localised Wannier functions (MLWFs).
+
+    Wannier90 is released under the GNU General Public License.
+    """
+    homepage = 'http://wannier.org'
+    url = 'http://wannier.org/code/wannier90-2.0.1.tar.gz'
+
+    version('2.0.1', '4edd742506eaba93317249d33261fb22')
+
+    depends_on('mpi')
+    depends_on('lapack')
+    depends_on('blas')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+
+        substitutions = {
+            '@F90': spack_fc,
+            '@MPIF90': self.spec['mpi'].mpifc,
+            '@LIBS': ' '.join([
+                self.spec['lapack'].lapack_shared_lib,
+                self.spec['lapack'].blas_shared_lib
+            ])
+        }
+        #######
+        # TODO : this part is replicated in PEXSI
+        # TODO : and may be a common pattern for Editable Makefiles
+        # TODO : see #1186
+        template = join_path(
+            os.path.dirname(inspect.getmodule(self).__file__),
+            'make.sys'
+        )
+        makefile = join_path(
+            self.stage.source_path,
+            'make.sys'
+        )
+
+        shutil.copy(template, makefile)
+        for key, value in substitutions.items():
+            filter_file(key, value, makefile)
+        ######
+
+        make('wannier')
+        mkdirp(self.prefix.bin)
+        install(
+            join_path(self.stage.source_path, 'wannier90.x'),
+            join_path(self.prefix.bin, 'wannier90.x')
+        )
+
+        make('post')
+        install(
+            join_path(self.stage.source_path, 'postw90.x'),
+            join_path(self.prefix.bin, 'postw90.x')
+        )
+
+        make('lib')
+        mkdirp(self.prefix.lib)
+        install(
+            join_path(self.stage.source_path, 'libwannier.a'),
+            join_path(self.prefix.lib, 'libwannier.a')
+        )
+
+        make('w90chk2chk')
+        install(
+            join_path(self.stage.source_path, 'w90chk2chk.x'),
+            join_path(self.prefix.bin, 'w90chk2chk.x')
+        )
+
+        make('w90vdw')
+        install(
+            join_path(self.stage.source_path, 'utility', 'w90vdw', 'w90vdw.x'),
+            join_path(self.prefix.bin, 'w90vdw.x')
+        )
+
+        make('w90pov')
+        install(
+            join_path(self.stage.source_path, 'utility', 'w90pov', 'w90pov'),
+            join_path(self.prefix.bin, 'w90pov')
+        )
+
+        install_tree(
+            join_path(self.stage.source_path, 'pseudo'),
+            join_path(self.prefix.bin, 'pseudo')
+        )
-- 
cgit v1.2.3-70-g09d2


From d3e04b3daf3f30729cfb90790cf4081364e911f1 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Wed, 21 Sep 2016 09:55:54 +0200
Subject: Close #1683 Apply ADIOS 1.10.0 Patch (HDF5 1.10+) (#1699)

* Close #1683 Apply ADIOS 1.10.0 Patch

Also correct version dependencies and comments.

* Clean Up ADIOS

- add develop
- simplify HDF5 options (parallel only)
- remove optional netCDF (not fully v4)
---
 .../repos/builtin/packages/adios/adios_1100.patch  | 29 ++++++++++++++++++++++
 var/spack/repos/builtin/packages/adios/package.py  | 22 +++++++++-------
 2 files changed, 42 insertions(+), 9 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/adios/adios_1100.patch

diff --git a/var/spack/repos/builtin/packages/adios/adios_1100.patch b/var/spack/repos/builtin/packages/adios/adios_1100.patch
new file mode 100644
index 0000000000..7a9f857c32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adios/adios_1100.patch
@@ -0,0 +1,29 @@
+From 3b21a8a4150962c6938baeceacd04f619cea2fbc Mon Sep 17 00:00:00 2001
+From: Norbert Podhorszki <pnorbert@ornl.gov>
+Date: Thu, 1 Sep 2016 16:26:23 -0400
+Subject: [PATCH] ifdef around 'bool' type. hdf5 1.10 defines bool and breaks
+ compiling bp2h5.c
+
+---
+ utils/bp2h5/bp2h5.c | 8 +++++---
+ 1 file changed, 5 insertions(+), 3 deletions(-)
+
+diff --git a/utils/bp2h5/bp2h5.c b/utils/bp2h5/bp2h5.c
+index 9c500c7..fa746bd 100644
+--- a/utils/bp2h5/bp2h5.c
++++ b/utils/bp2h5/bp2h5.c
+@@ -43,9 +43,11 @@
+ #include "dmalloc.h"
+ #endif
+ 
+-typedef int bool;
+-#define false 0
+-#define true  1
++#ifndef bool
++    typedef int bool;
++#   define false 0
++#   define true  1
++#endif
+ 
+ bool noindex = false;              // do no print array indices with data
+ bool printByteAsChar = false;      // print 8 bit integer arrays as string
diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 01834383b8..e240ce0858 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -36,6 +36,8 @@ class Adios(Package):
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
     url      = "https://github.com/ornladios/ADIOS/archive/v1.10.0.tar.gz"
 
+    version('develop', git='https://github.com/ornladios/ADIOS.git',
+            branch='master')
     version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
     version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
@@ -48,14 +50,14 @@ class Adios(Package):
     variant('mpi', default=True, description='Enable MPI support')
     variant('infiniband', default=False, description='Enable infiniband support')
 
+    # transforms
     variant('zlib', default=True, description='Enable szip transform support')
     variant('szip', default=False, description='Enable szip transform support')
-    variant('hdf5', default=False, description='Enable HDF5 transport support')
-    variant('netcdf', default=False, description='Enable NetCDF transport support')
+    # transports and serial file converters
+    variant('hdf5', default=False, description='Enable parallel HDF5 transport and serial bp2h5 converter')
 
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP
-    # module load cray-netcdf/4.3.3.1
     # module load cray-hdf5/1.8.14
     # module load python/2.7.10
 
@@ -69,9 +71,13 @@ class Adios(Package):
     # optional transformations
     depends_on('zlib', when='+zlib')
     depends_on('szip', when='+szip')
-    # optional transports
-    depends_on('hdf5', when='+hdf5')
-    depends_on('netcdf', when='+netcdf')
+    # optional transports & file converters
+    depends_on('hdf5@1.8:+mpi', when='+hdf5')
+
+    # Fix ADIOS <=1.10.0 compile error on HDF5 1.10+
+    #   https://github.com/ornladios/ADIOS/commit/3b21a8a41509
+    #   https://github.com/LLNL/spack/issues/1683
+    patch('adios_1100.patch', when='@:1.10.0^hdf5@1.10:')
 
     def validate(self, spec):
         """
@@ -114,9 +120,7 @@ class Adios(Package):
         if '+szip' in spec:
             extra_args.append('--with-szip=%s' % spec['szip'].prefix)
         if '+hdf5' in spec:
-            extra_args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
-        if '+netcdf' in spec:
-            extra_args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+            extra_args.append('--with-phdf5=%s' % spec['hdf5'].prefix)
 
         sh = which('sh')
         sh('./autogen.sh')
-- 
cgit v1.2.3-70-g09d2


From 94b24e88934aae11fd05c77600311ae99c980bc5 Mon Sep 17 00:00:00 2001
From: Matt Belhorn <belhornmp@ornl.gov>
Date: Wed, 21 Sep 2016 04:48:33 -0400
Subject: Adds all available CrayPE CPU targets to platform by default. (#1745)

---
 lib/spack/spack/platforms/cray.py | 109 +++++++++++++++++++++++---------------
 1 file changed, 67 insertions(+), 42 deletions(-)

diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 0059b49ff1..9138ad7afe 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -8,37 +8,21 @@ from spack.operating_systems.linux_distro import LinuxDistro
 from spack.operating_systems.cnl import Cnl
 from llnl.util.filesystem import join_path
 
-# Craype- module prefixes that are not valid CPU targets.
-NON_TARGETS = ('hugepages', 'network', 'target', 'accel', 'xtpe')
-
-
-def _target_from_clean_env(name):
-    '''Return the default back_end target as loaded in a clean login session.
-
-    A bash subshell is launched with a wiped environment and the list of loaded
-    modules is parsed for the first acceptable CrayPE target.
-    '''
-    # Based on the incantation:
-    # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
-    targets = []
-    if name != 'front_end':
-        env = which('env')
-        env.add_default_arg('-')
-        # CAUTION - $USER is generally needed to initialize the environment.
-        # There may be other variables needed for general success.
-        output = env('USER=%s' % os.environ['USER'],
-                     '/bin/bash', '--noprofile', '--norc', '-c',
-                     '. /etc/profile; module list -lt',
-                     output=str, error=str)
-        default_modules = [i for i in output.splitlines()
-                           if len(i.split()) == 1]
-        tty.debug("Found default modules:",
-                  *["      " + mod for mod in default_modules])
-        pattern = 'craype-(?!{0})(\S*)'.format('|'.join(NON_TARGETS))
-        for mod in default_modules:
-            if 'craype-' in mod:
-                targets.extend(re.findall(pattern, mod))
-    return targets[0] if targets else None
+
+def _get_modules_in_modulecmd_output(output):
+    '''Return list of valid modules parsed from modulecmd output string.'''
+    return [i for i in output.splitlines()
+            if len(i.split()) == 1]
+
+
+def _fill_craype_targets_from_modules(targets, modules):
+    '''Extend CrayPE CPU targets list with those found in list of modules.'''
+    # Craype- module prefixes that are not valid CPU targets.
+    non_targets = ('hugepages', 'network', 'target', 'accel', 'xtpe')
+    pattern = r'craype-(?!{0})(\S*)'.format('|'.join(non_targets))
+    for mod in modules:
+        if 'craype-' in mod:
+            targets.extend(re.findall(pattern, mod))
 
 
 class Cray(Platform):
@@ -56,7 +40,12 @@ class Cray(Platform):
         '''
         super(Cray, self).__init__('cray')
 
-        # Get targets from config or make best guess from environment:
+        # Make all craype targets available.
+        for target in self._avail_targets():
+            name = target.replace('-', '_')
+            self.add_target(name, Target(name, 'craype-%s' % target))
+
+        # Get aliased targets from config or best guess from environment:
         conf = spack.config.get_config('targets')
         for name in ('front_end', 'back_end'):
             _target = getattr(self, name, None)
@@ -64,18 +53,16 @@ class Cray(Platform):
                 _target = os.environ.get('SPACK_' + name.upper())
             if _target is None:
                 _target = conf.get(name)
-            if _target is None:
-                _target = _target_from_clean_env(name)
-            setattr(self, name, _target)
-
+            if _target is None and name == 'back_end':
+                _target = self._default_target_from_env()
             if _target is not None:
-                self.add_target(name, Target(_target, 'craype-' + _target))
-                self.add_target(_target, Target(_target, 'craype-' + _target))
+                safe_name = _target.replace('-', '_')
+                setattr(self, name, safe_name)
+                self.add_target(name, self.targets[safe_name])
 
         if self.back_end is not None:
             self.default = self.back_end
-            self.add_target(
-                'default', Target(self.default, 'craype-' + self.default))
+            self.add_target('default', self.targets[self.back_end])
         else:
             raise NoPlatformError()
 
@@ -90,7 +77,7 @@ class Cray(Platform):
         self.add_operating_system(self.front_os, front_distro)
 
     @classmethod
-    def setup_platform_environment(self, pkg, env):
+    def setup_platform_environment(cls, pkg, env):
         """ Change the linker to default dynamic to be more
             similar to linux/standard linker behavior
         """
@@ -101,5 +88,43 @@ class Cray(Platform):
             env.prepend_path('SPACK_ENV_PATH', cray_wrapper_names)
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return os.environ.get('CRAYPE_VERSION') is not None
+
+    def _default_target_from_env(self):
+        '''Set and return the default CrayPE target loaded in a clean login
+        session.
+
+        A bash subshell is launched with a wiped environment and the list of
+        loaded modules is parsed for the first acceptable CrayPE target.
+        '''
+        # Based on the incantation:
+        # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
+        if getattr(self, 'default', None) is None:
+            env = which('env')
+            env.add_default_arg('-')
+            # CAUTION - $USER is generally needed in the sub-environment.
+            # There may be other variables needed for general success.
+            output = env('USER=%s' % os.environ['USER'],
+                         'HOME=%s' % os.environ['HOME'],
+                         '/bin/bash', '--noprofile', '--norc', '-c',
+                         '. /etc/profile; module list -lt',
+                         output=str, error=str)
+            self._defmods = _get_modules_in_modulecmd_output(output)
+            targets = []
+            _fill_craype_targets_from_modules(targets, self._defmods)
+            self.default = targets[0] if targets else None
+            tty.debug("Found default modules:",
+                      *["     %s" % mod for mod in self._defmods])
+        return self.default
+
+    def _avail_targets(self):
+        '''Return a list of available CrayPE CPU targets.'''
+        if getattr(self, '_craype_targets', None) is None:
+            module = which('modulecmd', required=True)
+            module.add_default_arg('python')
+            output = module('avail', '-t', 'craype-', output=str, error=str)
+            craype_modules = _get_modules_in_modulecmd_output(output)
+            self._craype_targets = targets = []
+            _fill_craype_targets_from_modules(targets, craype_modules)
+        return self._craype_targets
-- 
cgit v1.2.3-70-g09d2


From 73012ec4c875a3f8aa7a0a244d7e3b73466a723e Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glennpj@gmail.com>
Date: Wed, 21 Sep 2016 03:56:20 -0500
Subject: Rework libgd package (#1679)

* Added missing libtiff dependency
* added dependency on fontconfig
* Added version 2.2.3
* use autotools rather than cmake

The cmake build was not producing a complete install.
* There was no versioning of the installed libraries.
* gdlib-config was missing
* pkgconfig directory was missing

These problems do not happen when built with autotools.
---
 var/spack/repos/builtin/packages/libgd/package.py | 35 ++++++++++++++++-------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index acfdebb972..6329adf8f3 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -40,18 +40,33 @@ class Libgd(Package):
     homepage = "https://github.com/libgd/libgd"
     url      = "https://github.com/libgd/libgd/archive/gd-2.1.1.tar.gz"
 
+    version('2.2.3', 'a67bd15fa33d4aac0a1c7904aed19f49')
     version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e')
 
+    # Build dependencies
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on('gettext', type='build')
+    depends_on('pkg-config', type='build')
+
     depends_on('libpng')
-    depends_on('cmake', type='build')
+    depends_on('libtiff')
+    depends_on('fontconfig')
 
     def install(self, spec, prefix):
-
-        with working_dir('spack-build', create=True):
-            cmake('..',
-                  '-DENABLE_JPEG:BOOL=ON',
-                  '-DENABLE_PNG:BOOL=ON',
-                  '-DENABLE_TIFF:BOOL=ON',
-                  *std_cmake_args)
-            make()
-            make("install")
+        autoreconf("--install", "--force",
+                   "-I", "m4",
+                   "-I", join_path(spec['gettext'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['pkg-config'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['automake'].prefix,
+                                   "share", "aclocal"),
+                   "-I", join_path(spec['libtool'].prefix,
+                                   "share", "aclocal")
+                   )
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From 899f3a7e37a5956255a4012e4690f3f539c8bbee Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Wed, 21 Sep 2016 06:56:56 -0400
Subject: Fixed bug propagating --dirty flag to sub-installs. (#1625)

* Fixed bug propagating --dirty flag to sub-installs.

* Fix syntax error

* Allow --dirty flag to be set with SPACK_DIRTY env var.

* Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install`

* flake8
---
 lib/spack/spack/cmd/diy.py     | 7 ++++++-
 lib/spack/spack/cmd/install.py | 6 ++++--
 lib/spack/spack/cmd/setup.py   | 7 ++++++-
 lib/spack/spack/package.py     | 3 ++-
 4 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 487654d261..1a3e2fd65c 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -52,6 +52,10 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND version.")
+    subparser.add_argument(
+        '--dirty', action='store_true', dest='dirty',
+        help="Install a package *without* cleaning the environment.  " +
+        "Or set SPACK_DIRTY environment variable")
 
 
 def diy(self, args):
@@ -100,4 +104,5 @@ def diy(self, args):
             keep_prefix=args.keep_prefix,
             ignore_deps=args.ignore_deps,
             verbose=not args.quiet,
-            keep_stage=True)   # don't remove source dir for DIY.
+            keep_stage=True,   # don't remove source dir for DIY.
+            dirty=args.dirty or ('SPACK_DIRTY' in os.environ))
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index 7663a97a28..a77af37ed0 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -28,6 +28,7 @@ import llnl.util.tty as tty
 
 import spack
 import spack.cmd
+import os
 
 description = "Build and install packages"
 
@@ -56,7 +57,8 @@ def setup_parser(subparser):
         help="Fake install. Just remove prefix and create a fake file.")
     subparser.add_argument(
         '--dirty', action='store_true', dest='dirty',
-        help="Install a package *without* cleaning the environment.")
+        help="Install a package *without* cleaning the environment.  " +
+        "Or set SPACK_DIRTY environment variable")
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER,
         help="specs of packages to install")
@@ -88,5 +90,5 @@ def install(parser, args):
                 run_tests=args.run_tests,
                 verbose=args.verbose,
                 fake=args.fake,
-                dirty=args.dirty,
+                dirty=args.dirty or ('SPACK_DIRTY' in os.environ),
                 explicit=True)
diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py
index b55e102c0e..66095ee628 100644
--- a/lib/spack/spack/cmd/setup.py
+++ b/lib/spack/spack/cmd/setup.py
@@ -46,6 +46,10 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="specs to use for install.  Must contain package AND version.")
+    subparser.add_argument(
+        '--dirty', action='store_true', dest='dirty',
+        help="Install a package *without* cleaning the environment.  " +
+        "Or set SPACK_DIRTY environment variable")
 
 
 def setup(self, args):
@@ -91,4 +95,5 @@ def setup(self, args):
             ignore_deps=args.ignore_deps,
             verbose=args.verbose,
             keep_stage=True,   # don't remove source dir for SETUP.
-            install_phases=set(['setup', 'provenance']))
+            install_phases=set(['setup', 'provenance']),
+            dirty=args.dirty or ('SPACK_DIRTY' in os.environ))
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 882901d887..38bc6fa3f4 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -916,7 +916,8 @@ class Package(object):
                                          skip_patch=skip_patch,
                                          verbose=verbose,
                                          make_jobs=make_jobs,
-                                         run_tests=run_tests)
+                                         run_tests=run_tests,
+                                         dirty=dirty)
 
         # Set run_tests flag before starting build.
         self.run_tests = run_tests
-- 
cgit v1.2.3-70-g09d2


From 851b58248dd12dd23b15075a97b26d301591343b Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glennpj@gmail.com>
Date: Wed, 21 Sep 2016 06:02:07 -0500
Subject: Build pkg-config files for ncurses (#1673)

---
 var/spack/repos/builtin/packages/ncurses/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index aaacbac7b1..e4fd5bf269 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -50,7 +50,10 @@ class Ncurses(Package):
             "--enable-widec",
             "--enable-overwrite",
             "--disable-lib-suffixes",
-            "--without-ada"]
+            "--without-ada",
+            "--enable-pc-files",
+            "--with-pkg-config-libdir={0}/lib/pkgconfig".format(prefix)
+        ]
         configure(*opts)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From c1284a9046bc54c34ec400bffa9458f084c0f9da Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glennpj@gmail.com>
Date: Wed, 21 Sep 2016 06:02:28 -0500
Subject: Stop python from linking with system ncurses (#1672)

Python will look to link with libncursesw in preference to libncurses. Since
ncurses in spack is built without suffixes there is no libncursesw and
python will link to the system libncursesw for _curses.so and
_curses_panel.so, as well as libpanelw for _curses_panel.so.

This PR introduces a patch that simple removes the check for ncursesw in
setup.py and therefore sets `curses_library` to `ncurses`.
---
 var/spack/repos/builtin/packages/python/ncurses.patch | 11 +++++++++++
 var/spack/repos/builtin/packages/python/package.py    |  2 ++
 2 files changed, 13 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/python/ncurses.patch

diff --git a/var/spack/repos/builtin/packages/python/ncurses.patch b/var/spack/repos/builtin/packages/python/ncurses.patch
new file mode 100644
index 0000000000..9054c03e7b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/ncurses.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2016-08-30 15:39:59.334926574 -0500
++++ b/setup.py	2016-08-30 15:46:57.227946339 -0500
+@@ -745,8 +745,6 @@
+         # use the same library for the readline and curses modules.
+         if 'curses' in readline_termcap_library:
+             curses_library = readline_termcap_library
+-        elif self.compiler.find_library_file(lib_dirs, 'ncursesw'):
+-            curses_library = 'ncursesw'
+         elif self.compiler.find_library_file(lib_dirs, 'ncurses'):
+             curses_library = 'ncurses'
+         elif self.compiler.find_library_file(lib_dirs, 'curses'):
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index e95bb4ba24..f3380cf75d 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -74,6 +74,8 @@ class Python(Package):
     depends_on("tk",  when="+tk")
     depends_on("tcl", when="+tk")
 
+    patch('ncurses.patch')
+
     @when('@2.7,3.4:')
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
-- 
cgit v1.2.3-70-g09d2


From 3d3614e52259913e8d96d811a2a95bc02637c63f Mon Sep 17 00:00:00 2001
From: Kelly Thompson <KineticTheory@users.noreply.github.com>
Date: Wed, 21 Sep 2016 05:10:30 -0600
Subject: Update to allow netlib-scalapack to build against netlib-lapack.
 (#1539)

---
 var/spack/repos/builtin/packages/netlib-scalapack/package.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 49b8633209..13e932e176 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -41,12 +41,14 @@ class NetlibScalapack(Package):
 
     variant('shared', default=True,
             description='Build the shared library version')
-    variant('fpic', default=False, description="Build with -fpic compiler option")
+    variant('fpic', default=False,
+            description="Build with -fpic compiler option")
 
     provides('scalapack')
 
     depends_on('mpi')
     depends_on('lapack')
+    depends_on('blas')
     depends_on('cmake', when='@2.0.0:', type='build')
 
     def install(self, spec, prefix):
@@ -54,18 +56,18 @@ class NetlibScalapack(Package):
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
                                              'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else
-                                             'ON'),
-            # forces scalapack to use find_package(LAPACK):
-            "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON",
+                                             'ON')
         ]
 
         # Make sure we use Spack's Lapack:
         options.extend([
             '-DLAPACK_FOUND=true',
-            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
             '-DLAPACK_LIBRARIES=%s' % (
                 spec['lapack'].lapack_shared_lib if '+shared' in spec else
                 spec['lapack'].lapack_static_lib),
+            '-DBLAS_LIBRARIES=%s' % (
+                spec['blas'].blas_shared_lib if '+shared' in spec else
+                spec['blas'].blas_static_lib)
         ])
 
         if '+fpic' in spec:
-- 
cgit v1.2.3-70-g09d2


From cf925ddc97301f92a05a9bb90f3f38a96eacc94e Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 21 Sep 2016 06:16:57 -0500
Subject: Add missing build dependencies to hdf package (#1812)

---
 var/spack/repos/builtin/packages/hdf/package.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index aafb345be6..9a44184256 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -38,13 +38,12 @@ class Hdf(Package):
 
     variant('szip', default=False, description="Enable szip support")
 
-    depends_on("jpeg")
-    depends_on("szip", when='+szip')
-    depends_on("zlib")
+    depends_on('jpeg')
+    depends_on('szip', when='+szip')
+    depends_on('zlib')
 
-    def url_for_version(self, version):
-        return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(
-            version) + "/src/hdf-" + str(version) + ".tar.gz"
+    depends_on('bison', type='build')
+    depends_on('flex',  type='build')
 
     def install(self, spec, prefix):
         config_args = [
@@ -66,4 +65,5 @@ class Hdf(Package):
         configure(*config_args)
 
         make()
-        make("install")
+        make('check')
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From 3d1c92e22cb0db9afd4cf956c15b5f3a74180706 Mon Sep 17 00:00:00 2001
From: Mayeul d'Avezac <m.davezac@ucl.ac.uk>
Date: Wed, 21 Sep 2016 12:18:35 +0100
Subject: Update espresso recipe to track change in spack internals (#1734)

---
 var/spack/repos/builtin/packages/espresso/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 3dca1ba187..d2c825513c 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -88,7 +88,7 @@ class Espresso(Package):
 
         # Add a list of directories to search
         search_list = []
-        for name, dependency_spec in spec.dependencies.iteritems():
+        for dependency_spec in spec.dependencies():
             search_list.extend([dependency_spec.prefix.lib,
                                 dependency_spec.prefix.lib64])
 
-- 
cgit v1.2.3-70-g09d2


From db0baaafe358a22b5bdfcf340b65ad23f9047176 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Wed, 21 Sep 2016 04:22:55 -0700
Subject: Add package for bamtools (#1571)

bamtools provides a C++ API & command-line toolkit for working with BAM
data.
---
 .../repos/builtin/packages/bamtools/package.py     | 45 ++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bamtools/package.py

diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py
new file mode 100644
index 0000000000..7bb1985003
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamtools/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bamtools(Package):
+    """C++ API & command-line toolkit for working with BAM data."""
+
+    homepage = "https://github.com/pezmaster31/bamtools"
+    url      = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz"
+
+    version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9')
+    version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc')
+    version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d')
+
+    depends_on('cmake', type='build')
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+
+            make()
+            make('install')
-- 
cgit v1.2.3-70-g09d2


From 51d869493ab85d4972e2d9f35be95e1b1c48dae9 Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Wed, 21 Sep 2016 04:23:03 -0700
Subject: Add package for bedtools2 (#1572)

Add package for bedtools2, with support for v2.25.0 and v2.26.0.
---
 .../repos/builtin/packages/bedtools2/package.py    | 43 ++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bedtools2/package.py

diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py
new file mode 100644
index 0000000000..46f3185154
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bedtools2/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bedtools2(Package):
+    """Collectively, the bedtools utilities are a swiss-army knife of
+       tools for a wide-range of genomics analysis tasks. The most
+       widely-used tools enable genome arithmetic: that is, set theory
+       on the genome."""
+
+    homepage = "https://github.com/arq5x/bedtools2"
+    url      = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz"
+
+    version('2.26.0', '52227e7efa6627f0f95d7d734973233d')
+    version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "install")
-- 
cgit v1.2.3-70-g09d2


From 6b6f868f2adcd5764a782678dbd0b1beaa597579 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 21 Sep 2016 04:35:15 -0700
Subject: Flake8 fixes.

---
 var/spack/repos/builtin/packages/qt/package.py | 46 +++++++++++++-------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 639875d29d..2dba05ce13 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -6,7 +6,7 @@
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/llnl/spack
+# For details, see https://github.com/llnl/spack  # NOQA: ignore=E501
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
@@ -29,9 +29,9 @@ import sys
 
 class Qt(Package):
     """Qt is a comprehensive cross-platform C++ application framework."""
-    homepage = 'http://qt.io'
-    url      = 'http://download.qt.io/archive/qt/5.7/5.7.0/single/qt-everywhere-opensource-src-5.7.0.tar.gz'
-    list_url = 'http://download.qt.io/archive/qt/'
+    homepage = 'http://qt.io'  # NOQA: ignore=E501
+    url      = 'http://download.qt.io/archive/qt/5.7/5.7.0/single/qt-everywhere-opensource-src-5.7.0.tar.gz'  # NOQA: ignore=E501
+    list_url = 'http://download.qt.io/archive/qt/'  # NOQA: ignore=E501
     list_depth = 4
 
     version('5.7.0',  '9a46cce61fc64c20c3ac0a0e0fa41b42')
@@ -53,7 +53,7 @@ class Qt(Package):
 
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
-    # https://github.com/xboxdrv/xboxdrv/issues/188
+    # https://github.com/xboxdrv/xboxdrv/issues/188  # NOQA: ignore=E501
     patch('btn_trigger_happy.patch', when='@5.7.0:')
 
     patch('qt4-corewlan-new-osx.patch', when='@4')
@@ -130,7 +130,7 @@ class Qt(Package):
                         'mkspecs/common/g++-base.conf')
 
             # Necessary to build with GCC 6 and other modern compilers
-            # http://stackoverflow.com/questions/10354371/
+            # http://stackoverflow.com/questions/10354371/  # NOQA: ignore=E501
             filter_file('(^QMAKE_CXXFLAGS .*)', r'\1 -std=gnu++98',
                         'mkspecs/common/gcc-base.conf')
 
@@ -179,21 +179,21 @@ class Qt(Package):
 
         if '@5:' in self.spec and sys.platform == 'darwin':
             config_args.extend([
-                    '-no-xinput2',
-                    '-no-xcb-xlib',
-                    '-no-pulseaudio',
-                    '-no-alsa',
-                    '-no-gtkstyle',
-                ])
+                '-no-xinput2',
+                '-no-xcb-xlib',
+                '-no-pulseaudio',
+                '-no-alsa',
+                '-no-gtkstyle',
+            ])
 
         if '@4' in self.spec and sys.platform == 'darwin':
             sdkpath = which('xcrun')('--show-sdk-path',
-                                     # XXX(macos): the 10.11 SDK fails to configure.
+                                     # XXX(macos): 10.11 SDK fails to configure
                                      '--sdk', 'macosx10.9',
                                      output=str)
             config_args.extend([
-                    '-sdk', sdkpath.strip(),
-                ])
+                '-sdk', sdkpath.strip(),
+            ])
             use_clang_platform = False
             if self.spec.compiler.name == 'clang' and \
                str(self.spec.compiler.version).endwith('-apple'):
@@ -204,15 +204,15 @@ class Qt(Package):
                 use_clang_platform = True
             if use_clang_platform:
                 config_args.extend([
-                        '-platform', 'unsupported/macx-clang',
-                    ])
+                    '-platform', 'unsupported/macx-clang',
+                ])
 
         return config_args
 
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 
-    @when('@3')
+    @when('@3')  # NOQA: ignore=F811
     def configure(self):
         # A user reported that this was necessary to link Qt3 on ubuntu
         os.environ['LD_LIBRARY_PATH'] = os.getcwd() + '/lib'
@@ -223,7 +223,7 @@ class Qt(Package):
                   '-release',
                   '-fast')
 
-    @when('@4')
+    @when('@4')  # NOQA: ignore=F811
     def configure(self):
         configure('-fast',
                   '-no-webkit',
@@ -231,7 +231,7 @@ class Qt(Package):
                   '-arch', str(self.spec.architecture.target),
                   *self.common_config_args)
 
-    @when('@5.0:5.6')
+    @when('@5.0:5.6')  # NOQA: ignore=F811
     def configure(self):
         configure('-no-eglfs',
                   '-no-directfb',
@@ -239,14 +239,14 @@ class Qt(Package):
                   '-skip', 'qtwebkit',
                   *self.common_config_args)
 
-    @when('@5.7:')
+    @when('@5.7:')  # NOQA: ignore=F811
     def configure(self):
         args = self.common_config_args
 
         if not sys.platform == 'darwin':
             args.extend([
-                    '-qt-xcb',
-                ])
+                '-qt-xcb',
+            ])
 
         configure('-no-eglfs',
                   '-no-directfb',
-- 
cgit v1.2.3-70-g09d2


From d848559f70ad67842150b51d2792843f3cce4621 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Wed, 21 Sep 2016 21:27:59 +0200
Subject: Reworking of `lapack_shared_libs` and similar properties (#1682)

* Turned <provider>_libs into an iterable

Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions

* atlas : added pthread variant

* intel packages : added lapack_libs and blas_libs

* find_library_path : removed unused function

* PR review : fixed last issues

* LibraryList : added test on __add__ return type

* LibraryList : added __radd__ fixed unit tests

fix : failing unit tests due to missing `self`

* cp2k and dependecies : fixed blas-lapack related statements in package.py
---
 lib/spack/docs/packaging_guide.rst                 |   9 +-
 lib/spack/llnl/util/filesystem.py                  | 197 +++++++++++++++++----
 lib/spack/llnl/util/lang.py                        |  16 ++
 lib/spack/spack/spec.py                            |   7 +
 lib/spack/spack/test/__init__.py                   |   1 +
 lib/spack/spack/test/library_list.py               | 111 ++++++++++++
 .../repos/builtin/packages/armadillo/package.py    |  14 +-
 .../repos/builtin/packages/arpack-ng/package.py    |  34 ++--
 var/spack/repos/builtin/packages/atlas/package.py  |  36 ++--
 var/spack/repos/builtin/packages/cp2k/package.py   |  25 ++-
 var/spack/repos/builtin/packages/dealii/package.py |   5 +-
 var/spack/repos/builtin/packages/elk/package.py    |   6 +-
 var/spack/repos/builtin/packages/gmsh/package.py   |   6 +-
 var/spack/repos/builtin/packages/hpl/package.py    |   2 +-
 var/spack/repos/builtin/packages/hypre/package.py  |   9 +-
 .../packages/intel-parallel-studio/package.py      |  44 +++--
 var/spack/repos/builtin/packages/mkl/package.py    |  48 ++---
 var/spack/repos/builtin/packages/mumps/package.py  |   8 +-
 .../builtin/packages/netlib-lapack/package.py      |  29 ++-
 .../builtin/packages/netlib-scalapack/package.py   |  46 ++---
 var/spack/repos/builtin/packages/nwchem/package.py |  13 +-
 .../repos/builtin/packages/octopus/package.py      |   8 +-
 .../repos/builtin/packages/openblas/package.py     |  31 ++--
 var/spack/repos/builtin/packages/opium/package.py  |  10 +-
 var/spack/repos/builtin/packages/pexsi/package.py  |   4 +-
 var/spack/repos/builtin/packages/psi4/package.py   |  11 +-
 .../repos/builtin/packages/py-scipy/package.py     |   4 +-
 .../repos/builtin/packages/suite-sparse/package.py |   4 +-
 .../repos/builtin/packages/sundials/package.py     |  10 +-
 .../repos/builtin/packages/superlu-dist/package.py |   5 +-
 .../repos/builtin/packages/superlu/package.py      |   2 +-
 .../repos/builtin/packages/trilinos/package.py     |   8 +-
 .../repos/builtin/packages/wannier90/package.py    |   7 +-
 33 files changed, 526 insertions(+), 244 deletions(-)
 create mode 100644 lib/spack/spack/test/library_list.py

diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 6936b5e423..0294f32748 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -2090,12 +2090,11 @@ Blas and Lapack libraries
 
 Different packages provide implementation of ``Blas`` and ``Lapack`` routines.
 The names of the resulting static and/or shared libraries differ from package
-to package. In order to make the ``install()`` method indifferent to the
+to package. In order to make the ``install()`` method independent of the
 choice of ``Blas`` implementation, each package which provides it
-sets up ``self.spec.blas_shared_lib`` and ``self.spec.blas_static_lib`` to
-point to the shared and static ``Blas`` libraries, respectively. The same
-applies to packages which provide ``Lapack``. Package developers are advised to
-use these variables, for example ``spec['blas'].blas_shared_lib`` instead of
+sets up ``self.spec.blas_libs`` to point to the correct ``Blas`` libraries.
+The same applies to packages which provide ``Lapack``. Package developers are advised to
+use these variables, for example ``spec['blas'].blas_libs.joined()`` instead of
 hard-coding ``join_path(spec['blas'].prefix.lib, 'libopenblas.so')``.
 
 ^^^^^^^^^^^^^^^^^^^^^
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 22ca85abf9..c3ecfde4f4 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -22,18 +22,22 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
+import collections
+import errno
+import fileinput
+import getpass
 import glob
+import numbers
+import os
 import re
 import shutil
 import stat
-import errno
-import getpass
-from contextlib import contextmanager
 import subprocess
-import fileinput
+import sys
+from contextlib import contextmanager
 
 import llnl.util.tty as tty
+from llnl.util.lang import dedupe
 
 __all__ = ['set_install_permissions', 'install', 'install_tree',
            'traverse_tree',
@@ -42,8 +46,8 @@ __all__ = ['set_install_permissions', 'install', 'install_tree',
            'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree', 'find_library_path',
-           'fix_darwin_install_name', 'to_link_flags', 'to_lib_name']
+           'remove_dead_links', 'remove_linked_tree',
+           'fix_darwin_install_name', 'find_libraries', 'LibraryList']
 
 
 def filter_file(regex, repl, *filenames, **kwargs):
@@ -326,7 +330,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     follow_links = kwargs.get('follow_link', False)
 
     # Yield in pre or post order?
-    order  = kwargs.get('order', 'pre')
+    order = kwargs.get('order', 'pre')
     if order not in ('pre', 'post'):
         raise ValueError("Order must be 'pre' or 'post'.")
 
@@ -338,7 +342,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         return
 
     source_path = os.path.join(source_root, rel_path)
-    dest_path   = os.path.join(dest_root, rel_path)
+    dest_path = os.path.join(dest_root, rel_path)
 
     # preorder yields directories before children
     if order == 'pre':
@@ -346,8 +350,8 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
 
     for f in os.listdir(source_path):
         source_child = os.path.join(source_path, f)
-        dest_child   = os.path.join(dest_path, f)
-        rel_child    = os.path.join(rel_path, f)
+        dest_child = os.path.join(dest_path, f)
+        rel_child = os.path.join(rel_path, f)
 
         # Treat as a directory
         if os.path.isdir(source_child) and (
@@ -440,35 +444,162 @@ def fix_darwin_install_name(path):
                         stdout=subprocess.PIPE).communicate()[0]
                     break
 
+# Utilities for libraries
+
 
-def to_lib_name(library):
-    """Transforms a path to the library /path/to/lib<name>.xyz into <name>
+class LibraryList(collections.Sequence):
+    """Sequence of absolute paths to libraries
+
+    Provides a few convenience methods to manipulate library paths and get
+    commonly used compiler flags or names
     """
-    # Assume libXYZ.suffix
-    return os.path.basename(library)[3:].split(".")[0]
 
+    def __init__(self, libraries):
+        self.libraries = list(libraries)
 
-def to_link_flags(library):
-    """Transforms a path to a <library> into linking flags -L<dir> -l<name>.
+    @property
+    def directories(self):
+        """Stable de-duplication of the directories where the libraries
+        reside
 
-    Return:
-      A string of linking flags.
-    """
-    dir  = os.path.dirname(library)
-    name = to_lib_name(library)
-    res = '-L%s -l%s' % (dir, name)
-    return res
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/libc.a'])
+        >>> assert l.directories == ['/dir1', '/dir2']
+        """
+        return list(dedupe(
+            os.path.dirname(x) for x in self.libraries if os.path.dirname(x)
+        ))
+
+    @property
+    def basenames(self):
+        """Stable de-duplication of the base-names in the list
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir3/liba.a'])
+        >>> assert l.basenames == ['liba.a', 'libb.a']
+        """
+        return list(dedupe(os.path.basename(x) for x in self.libraries))
+
+    @property
+    def names(self):
+        """Stable de-duplication of library names in the list
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir3/liba.so'])
+        >>> assert l.names == ['a', 'b']
+        """
+        return list(dedupe(x.split('.')[0][3:] for x in self.basenames))
+
+    @property
+    def search_flags(self):
+        """Search flags for the libraries
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-L/dir1 -L/dir2'
+        """
+        return ' '.join(['-L' + x for x in self.directories])
+
+    @property
+    def link_flags(self):
+        """Link flags for the libraries
+
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-la -lb'
+        """
+        return ' '.join(['-l' + name for name in self.names])
 
+    @property
+    def ld_flags(self):
+        """Search flags + link flags
 
-def find_library_path(libname, *paths):
-    """Searches for a file called <libname> in each path.
+        >>> l = LibraryList(['/dir1/liba.a', '/dir2/libb.a', '/dir1/liba.so'])
+        >>> assert l.search_flags == '-L/dir1 -L/dir2 -la -lb'
+        """
+        return self.search_flags + ' ' + self.link_flags
 
-    Return:
-      directory where the library was found, if found.  None otherwise.
+    def __getitem__(self, item):
+        cls = type(self)
+        if isinstance(item, numbers.Integral):
+            return self.libraries[item]
+        return cls(self.libraries[item])
 
+    def __add__(self, other):
+        return LibraryList(dedupe(self.libraries + list(other)))
+
+    def __radd__(self, other):
+        return self.__add__(other)
+
+    def __eq__(self, other):
+        return self.libraries == other.libraries
+
+    def __len__(self):
+        return len(self.libraries)
+
+    def joined(self, separator=' '):
+        return separator.join(self.libraries)
+
+    def __repr__(self):
+        return self.__class__.__name__ + '(' + repr(self.libraries) + ')'
+
+    def __str__(self):
+        return self.joined()
+
+
+def find_libraries(args, root, shared=True, recurse=False):
+    """Returns an iterable object containing a list of full paths to
+    libraries if found.
+
+    Args:
+        args: iterable object containing a list of library names to \
+            search for (e.g. 'libhdf5')
+        root: root folder where to start searching
+        shared: if True searches for shared libraries, otherwise for static
+        recurse: if False search only root folder, if True descends top-down \
+            from the root
+
+    Returns:
+        list of full paths to the libraries that have been found
     """
-    for path in paths:
-        library = join_path(path, libname)
-        if os.path.exists(library):
-            return path
-    return None
+    if not isinstance(args, collections.Sequence) or isinstance(args, str):
+        message = '{0} expects a sequence of strings as first argument'
+        message += ' [got {1} instead]'
+        raise TypeError(message.format(find_libraries.__name__, type(args)))
+
+    # Construct the right suffix for the library
+    if shared is True:
+        suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+    else:
+        suffix = 'a'
+    # List of libraries we are searching with suffixes
+    libraries = ['{0}.{1}'.format(lib, suffix) for lib in args]
+    # Search method
+    if recurse is False:
+        search_method = _find_libraries_non_recursive
+    else:
+        search_method = _find_libraries_recursive
+
+    return search_method(libraries, root)
+
+
+def _find_libraries_recursive(libraries, root):
+    library_dict = collections.defaultdict(list)
+    for path, _, files in os.walk(root):
+        for lib in libraries:
+            if lib in files:
+                library_dict[lib].append(
+                    join_path(path, lib)
+                )
+    answer = []
+    for lib in libraries:
+        answer.extend(library_dict[lib])
+    return LibraryList(answer)
+
+
+def _find_libraries_non_recursive(libraries, root):
+
+    def lib_or_none(lib):
+        library = join_path(root, lib)
+        if not os.path.exists(library):
+            return None
+        return library
+
+    return LibraryList(
+        [lib_or_none(lib) for lib in libraries if lib_or_none(lib) is not None]
+    )
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index df32012e2d..253334c416 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -374,6 +374,22 @@ def DictWrapper(dictionary):
     return wrapper()
 
 
+def dedupe(sequence):
+    """Yields a stable de-duplication of an hashable sequence
+
+    Args:
+        sequence: hashable sequence to be de-duplicated
+
+    Returns:
+        stable de-duplication of the sequence
+    """
+    seen = set()
+    for x in sequence:
+        if x not in seen:
+            yield x
+            seen.add(x)
+
+
 class RequiredAttributeError(ValueError):
 
     def __init__(self, message):
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 8b0486c4da..158d76e568 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -527,6 +527,13 @@ class Spec(object):
             # XXX(deptype): default deptypes
             self._add_dependency(spec, ('build', 'link'))
 
+    def __getattr__(self, item):
+        """Delegate to self.package if the attribute is not in the spec"""
+        # This line is to avoid infinite recursion in case package is
+        # not present among self attributes
+        package = super(Spec, self).__getattribute__('package')
+        return getattr(package, item)
+
     def get_dependency(self, name):
         dep = self._dependencies.get(name)
         if dep is not None:
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index db683917b5..0a946ff2ff 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -53,6 +53,7 @@ test_names = [
     'git_fetch',
     'hg_fetch',
     'install',
+    'library_list',
     'link_tree',
     'lock',
     'make_executable',
diff --git a/lib/spack/spack/test/library_list.py b/lib/spack/spack/test/library_list.py
new file mode 100644
index 0000000000..7fc2fd222f
--- /dev/null
+++ b/lib/spack/spack/test/library_list.py
@@ -0,0 +1,111 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import unittest
+
+from llnl.util.filesystem import LibraryList
+
+
+class LibraryListTest(unittest.TestCase):
+    def setUp(self):
+        l = [
+            '/dir1/liblapack.a',
+            '/dir2/libfoo.dylib',
+            '/dir1/libblas.a',
+            '/dir3/libbar.so',
+            'libbaz.so'
+        ]
+        self.liblist = LibraryList(l)
+
+    def test_repr(self):
+        x = eval(repr(self.liblist))
+        self.assertEqual(self.liblist, x)
+
+    def test_joined_and_str(self):
+        s1 = self.liblist.joined()
+        self.assertEqual(
+            s1,
+            '/dir1/liblapack.a /dir2/libfoo.dylib /dir1/libblas.a /dir3/libbar.so libbaz.so'  # NOQA: ignore=E501
+        )
+        s2 = str(self.liblist)
+        self.assertEqual(s1, s2)
+        s3 = self.liblist.joined(';')
+        self.assertEqual(
+            s3,
+            '/dir1/liblapack.a;/dir2/libfoo.dylib;/dir1/libblas.a;/dir3/libbar.so;libbaz.so'  # NOQA: ignore=E501
+        )
+
+    def test_flags(self):
+        search_flags = self.liblist.search_flags
+        self.assertTrue('-L/dir1' in search_flags)
+        self.assertTrue('-L/dir2' in search_flags)
+        self.assertTrue('-L/dir3' in search_flags)
+        self.assertTrue(isinstance(search_flags, str))
+
+        link_flags = self.liblist.link_flags
+        self.assertEqual(
+            link_flags,
+            '-llapack -lfoo -lblas -lbar -lbaz'
+        )
+
+        ld_flags = self.liblist.ld_flags
+        self.assertEqual(ld_flags, search_flags + ' ' + link_flags)
+
+    def test_paths_manipulation(self):
+        names = self.liblist.names
+        self.assertEqual(names, ['lapack', 'foo', 'blas', 'bar', 'baz'])
+
+        directories = self.liblist.directories
+        self.assertEqual(directories, ['/dir1', '/dir2', '/dir3'])
+
+    def test_get_item(self):
+        a = self.liblist[0]
+        self.assertEqual(a, '/dir1/liblapack.a')
+
+        b = self.liblist[:]
+        self.assertEqual(type(b), type(self.liblist))
+        self.assertEqual(self.liblist, b)
+        self.assertTrue(self.liblist is not b)
+
+    def test_add(self):
+        pylist = [
+            '/dir1/liblapack.a',  # removed from the final list
+            '/dir2/libbaz.so',
+            '/dir4/libnew.a'
+        ]
+        another = LibraryList(pylist)
+        l = self.liblist + another
+        self.assertEqual(len(l), 7)
+        # Invariant : l == l + l
+        self.assertEqual(l, l + l)
+        # Always produce an instance of LibraryList
+        self.assertEqual(
+            type(self.liblist),
+            type(self.liblist + pylist)
+        )
+        self.assertEqual(
+            type(pylist + self.liblist),
+            type(self.liblist)
+        )
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
index 4356f60aca..fdd682f5e5 100644
--- a/var/spack/repos/builtin/packages/armadillo/package.py
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -46,18 +46,20 @@ class Armadillo(Package):
     depends_on('hdf5', when='+hdf5')
 
     def install(self, spec, prefix):
+        arpack = find_libraries(['libarpack'], root=spec[
+                                'arpack-ng'].prefix.lib, shared=True)
+        superlu = find_libraries(['libsuperlu'], root=spec[
+                                 'superlu'].prefix, shared=False, recurse=True)
         cmake_args = [
             # ARPACK support
-            '-DARPACK_LIBRARY={0}/libarpack.{1}'.format(
-                spec['arpack-ng'].prefix.lib, dso_suffix),
+            '-DARPACK_LIBRARY={0}'.format(arpack.joined()),
             # BLAS support
-            '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_libs.joined()),
             # LAPACK support
-            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_libs.joined()),
             # SuperLU support
             '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
-            '-DSuperLU_LIBRARY={0}/libsuperlu.a'.format(
-                spec['superlu'].prefix.lib64),
+            '-DSuperLU_LIBRARY={0}'.format(superlu.joined()),
             # HDF5 support
             '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
         ]
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 0e71125d41..7f92bc1950 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -88,17 +88,16 @@ class ArpackNg(Package):
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
         # Make sure we use Spack's blas/lapack:
+        lapack_libs = spec['lapack'].lapack_libs.joined()
+        blas_libs = spec['blas'].blas_libs.joined()
+
         options.extend([
             '-DLAPACK_FOUND=true',
-            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
-            '-DLAPACK_LIBRARIES=%s' % (
-                spec['lapack'].lapack_shared_lib if '+shared' in spec else
-                spec['lapack'].lapack_static_lib),
+            '-DLAPACK_INCLUDE_DIRS={0}'.format(spec['lapack'].prefix.include),
+            '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
             '-DBLAS_FOUND=true',
-            '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include,
-            '-DBLAS_LIBRARIES=%s' % (
-                spec['blas'].blas_shared_lib if '+shared' in spec else
-                spec['blas'].blas_static_lib)
+            '-DBLAS_INCLUDE_DIRS={0}'.format(spec['blas'].prefix.include),
+            '-DBLAS_LIBRARIES={0}'.format(blas_libs)
         ])
 
         if '+mpi' in spec:
@@ -129,19 +128,12 @@ class ArpackNg(Package):
                 'F77=%s' % spec['mpi'].mpif77
             ])
 
-        if '+shared' in spec:
-            options.extend([
-                '--with-blas=%s' % to_link_flags(
-                    spec['blas'].blas_shared_lib),
-                '--with-lapack=%s' % to_link_flags(
-                    spec['lapack'].lapack_shared_lib)
-            ])
-        else:
-            options.extend([
-                '--with-blas=%s' % spec['blas'].blas_static_lib,
-                '--with-lapack=%s' % spec['lapack'].lapack_static_lib,
-                '--enable-shared=no'
-            ])
+        options.extend([
+            '--with-blas={0}'.format(spec['blas'].blas_libs.ld_flags),
+            '--with-lapack={0}'.format(spec['lapack'].lapack_libs.ld_flags)
+        ])
+        if '+shared' not in spec:
+            options.append('--enable-shared=no')
 
         bootstrap()
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index f9d5da6166..e1914aac98 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -51,6 +51,7 @@ class Atlas(Package):
             url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
 
     variant('shared', default=True, description='Builds shared library')
+    variant('pthread', default=False, description='Use multithreaded libraries')
 
     provides('blas')
     provides('lapack')
@@ -107,18 +108,32 @@ class Atlas(Package):
             make("install")
             self.install_test()
 
-    def setup_dependent_package(self, module, dspec):
+    @property
+    def blas_libs(self):
         # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack,
         # serial BLAS), and all ATLAS symbols needed to support them. Whereas
         # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version.
-        name = 'libsatlas.%s' % dso_suffix
-        libdir = find_library_path(name,
-                                   self.prefix.lib64,
-                                   self.prefix.lib)
-
+        is_threaded = '+pthread' in self.spec
         if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(libdir, name)
-            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+            to_find = ['libtatlas'] if is_threaded else ['libsatlas']
+            shared = True
+        else:
+            interfaces = [
+                'libptcblas',
+                'libptf77blas'
+            ] if is_threaded else [
+                'libcblas',
+                'libf77blas'
+            ]
+            to_find = ['liblapack'] + interfaces + ['libatlas']
+            shared = False
+        return find_libraries(
+            to_find, root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
 
     def install_test(self):
         source_file = join_path(os.path.dirname(self.module.__file__),
@@ -126,9 +141,8 @@ class Atlas(Package):
         blessed_file = join_path(os.path.dirname(self.module.__file__),
                                  'test_cblas_dgemm.output')
 
-        include_flags = ["-I%s" % join_path(self.spec.prefix, "include")]
-        link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"),
-                      "-lsatlas"]
+        include_flags = ["-I%s" % self.spec.prefix.include]
+        link_flags = self.lapack_libs.ld_flags
 
         output = compile_c_and_execute(source_file, include_flags, link_flags)
         compare_output_file(output, blessed_file)
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 785de08d34..15606cd80a 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -95,7 +95,8 @@ class Cp2k(Package):
             fcflags.extend([
                 '-I' + spec['fftw'].prefix.include
             ])
-            ldflags = ['-L' + spec['fftw'].prefix.lib]
+            fftw = find_libraries(['libfftw3'], root=spec['fftw'].prefix.lib)
+            ldflags = [fftw.search_flags]
             libs = []
             if '+plumed' in self.spec:
                 # Include Plumed.inc in the Makefile
@@ -157,9 +158,8 @@ class Cp2k(Package):
                     ),
                     '-I' + join_path(spec['pexsi'].prefix, 'fortran')
                 ])
-                ldflags.extend([
-                    '-L' + spec['scalapack'].prefix.lib
-                ])
+                scalapack = spec['scalapack'].scalapack_libs
+                ldflags.append(scalapack.search_flags)
                 libs.extend([
                     join_path(spec['elpa'].prefix.lib,
                               'libelpa.{0}'.format(dso_suffix)),
@@ -176,20 +176,15 @@ class Cp2k(Package):
                         'libmetis.{0}'.format(dso_suffix)
                     ),
                 ])
-                libs.extend(spec['scalapack'].scalapack_shared_libs)
+                libs.extend(scalapack)
                 libs.extend(self.spec['mpi'].mpicxx_shared_libs)
                 libs.extend(self.compiler.stdcxx_libs)
             # LAPACK / BLAS
-            ldflags.extend([
-                '-L' + spec['lapack'].prefix.lib,
-                '-L' + spec['blas'].prefix.lib
-            ])
-            libs.extend([
-                join_path(spec['fftw'].prefix.lib,
-                          'libfftw3.{0}'.format(dso_suffix)),
-                spec['lapack'].lapack_shared_lib,
-                spec['blas'].blas_shared_lib
-            ])
+            lapack = spec['lapack'].lapack_libs
+            blas = spec['blas'].blas_libs
+
+            ldflags.append((lapack + blas).search_flags)
+            libs.extend([str(x) for x in (fftw, lapack, blas)])
 
             # Write compiler flags to file
             mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags)))
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 9e8c639128..89732f98b8 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -123,6 +123,7 @@ class Dealii(Package):
                 options.remove(word)
 
         dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
         options.extend([
             '-DCMAKE_BUILD_TYPE=DebugRelease',
             '-DDEAL_II_COMPONENT_EXAMPLES=ON',
@@ -135,9 +136,7 @@ class Dealii(Package):
             '-DLAPACK_FOUND=true',
             '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
                 spec['lapack'].prefix.include, spec['blas'].prefix.include),
-            '-DLAPACK_LIBRARIES=%s;%s' % (
-                spec['lapack'].lapack_shared_lib,
-                spec['blas'].blas_shared_lib),
+            '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';'),
             '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py
index b089e585dd..acaf863935 100644
--- a/var/spack/repos/builtin/packages/elk/package.py
+++ b/var/spack/repos/builtin/packages/elk/package.py
@@ -87,12 +87,12 @@ class Elk(Package):
         # BLAS/LAPACK support
         # Note: BLAS/LAPACK must be compiled with OpenMP support
         # if the +openmp variant is chosen
-        blas   = 'blas.a'
+        blas = 'blas.a'
         lapack = 'lapack.a'
         if '+blas' in spec:
-            blas   = spec['blas'].blas_shared_lib
+            blas = spec['blas'].blas_libs.joined()
         if '+lapack' in spec:
-            lapack = spec['lapack'].lapack_shared_lib
+            lapack = spec['lapack'].lapack_libs.joined()
         # lapack must come before blas
         config['LIB_LPK'] = ' '.join([lapack, blas])
 
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 1d375f2186..dd142866e5 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -87,9 +87,9 @@ class Gmsh(Package):
         options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF')
 
         # Make sure GMSH picks up correct BlasLapack by providing linker flags
-        options.append('-DBLAS_LAPACK_LIBRARIES=%s %s' %
-                       (to_link_flags(spec['lapack'].lapack_shared_lib),
-                        to_link_flags(spec['blas'].blas_shared_lib)))
+        blas_lapack = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options.append(
+            '-DBLAS_LAPACK_LIBRARIES={0}'.format(blas_lapack.ld_flags))
 
         # Gmsh does not have an option to compile against external metis.
         # Its own Metis, however, fails to build
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
index efd5c8bb1d..fa0013de17 100644
--- a/var/spack/repos/builtin/packages/hpl/package.py
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -78,7 +78,7 @@ class Hpl(Package):
             'MPlib        = -L{0}'.format(spec['mpi'].prefix.lib),
             # Linear Algebra library (BLAS or VSIPL)
             'LAinc        = {0}'.format(spec['blas'].prefix.include),
-            'LAlib        = {0}'.format(spec['blas'].blas_shared_lib),
+            'LAlib        = {0}'.format(spec['blas'].blas_libs.joined()),
             # F77 / C interface
             'F2CDEFS      = -DAdd_ -DF77_INTEGER=int -DStringSunStyle',
             # HPL includes / libraries / specifics
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index fdc236dcf4..96ed8411dd 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -60,13 +60,14 @@ class Hypre(Package):
         # to command the linker to include whole static libs' content into the
         # shared lib
         # Note: --with-(lapack|blas)_libs= needs space separated list of names
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
+
         configure_args = [
             '--prefix=%s' % prefix,
-            '--with-lapack-libs=%s' % to_lib_name(
-                spec['lapack'].lapack_shared_lib),
+            '--with-lapack-libs=%s' % lapack.names,
             '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
-            '--with-blas-libs=%s' % to_lib_name(
-                spec['blas'].blas_shared_lib),
+            '--with-blas-libs=%s' % blas.names,
             '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 65db3351a1..74bdba455f 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -45,6 +45,10 @@ class IntelParallelStudio(IntelInstaller):
     variant('tools', default=True, description="Install the Intel Advisor, "
             "VTune Amplifier, and Inspector tools")
 
+    variant('shared', default=True, description='Builds shared library')
+    variant('ilp64', default=False, description='64 bit integers')
+    variant('openmp', default=False, description='OpenMP multithreading layer')
+
     provides('mpi', when='@cluster:+mpi')
     provides('mkl', when='+mkl')
     provides('daal', when='+daal')
@@ -55,6 +59,28 @@ class IntelParallelStudio(IntelInstaller):
     provides('lapack', when='+mkl')
     # TODO: MKL also provides implementation of Scalapack.
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        suffix = dso_suffix if '+shared' in self.spec else 'a'
+        mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
+        mkl_threading = ['libmkl_intel_thread'] if '+openmp' in self.spec else ['libmkl_sequential']  # NOQA: ignore=E501
+        mkl_libs = find_libraries(
+            mkl_integer + ['libmkl_core'] + mkl_threading,
+            root=join_path(self.prefix.lib, 'intel64'),
+            shared=shared
+        )
+        system_libs = [
+            'libpthread.{0}'.format(suffix),
+            'libm.{0}'.format(suffix),
+            'libdl.{0}'.format(suffix)
+        ]
+        return mkl_libs + system_libs
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
+
     def check_variants(self, spec):
         error_message = '\t{variant} can not be turned off if "+all" is set'
 
@@ -171,24 +197,6 @@ class IntelParallelStudio(IntelInstaller):
         os.symlink(os.path.join(self.prefix.man, "common", "man1"),
                    os.path.join(self.prefix.man, "man1"))
 
-    def setup_dependent_package(self, module, dspec):
-        # For now use Single Dynamic Library:
-        # To set the threading layer at run time, use the
-        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
-        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
-        # To set interface layer at run time, use the mkl_set_interface_layer
-        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
-
-        # Otherwise one would need to specify several libraries
-        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
-        # different interface and threading layers.
-
-        name = 'libmkl_rt.%s' % dso_suffix
-        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
-
-        self.spec.blas_shared_lib   = join_path(libdir, name)
-        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def setup_environment(self, spack_env, run_env):
         # TODO: Determine variables needed for the professional edition.
 
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index 71a233ff3e..a7353d57c4 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -24,13 +24,40 @@ class Mkl(IntelInstaller):
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
 
+    variant('shared', default=True, description='Builds shared library')
+    variant('ilp64', default=False, description='64 bit integers')
+    variant('openmp', default=False, description='OpenMP multithreading layer')
+
     # virtual dependency
     provides('blas')
     provides('lapack')
     # TODO: MKL also provides implementation of Scalapack.
 
-    def install(self, spec, prefix):
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        suffix = dso_suffix if '+shared' in self.spec else 'a'
+        mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
+        mkl_threading = ['libmkl_sequential']
+        if '+openmp' in spec:
+            mkl_threading = ['libmkl_intel_thread'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        mkl_libs = find_libraries(
+            mkl_integer + ['libmkl_core'] + mkl_threading,
+            root=join_path(self.prefix.lib, 'intel64'),
+            shared=shared
+        )
+        system_libs = [
+            'libpthread.{0}'.format(suffix),
+            'libm.{0}'.format(suffix),
+            'libdl.{0}'.format(suffix)
+        ]
+        return mkl_libs + system_libs
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
 
+    def install(self, spec, prefix):
         self.intel_prefix = os.path.join(prefix, "pkg")
         IntelInstaller.install(self, spec, prefix)
 
@@ -45,25 +72,6 @@ class Mkl(IntelInstaller):
             os.symlink(os.path.join(mkl_lib_dir, f),
                        os.path.join(self.prefix, "lib", f))
 
-    def setup_dependent_package(self, module, dspec):
-        # For now use Single Dynamic Library:
-        # To set the threading layer at run time, use the
-        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
-        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
-        # To set interface layer at run time, use the mkl_set_interface_layer
-        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
-
-        # Otherwise one would need to specify several libraries
-        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
-        # different interface and threading layers.
-
-        name = 'libmkl_rt.%s' % dso_suffix
-        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
-
-        # Now set blas/lapack libs:
-        self.spec.blas_shared_lib   = join_path(libdir, name)
-        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up MKLROOT for everyone using MKL package
         spack_env.set('MKLROOT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 32bc42a9c3..3466f091a0 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -75,9 +75,8 @@ class Mumps(Package):
             raise RuntimeError(
                 'You cannot use the variants parmetis or ptscotch without mpi')
 
-        makefile_conf = ["LIBBLAS = %s" % to_link_flags(
-            self.spec['blas'].blas_shared_lib)
-        ]
+        blas = self.spec['blas'].blas_libs
+        makefile_conf = ["LIBBLAS = %s" % blas.ld_flags]
 
         orderings = ['-Dpord']
 
@@ -136,11 +135,12 @@ class Mumps(Package):
                  'OPTC    = %s -O ' % fpic])
 
         if '+mpi' in self.spec:
+            scalapack = self.spec['scalapack'].scalapack_libs
             makefile_conf.extend(
                 ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
                  "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
                  "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                 "SCALAP = %s" % self.spec['scalapack'].fc_link,
+                 "SCALAP = %s" % scalapack.ld_flags,
                  "MUMPS_TYPE = par"])
         else:
             makefile_conf.extend(
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 93d64fb466..b73fe850d7 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -67,6 +67,20 @@ class NetlibLapack(Package):
                 '${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
                 'CBLAS/CMakeLists.txt', string=True)
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libblas'], root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['liblapack'], root=self.prefix, shared=shared, recurse=True
+        )
+
     def install_one(self, spec, prefix, shared):
         cmake_args = [
             '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
@@ -100,18 +114,3 @@ class NetlibLapack(Package):
         # Build shared libraries if requested.
         if '+shared' in spec:
             self.install_one(spec, prefix, True)
-
-    def setup_dependent_package(self, module, dspec):
-        # This is WIP for a prototype interface for virtual packages.
-        # We can update this as more builds start depending on BLAS/LAPACK.
-        libdir = find_library_path(
-            'libblas.a', self.prefix.lib64, self.prefix.lib)
-
-        self.spec.blas_static_lib   = join_path(libdir, 'libblas.a')
-        self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a')
-
-        if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(
-                libdir, 'libblas.%s' % dso_suffix)
-            self.spec.lapack_shared_lib = join_path(
-                libdir, 'liblapack.%s' % dso_suffix)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 13e932e176..fe9f1a3023 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -28,10 +28,11 @@ import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for
-    parallel distributed memory machines"""
+    parallel distributed memory machines
+    """
 
     homepage = "http://www.netlib.org/scalapack/"
-    url      = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
+    url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
 
     version('2.0.2', '2f75e600a2ba155ed9ce974a1c4b536f')
     version('2.0.1', '17b8cde589ea0423afe1ec43e7499161')
@@ -39,10 +40,16 @@ class NetlibScalapack(Package):
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
 
-    variant('shared', default=True,
-            description='Build the shared library version')
-    variant('fpic', default=False,
-            description="Build with -fpic compiler option")
+    variant(
+        'shared',
+        default=True,
+        description='Build the shared library version'
+    )
+    variant(
+        'fpic',
+        default=False,
+        description='Build with -fpic compiler option'
+    )
 
     provides('scalapack')
 
@@ -51,6 +58,13 @@ class NetlibScalapack(Package):
     depends_on('blas')
     depends_on('cmake', when='@2.0.0:', type='build')
 
+    @property
+    def scalapack_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libscalapack'], root=self.prefix, shared=shared, recurse=True
+        )
+
     def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
@@ -60,14 +74,13 @@ class NetlibScalapack(Package):
         ]
 
         # Make sure we use Spack's Lapack:
+        blas = spec['blas'].blas_libs
+        lapack = spec['lapack'].lapack_libs
         options.extend([
             '-DLAPACK_FOUND=true',
-            '-DLAPACK_LIBRARIES=%s' % (
-                spec['lapack'].lapack_shared_lib if '+shared' in spec else
-                spec['lapack'].lapack_static_lib),
-            '-DBLAS_LIBRARIES=%s' % (
-                spec['blas'].blas_shared_lib if '+shared' in spec else
-                spec['blas'].blas_static_lib)
+            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
+            '-DLAPACK_LIBRARIES=%s' % (lapack.joined()),
+            '-DBLAS_LIBRARIES=%s' % (blas.joined())
         ])
 
         if '+fpic' in spec:
@@ -86,12 +99,3 @@ class NetlibScalapack(Package):
         # The shared libraries are not installed correctly on Darwin:
         if (sys.platform == 'darwin') and ('+shared' in spec):
             fix_darwin_install_name(prefix.lib)
-
-    def setup_dependent_package(self, module, dependent_spec):
-        spec = self.spec
-        lib_suffix = dso_suffix if '+shared' in spec else 'a'
-
-        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
-        spec.cc_link = spec.fc_link
-        spec.libraries = [join_path(spec.prefix.lib,
-                                    'libscalapack.%s' % lib_suffix)]
diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py
index 13c710a35a..b15c1c02fd 100644
--- a/var/spack/repos/builtin/packages/nwchem/package.py
+++ b/var/spack/repos/builtin/packages/nwchem/package.py
@@ -66,6 +66,9 @@ class Nwchem(Package):
     patch('Gcc6_macs_optfix.patch', when='@6.6', level=0)
 
     def install(self, spec, prefix):
+        scalapack = spec['scalapack'].scalapack_libs
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
         # see http://www.nwchem-sw.org/index.php/Compiling_NWChem
         args = []
         args.extend([
@@ -79,13 +82,11 @@ class Nwchem(Package):
             'USE_PYTHONCONFIG=y',
             'PYTHONVERSION=%s' % spec['python'].version.up_to(2),
             'PYTHONHOME=%s' % spec['python'].prefix,
-            'BLASOPT=%s %s' % (
-                to_link_flags(spec['lapack'].lapack_shared_lib),
-                to_link_flags(spec['blas'].blas_shared_lib)),
-            'BLAS_LIB=%s' % to_link_flags(spec['blas'].blas_shared_lib),
-            'LAPACK_LIB=%s' % to_link_flags(spec['lapack'].lapack_shared_lib),
+            'BLASOPT=%s' % ((lapack + blas).ld_flags),
+            'BLAS_LIB=%s' % blas.ld_flags,
+            'LAPACK_LIB=%s' % lapack.ld_flags,
             'USE_SCALAPACK=y',
-            'SCALAPACK=%s' % spec['scalapack'].fc_link,
+            'SCALAPACK=%s' % scalapack.ld_flags,
             'NWCHEM_MODULES=all python',
             'NWCHEM_LONG_PATHS=Y'  # by default NWCHEM_TOP is 64 char max
         ])
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index ff4a106940..adb760f06d 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -46,13 +46,13 @@ class Octopus(Package):
     # FEAST, Libfm, PFFT, ISF, PNFFT
 
     def install(self, spec, prefix):
+        lapack = spec['lapack'].lapack_libs
+        blas = spec['blas'].blas_libs
         args = []
         args.extend([
             '--prefix=%s' % prefix,
-            '--with-blas=%s' % to_link_flags(
-                spec['blas'].blas_shared_lib),
-            '--with-lapack=%s' % to_link_flags(
-                spec['lapack'].lapack_shared_lib),
+            '--with-blas=%s' % blas.ld_flags,
+            '--with-lapack=%s' % lapack.ld_flags,
             '--with-gsl-prefix=%s' % spec['gsl'].prefix,
             '--with-libxc-prefix=%s' % spec['libxc'].prefix,
             'CC=%s' % spec['mpi'].mpicc,
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 23c7b02daf..89c35fb991 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -30,7 +30,7 @@ import os
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
     homepage = "http://www.openblas.net"
-    url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
+    url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
 
     version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
@@ -51,6 +51,17 @@ class Openblas(Package):
 
     patch('make.patch')
 
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            ['libopenblas'], root=self.prefix, shared=shared, recurse=True
+        )
+
+    @property
+    def lapack_libs(self):
+        return self.blas_libs
+
     def install(self, spec, prefix):
         # As of 06/2016 there is no mechanism to specify that packages which
         # depends on Blas/Lapack need C or/and Fortran symbols. For now
@@ -100,6 +111,9 @@ class Openblas(Package):
         # no quotes around prefix (spack doesn't use a shell)
         make('install', "PREFIX=%s" % prefix, *make_defs)
 
+        # TODO : the links below are mainly there because client
+        # TODO : packages are wrongly written. Check if they can be removed
+
         # Blas virtual package should provide blas.a and libblas.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
@@ -120,21 +134,6 @@ class Openblas(Package):
         # test.
         self.check_install(spec)
 
-    def setup_dependent_package(self, module, dspec):
-        # This is WIP for a prototype interface for virtual packages.
-        # We can update this as more builds start depending on BLAS/LAPACK.
-        libdir = find_library_path('libopenblas.a',
-                                   self.prefix.lib64,
-                                   self.prefix.lib)
-
-        self.spec.blas_static_lib   = join_path(libdir, 'libopenblas.a')
-        self.spec.lapack_static_lib = self.spec.blas_static_lib
-
-        if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(libdir, 'libopenblas.%s' %
-                                                    dso_suffix)
-            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
-
     def check_install(self, spec):
         source_file = join_path(os.path.dirname(self.module.__file__),
                                 'test_cblas_dgemm.c')
diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py
index 2c81d92cc0..521f917230 100644
--- a/var/spack/repos/builtin/packages/opium/package.py
+++ b/var/spack/repos/builtin/packages/opium/package.py
@@ -29,7 +29,7 @@ class Opium(Package):
     """DFT pseudopotential generation project"""
 
     homepage = "https://opium.sourceforge.net/index.html"
-    url      = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz"
+    url = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz"
 
     version('3.8', 'f710c0f869e70352b4a510c31e13bf9f')
 
@@ -37,12 +37,8 @@ class Opium(Package):
     depends_on('lapack')
 
     def install(self, spec, prefix):
-        options = [
-            'LDFLAGS=%s %s' % (
-                to_link_flags(spec['lapack'].lapack_shared_lib),
-                to_link_flags(spec['blas'].blas_shared_lib)
-            )
-        ]
+        libs = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options = ['LDFLAGS=%s' % libs.ld_flags]
 
         configure(*options)
         with working_dir("src", create=False):
diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py
index e74ad6df01..9fc71d4c52 100644
--- a/var/spack/repos/builtin/packages/pexsi/package.py
+++ b/var/spack/repos/builtin/packages/pexsi/package.py
@@ -67,8 +67,8 @@ class Pexsi(Package):
             '@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
             '@LAPACK_PREFIX': self.spec['lapack'].prefix,
             '@BLAS_PREFIX': self.spec['blas'].prefix,
-            '@LAPACK_LIBS': self.spec['lapack'].lapack_shared_lib,
-            '@BLAS_LIBS': self.spec['lapack'].blas_shared_lib,
+            '@LAPACK_LIBS': self.spec['lapack'].lapack_libs.joined(),
+            '@BLAS_LIBS': self.spec['lapack'].blas_libs.joined(),
             '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs)
         }
 
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index 6296d0cee6..566aa50f44 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -32,7 +32,7 @@ class Psi4(Package):
     a variety of molecular properties."""
 
     homepage = "http://www.psicode.org/"
-    url      = "https://github.com/psi4/psi4/archive/0.5.tar.gz"
+    url = "https://github.com/psi4/psi4/archive/0.5.tar.gz"
 
     version('0.5', '53041b8a9be3958384171d0d22f9fdd0')
 
@@ -62,9 +62,10 @@ class Psi4(Package):
     def install(self, spec, prefix):
         cmake_args = [
             '-DBLAS_TYPE={0}'.format(spec['blas'].name.upper()),
-            '-DBLAS_LIBRARIES={0}'.format(spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARIES={0}'.format(spec['blas'].blas_libs.joined()),
             '-DLAPACK_TYPE={0}'.format(spec['lapack'].name.upper()),
-            '-DLAPACK_LIBRARIES={0}'.format(spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARIES={0}'.format(
+                spec['lapack'].lapack_libs.joined()),
             '-DBOOST_INCLUDEDIR={0}'.format(spec['boost'].prefix.include),
             '-DBOOST_LIBRARYDIR={0}'.format(spec['boost'].prefix.lib),
             '-DENABLE_CHEMPS2=OFF'
@@ -90,9 +91,9 @@ class Psi4(Package):
 
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
 
-        cc_files  = ['bin/psi4-config']
+        cc_files = ['bin/psi4-config']
         cxx_files = ['bin/psi4-config', 'include/psi4/psiconfig.h']
-        template  = 'share/psi4/plugin/Makefile.template'
+        template = 'share/psi4/plugin/Makefile.template'
 
         for filename in cc_files:
             filter_file(os.environ['CC'], self.compiler.cc,
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 83a69c5682..68b2cb13e0 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -47,7 +47,7 @@ class PyScipy(Package):
             env['ATLAS'] = join_path(
                 spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix)
         else:
-            env['BLAS']   = spec['blas'].blas_shared_lib
-            env['LAPACK'] = spec['lapack'].lapack_shared_lib
+            env['BLAS'] = spec['blas'].blas_libs.joined()
+            env['LAPACK'] = spec['lapack'].lapack_libs.joined()
 
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index a71bfd8bd4..22f069885d 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -80,8 +80,8 @@ class SuiteSparse(Package):
 
         # Make sure Spack's Blas/Lapack is used. Otherwise System's
         # Blas/Lapack might be picked up.
-        blas = to_link_flags(spec['blas'].blas_shared_lib)
-        lapack = to_link_flags(spec['lapack'].lapack_shared_lib)
+        blas = spec['blas'].blas_libs.ld_flags
+        lapack = spec['lapack'].lapack_libs.ld_flags
         if '@4.5.1' in spec:
             # adding -lstdc++ is clearly an ugly way to do this, but it follows
             # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index 7582954ab1..6ee247b7ea 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -31,7 +31,7 @@ class Sundials(Package):
     Solvers)"""
 
     homepage = "http://computation.llnl.gov/casc/sundials/"
-    url      = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
+    url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
 
     version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
 
@@ -79,9 +79,9 @@ class Sundials(Package):
         if '+lapack' in spec:
             cmake_args.extend([
                 '-DLAPACK_ENABLE=ON',
-                '-DLAPACK_LIBRARIES={0};{1}'.format(
-                    spec['lapack'].lapack_shared_lib,
-                    spec['blas'].blas_shared_lib
+                '-DLAPACK_LIBRARIES={0}'.format(
+                    (spec['lapack'].lapack_libs +
+                     spec['blas'].blas_libs).joined(';')
                 )
             ])
         else:
@@ -113,7 +113,7 @@ class Sundials(Package):
             elif '+pthread' in spec:
                 cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread')
             else:
-                msg  = 'You must choose either +openmp or +pthread when '
+                msg = 'You must choose either +openmp or +pthread when '
                 msg += 'building with SuperLU_MT'
                 raise RuntimeError(msg)
         else:
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 85b7f689d0..a29b74bf08 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -46,15 +46,14 @@ class SuperluDist(Package):
     depends_on('metis@5:')
 
     def install(self, spec, prefix):
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
         makefile_inc = []
         makefile_inc.extend([
             'PLAT         = _mac_x',
             'DSuperLUroot = %s' % self.stage.source_path,
             'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
             'BLASDEF      = -DUSE_VENDOR_BLAS',
-            'BLASLIB      = %s %s' %
-                (to_link_flags(spec['lapack'].lapack_shared_lib),
-                 to_link_flags(spec['blas'].blas_shared_lib)),
+            'BLASLIB      = %s' % lapack_blas.ld_flags,
             'METISLIB     = -L%s -lmetis' % spec['metis'].prefix.lib,
             'PARMETISLIB  = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
             'FLIBS        =',
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
index c634c1d1ba..d9cff650b6 100644
--- a/var/spack/repos/builtin/packages/superlu/package.py
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -42,7 +42,7 @@ class Superlu(Package):
             '-DCMAKE_POSITION_INDEPENDENT_CODE=ON',
             # BLAS support
             '-Denable_blaslib=OFF',
-            '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_shared_lib)
+            '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_libs.joined())
         ]
 
         cmake_args.extend(std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3a88f67340..716d8f8eb6 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -132,6 +132,8 @@ class Trilinos(Package):
 
         mpi_bin = spec['mpi'].prefix.bin
         # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
+        blas = spec['blas'].blas_libs
+        lapack = spec['lapack'].lapack_libs
         options.extend([
             '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@@ -145,12 +147,10 @@ class Trilinos(Package):
             '-DTPL_ENABLE_MPI:BOOL=ON',
             '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
             '-DTPL_ENABLE_BLAS=ON',
-            '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
-                spec['blas'].blas_shared_lib),
+            '-DBLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
             '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
             '-DTPL_ENABLE_LAPACK=ON',
-            '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
-                spec['lapack'].lapack_shared_lib),
+            '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
             '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py
index 189e568cdc..119d2cf769 100644
--- a/var/spack/repos/builtin/packages/wannier90/package.py
+++ b/var/spack/repos/builtin/packages/wannier90/package.py
@@ -47,13 +47,12 @@ class Wannier90(Package):
 
     def install(self, spec, prefix):
 
+        lapack = self.spec['lapack'].lapack_libs
+        blas = self.spec['blas'].blas_libs
         substitutions = {
             '@F90': spack_fc,
             '@MPIF90': self.spec['mpi'].mpifc,
-            '@LIBS': ' '.join([
-                self.spec['lapack'].lapack_shared_lib,
-                self.spec['lapack'].blas_shared_lib
-            ])
+            '@LIBS': (lapack + blas).joined()
         }
         #######
         # TODO : this part is replicated in PEXSI
-- 
cgit v1.2.3-70-g09d2


From 1db25526445f6d8764708c39315f77be3f2d57c8 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Thu, 22 Sep 2016 09:31:28 +0200
Subject: fix : stops infinite recursion for python 2.6 (#1823)

---
 lib/spack/spack/spec.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 158d76e568..c92594da72 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -531,8 +531,9 @@ class Spec(object):
         """Delegate to self.package if the attribute is not in the spec"""
         # This line is to avoid infinite recursion in case package is
         # not present among self attributes
-        package = super(Spec, self).__getattribute__('package')
-        return getattr(package, item)
+        if item.endswith('libs'):
+            return getattr(self.package, item)
+        raise AttributeError()
 
     def get_dependency(self, name):
         dep = self._dependencies.get(name)
-- 
cgit v1.2.3-70-g09d2


From 98f9dd266fe53444c77bcb6b810dda788c1fa558 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Thu, 22 Sep 2016 03:43:33 -0400
Subject: Remove SPACK_DIRTY env var (#1818)

* Removed SPACK_DIRTY env var support.

* Finished removing SPACK_DIRTY support.

* Minor changes.
---
 lib/spack/spack/cmd/diy.py     | 5 ++---
 lib/spack/spack/cmd/install.py | 6 ++----
 lib/spack/spack/cmd/setup.py   | 5 ++---
 3 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 1a3e2fd65c..9833e8cdce 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -54,8 +54,7 @@ def setup_parser(subparser):
         help="specs to use for install.  Must contain package AND version.")
     subparser.add_argument(
         '--dirty', action='store_true', dest='dirty',
-        help="Install a package *without* cleaning the environment.  " +
-        "Or set SPACK_DIRTY environment variable")
+        help="Install a package *without* cleaning the environment.")
 
 
 def diy(self, args):
@@ -105,4 +104,4 @@ def diy(self, args):
             ignore_deps=args.ignore_deps,
             verbose=not args.quiet,
             keep_stage=True,   # don't remove source dir for DIY.
-            dirty=args.dirty or ('SPACK_DIRTY' in os.environ))
+            dirty=args.dirty)
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index a77af37ed0..7663a97a28 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -28,7 +28,6 @@ import llnl.util.tty as tty
 
 import spack
 import spack.cmd
-import os
 
 description = "Build and install packages"
 
@@ -57,8 +56,7 @@ def setup_parser(subparser):
         help="Fake install. Just remove prefix and create a fake file.")
     subparser.add_argument(
         '--dirty', action='store_true', dest='dirty',
-        help="Install a package *without* cleaning the environment.  " +
-        "Or set SPACK_DIRTY environment variable")
+        help="Install a package *without* cleaning the environment.")
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER,
         help="specs of packages to install")
@@ -90,5 +88,5 @@ def install(parser, args):
                 run_tests=args.run_tests,
                 verbose=args.verbose,
                 fake=args.fake,
-                dirty=args.dirty or ('SPACK_DIRTY' in os.environ),
+                dirty=args.dirty,
                 explicit=True)
diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py
index 66095ee628..4dfa13eccf 100644
--- a/lib/spack/spack/cmd/setup.py
+++ b/lib/spack/spack/cmd/setup.py
@@ -48,8 +48,7 @@ def setup_parser(subparser):
         help="specs to use for install.  Must contain package AND version.")
     subparser.add_argument(
         '--dirty', action='store_true', dest='dirty',
-        help="Install a package *without* cleaning the environment.  " +
-        "Or set SPACK_DIRTY environment variable")
+        help="Install a package *without* cleaning the environment.")
 
 
 def setup(self, args):
@@ -96,4 +95,4 @@ def setup(self, args):
             verbose=args.verbose,
             keep_stage=True,   # don't remove source dir for SETUP.
             install_phases=set(['setup', 'provenance']),
-            dirty=args.dirty or ('SPACK_DIRTY' in os.environ))
+            dirty=args.dirty)
-- 
cgit v1.2.3-70-g09d2


From 025b779a30476dd2b6ba9851e4ef1d57812b97c7 Mon Sep 17 00:00:00 2001
From: Eric <muffgaga@gmx.de>
Date: Thu, 22 Sep 2016 09:43:47 +0200
Subject: Fix sbang for perl (#1802)

* Perform shebang fix for all files

* Fix sbang for perl scripts

Otherwise perl would look at the #! line and call sbang again, resulting
in an infinite loop.
---
 bin/sbang                      |  8 ++++++--
 lib/spack/spack/hooks/sbang.py | 12 +++++++-----
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/bin/sbang b/bin/sbang
index 1ea5f06592..e71074b330 100755
--- a/bin/sbang
+++ b/bin/sbang
@@ -111,8 +111,12 @@ while read line && ((lines < 2)) ; do
 done < "$script"
 
 # Invoke any interpreter found, or raise an error if none was found.
-if [ -n "$interpreter" ]; then
-    exec $interpreter "$@"
+if [[ -n "$interpreter" ]]; then
+    if [[ "${interpreter##*/}" = "perl" ]]; then
+        exec $interpreter -x "$@"
+    else
+        exec $interpreter "$@"
+    fi
 else
     echo "error: sbang found no interpreter in $script"
     exit 1
diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
index 02c1ce3816..6f9736a018 100644
--- a/lib/spack/spack/hooks/sbang.py
+++ b/lib/spack/spack/hooks/sbang.py
@@ -81,8 +81,10 @@ def filter_shebang(path):
     tty.warn("Patched overlong shebang in %s" % path)
 
 
-def filter_shebangs_in_directory(directory):
-    for file in os.listdir(directory):
+def filter_shebangs_in_directory(directory, filenames=None):
+    if filenames is None:
+        filenames = os.listdir(directory)
+    for file in filenames:
         path = os.path.join(directory, file)
 
         # only handle files
@@ -104,6 +106,6 @@ def post_install(pkg):
     """This hook edits scripts so that they call /bin/bash
        $spack_prefix/bin/sbang instead of something longer than the
        shebang limit."""
-    if not os.path.isdir(pkg.prefix.bin):
-        return
-    filter_shebangs_in_directory(pkg.prefix.bin)
+
+    for directory, _, filenames in os.walk(pkg.prefix):
+        filter_shebangs_in_directory(directory, filenames)
-- 
cgit v1.2.3-70-g09d2


From 7ad6c35627128b3f70334e0c698954b7bc691698 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 22 Sep 2016 03:48:00 -0400
Subject: New package "charm" for the Charm++ parallel programming framework
 (#1766)

---
 var/spack/repos/builtin/packages/charm/mpi.patch  |  19 +++
 var/spack/repos/builtin/packages/charm/package.py | 172 ++++++++++++++++++++++
 2 files changed, 191 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/charm/mpi.patch
 create mode 100644 var/spack/repos/builtin/packages/charm/package.py

diff --git a/var/spack/repos/builtin/packages/charm/mpi.patch b/var/spack/repos/builtin/packages/charm/mpi.patch
new file mode 100644
index 0000000000..e909d5f876
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charm/mpi.patch
@@ -0,0 +1,19 @@
+--- old/src/scripts/configure
++++ new/src/scripts/configure
+@@ -3293,10 +3293,16 @@
+         test_link "whether -lmpi" "ok" "no" "-lmpi"
+         if test $pass -eq 1
+         then
+                 add_flag CMK_SYSLIBS='"$CMK_SYSLIBS -lmpi"' "mpi lib"
+         else
++          test_link "whether -lmpi -lmpi_cxx" "ok" "no" "-lmpi -lmpi_cxx"
++          if test $pass -eq 1
++          then
++            add_flag CMK_SYSLIBS='"$CMK_SYSLIBS -lmpi -lmpi_cxx"' "mpi lib"
++          else
+                 echo "Error: can not find mpi library"
+                 test_finish 1
++          fi
+         fi
+       fi
+     else
diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py
new file mode 100644
index 0000000000..d67ac80de1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charm/package.py
@@ -0,0 +1,172 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import platform
+import shutil
+import sys
+from spack import *
+
+
+class Charm(Package):
+    """Charm++ is a parallel programming framework in C++ supported by
+    an adaptive runtime system, which enhances user productivity and
+    allows programs to run portably from small multicore computers
+    (your laptop) to the largest supercomputers."""
+
+    homepage = "http://charmplusplus.org"
+    url      = "http://charm.cs.illinois.edu/distrib/charm-6.7.1.tar.gz"
+
+    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
+    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
+    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
+    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
+    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
+
+    # Support OpenMPI; see
+    # <https://charm.cs.illinois.edu/redmine/issues/1206>
+    patch("mpi.patch")
+
+    # Communication mechanisms (choose exactly one)
+    # TODO: Support Blue Gene/Q PAMI, Cray GNI, Cray shmem, CUDA
+    variant("mpi", default=False,
+            description="Use MPI as communication mechanism")
+    variant("multicore", default=False,
+            description="Disable inter-node communication")
+    variant("net", default=False,
+            description="Use net communication mechanism")
+    variant("netlrts", default=True,
+            description="Use netlrts communication mechanism")
+    variant("verbs", default=False,
+            description="Use Infiniband as communication mechanism")
+
+    # Other options
+    # Something is off with PAPI -- there are build errors. Maybe
+    # Charm++ expects a particular version?
+    variant("papi", default=False, description="Enable PAPI integration")
+    variant("smp", default=True,
+            description=(
+                "Enable SMP parallelism (does not work with +multicore)"))
+    variant("tcp", default=False,
+            description="Use TCP as transport mechanism (requires +net)")
+
+    # Note: We could add variants for AMPI, LIBS, bigemulator, msa, Tau
+    # Note: We could support shared libraries
+
+    depends_on("mpi", when="+mpi")
+    depends_on("papi", when="+papi")
+
+    def install(self, spec, prefix):
+        target = "charm++"
+
+        # Note: Turn this into a multi-valued variant, once these
+        # exist in Spack
+        if sum(["+mpi" in spec,
+                "+multicore" in spec,
+                "+net" in spec,
+                "+netlrts" in spec,
+                "+verbs" in spec]) != 1:
+            raise InstallError(
+                "Exactly one communication mechanism "
+                "(+mpi, +multicore, +net, +netlrts, or +verbs) "
+                "must be enabled")
+        if "+mpi" in spec:
+            comm = "mpi"
+        if "+multicore" in spec:
+            comm = "multicore"
+        if "+net" in spec:
+            comm = "net"
+        if "+netlrts" in spec:
+            comm = "netlrts"
+        if "+verbs" in spec:
+            comm = "verbs"
+
+        plat = sys.platform
+        if plat.startswith("linux"):
+            plat = "linux"
+        mach = platform.machine()
+
+        # Define Charm++ version names for various (plat, mach, comm)
+        # combinations. Note that not all combinations are supported.
+        versions = {
+            ("darwin", "i386", "multicore"): "multicore-darwin-x86",
+            ("darwin", "i386", "net"): "net-darwin-x86",
+            ("darwin", "x86_64", "mpi"): "mpi-darwin-x86_64",
+            ("darwin", "x86_64", "multicore"): "multicore-darwin-x86_64",
+            ("darwin", "x86_64", "net"): "net-darwin-x86_64",
+            ("darwin", "x86_64", "netlrts"): "netlrts-darwin-x86_64",
+            ("linux", "i386", "mpi"): "mpi-linux",
+            ("linux", "i386", "multicore"): "multicore-linux32",
+            ("linux", "i386", "net"): "net-linux",
+            ("linux", "i386", "netlrts"): "netlrts-linux",
+            ("linux", "x86_64", "mpi"): "mpi-linux-x86_64",
+            ("linux", "x86_64", "multicore"): "multicore-linux64",
+            ("linux", "x86_64", "net"): "net-linux-x86_64",
+            ("linux", "x86_64", "netlrts"): "netlrts-linux-x86_64",
+            ("linux", "x86_64", "verbs"): "verbs-linux-x86_64",
+        }
+        if (plat, mach, comm) not in versions:
+            raise InstallError(
+                "The communication mechanism %s is not supported "
+                "on a %s platform with a %s CPU" %
+                (comm, plat, mach))
+        version = versions[(plat, mach, comm)]
+
+        # We assume that Spack's compiler wrappers make this work. If
+        # not, then we need to query the compiler vendor from Spack
+        # here.
+        compiler = "gcc"
+
+        options = [compiler,
+                   "--with-production",   # Note: turn this into a variant
+                   "-j%d" % make_jobs,
+                   "--destination=%s" % prefix]
+        if "+mpi" in spec:
+            options.append("--basedir=%s" % spec["mpi"].prefix)
+        if "+papi" in spec:
+            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
+        if "+smp" in spec:
+            if "+multicore" in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError("Cannot combine +smp with +multicore")
+            options.append("smp")
+        if "+tcp" in spec:
+            if "+net" not in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError(
+                    "The +tcp variant requires "
+                    "the +net communication mechanism")
+            options.append("tcp")
+
+        # Call "make" via the build script
+        # Note: This builds Charm++ in the "tmp" subdirectory of the
+        # install directory. Maybe we could set up a symbolic link
+        # back to the build tree to prevent this? Alternatively, we
+        # could dissect the build script; the build instructions say
+        # this wouldn't be difficult.
+        build = Executable(join_path(".", "build"))
+        build(target, version, *options)
+        shutil.rmtree(join_path(prefix, "tmp"))
-- 
cgit v1.2.3-70-g09d2


From 64c3b11478e02a5fa1eb9b60c09d514245181275 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Thu, 22 Sep 2016 14:03:49 -0400
Subject: suitesparse: Added +fpic (for linking with shared libraries) (#1542)

---
 var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 22f069885d..d6d8f71313 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -36,6 +36,7 @@ class SuiteSparse(Package):
     version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
 
     variant('tbb', default=True, description='Build with Intel TBB')
+    variant('fpic', default=True, description='Build position independent code (required to link with shared libraries)')
 
     depends_on('blas')
     depends_on('lapack')
@@ -63,6 +64,8 @@ class SuiteSparse(Package):
             'CXX=c++',
             'F77=f77',
         ])
+        if '+fpic' in spec:
+            make_args.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC'])
 
         # use Spack's metis in CHOLMOD/Partition module,
         # otherwise internal Metis will be compiled
-- 
cgit v1.2.3-70-g09d2


From f1f301ad3b994bd4c3d17db4a4bf5e5be2fa5ed8 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 22 Sep 2016 13:33:29 -0500
Subject: Fix spack checksum output indentation (#1826)

---
 lib/spack/spack/cmd/checksum.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index aedb0fd99c..2e24d0527e 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -113,6 +113,6 @@ def checksum(parser, args):
         tty.die("Could not fetch any versions for %s" % pkg.name)
 
     version_lines = [
-        "    version('%s', '%s')" % (v, h) for v, h in version_hashes
+        "  version('%s', '%s')" % (v, h) for v, h in version_hashes
     ]
     tty.msg("Checksummed new versions of %s:" % pkg.name, *version_lines)
-- 
cgit v1.2.3-70-g09d2


From c7860322f5a07450ca7a5a60e97be95eeb33fc23 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <mathstuf@users.noreply.github.com>
Date: Thu, 22 Sep 2016 14:47:25 -0400
Subject: package: fix variable name usage (#1829)

---
 lib/spack/spack/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 38bc6fa3f4..fe19e5d400 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -722,7 +722,7 @@ class Package(object):
 
             if not ignore_checksum:
                 raise FetchError("Will not fetch %s" %
-                                 self.spec.format('$_$@'), checksum_msg)
+                                 self.spec.format('$_$@'), ck_msg)
 
         self.stage.fetch(mirror_only)
 
-- 
cgit v1.2.3-70-g09d2


From a638b62ab14117b3d8339f766eb673147ec85be8 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 22 Sep 2016 13:50:50 -0500
Subject: Updates to CGAL and ICU4C packages (#1828)

---
 var/spack/repos/builtin/packages/cgal/package.py  | 49 ++++++++++++++---------
 var/spack/repos/builtin/packages/icu4c/package.py | 19 +++++----
 2 files changed, 42 insertions(+), 26 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index e522b4a5a0..d986f77487 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -22,44 +22,57 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
 
 
 class Cgal(Package):
-    """CGAL is a software project that provides easy access to efficient and
-       reliable geometric algorithms in the form of a C++ library. CGAL
-       is used in various areas needing geometric computation, such as
-       geographic information systems, computer aided design, molecular
-       biology, medical imaging, computer graphics, and robotics.
-
+    """The Computational Geometry Algorithms Library (CGAL) is a C++ library
+    that aims to provide easy access to efficient and reliable algorithms in
+    computational geometry. CGAL is used in various areas needing geometric
+    computation, such as geographic information systems, computer aided design,
+    molecular biology, medical imaging, computer graphics, and robotics.
     """
     homepage = 'http://www.cgal.org/'
     url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
 
+    version('4.9', '7b628db3e5614347f776c046b7666089')
     version('4.7', '4826714810f3b4c65cac96b90fb03b67')
     version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
 
-    # Installation instructions :
-    # http://doc.cgal.org/latest/Manual/installation.html
     variant('shared', default=True,
             description='Enables the build of shared libraries')
     variant('debug', default=False,
             description='Builds a debug version of the libraries')
 
+    # Essential Third Party Libraries
     depends_on('boost')
-    depends_on('mpfr')
     depends_on('gmp')
+    depends_on('mpfr')
     depends_on('zlib')
-    depends_on('cmake', type='build')
+    # depends_on('opengl')
+    depends_on('qt@5:')
 
-    # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
-    # FIXME : Optional third party libraries missing
+    # Optional Third Party Libraries
+    # depends_on('leda')
+    # depends_on('mpfi')
+    # depends_on('rs')
+    # depends_on('rs3')
+    # depends_on('ntl')
+    # depends_on('eigen')
+    # depends_on('libqglviewer')
+    # depends_on('esbtl')
+    # depends_on('intel-tbb')
+
+    # Build dependencies
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
+        # Installation instructions:
+        # http://doc.cgal.org/latest/Manual/installation.html
 
         options = []
         options.extend(std_cmake_args)
+
         # CGAL supports only Release and Debug build type. Any other build type
         # will raise an error at configure time
         if '+debug' in spec:
@@ -72,9 +85,7 @@ class Cgal(Package):
         else:
             options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
 
-        build_directory = join_path(self.stage.path, 'spack-build')
-        source_directory = self.stage.source_path
-        with working_dir(build_directory, create=True):
-            cmake(source_directory, *options)
-            make()
-            make("install")
+        cmake('.', *options)
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index 2bcf86cd13..615c59f92d 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -28,17 +28,22 @@ from spack import *
 class Icu4c(Package):
     """ICU is a mature, widely used set of C/C++ and Java libraries providing
        Unicode and Globalization support for software applications.
-
     """
-
     homepage = "http://site.icu-project.org/"
-    url      = "http://downloads.sourceforge.net/project/icu/ICU4C/54.1/icu4c-54_1-src.tgz"
+    url      = "http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz"
 
-    version('54_1', 'e844caed8f2ca24c088505b0d6271bc0')
+    version('57.1', '976734806026a4ef8bdd17937c8898b9')
+
+    def url_for_version(self, version):
+        base_url = "http://download.icu-project.org/files/icu4c"
+        return "{0}/{1}/icu4c-{2}-src.tgz".format(
+            base_url, version, version.underscored)
 
     def install(self, spec, prefix):
-        cd("source")
-        configure("--prefix=%s" % prefix)
+        cd('source')
+
+        configure('--prefix={0}'.format(prefix))
 
         make()
-        make("install")
+        make('check')
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From 462a4a1353bfcf68e75036d322bd3b668d2b8756 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 22 Sep 2016 22:47:22 +0200
Subject: boost: fix a bug which broke it on macOS with clang+gfortran (#1816)

* dealii: add missing python dependency

* boost: fix a bug which  broke it on macOS with clang+gfortran

Boost was using gcc compiler instead of clang++, which lead to
cryptic Undefined symbols linking errors for boost::python::objects::function_object()
when building other packages against boost+python.

* boost: add exceptions for intel

* boost: use spack_cxx
---
 var/spack/repos/builtin/packages/boost/package.py  | 22 ++++++++++++++++++----
 var/spack/repos/builtin/packages/dealii/package.py |  1 +
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 0d4ccc7ea3..2b78dbd858 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -138,15 +138,13 @@ class Boost(Package):
     def determine_toolset(self, spec):
         if spec.satisfies("platform=darwin"):
             return 'darwin'
-        else:
-            platform = 'linux'
 
         toolsets = {'g++': 'gcc',
                     'icpc': 'intel',
                     'clang++': 'clang'}
 
         if spec.satisfies('@1.47:'):
-            toolsets['icpc'] += '-' + platform
+            toolsets['icpc'] += '-linux'
         for cc, toolset in toolsets.iteritems():
             if cc in self.compiler.cxx_names:
                 return toolset
@@ -164,6 +162,16 @@ class Boost(Package):
                            join_path(spec['python'].prefix.bin, 'python'))
 
         with open('user-config.jam', 'w') as f:
+            # Boost may end up using gcc even though clang+gfortran is set in
+            # compilers.yaml. Make sure this does not happen:
+            if not spec.satisfies('%intel'):
+                # using intel-linux : : spack_cxx in user-config.jam leads to
+                # error: at project-config.jam:12
+                # error: duplicate initialization of intel-linux with the following parameters:  # noqa
+                # error: version = <unspecified>
+                # error: previous initialization at ./user-config.jam:1
+                f.write("using {0} : : {1} ;\n".format(boostToolsetId,
+                                                       spack_cxx))
 
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
@@ -204,7 +212,13 @@ class Boost(Package):
 
         options.extend([
             'link=%s' % ','.join(linkTypes),
-            '--layout=tagged'])
+            '--layout=tagged'
+        ])
+
+        if not spec.satisfies('%intel'):
+            options.extend([
+                'toolset=%s' % self.determine_toolset(spec)
+            ])
 
         return threadingOpts
 
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 89732f98b8..0d293e5d92 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -104,6 +104,7 @@ class Dealii(Package):
     depends_on("oce",              when='+oce')
     depends_on("p4est",            when='+p4est+mpi')
     depends_on("petsc+mpi",        when='@8.4.2:+petsc+mpi')
+    depends_on('python',           when='@8.5.0:+python')
     depends_on("slepc",            when='@8.4.2:+slepc+petsc+mpi')
     depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi')
     depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi')
-- 
cgit v1.2.3-70-g09d2


From c0ebbc97c9a5da9e6ba2319938b6ef3dc8aca0b3 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 23 Sep 2016 11:21:15 -0400
Subject: Update OpenSSL (#1836)

This is a security update with priority "HIGH".
---
 var/spack/repos/builtin/packages/openssl/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 40c8b1b9f1..e5dce49918 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -36,11 +36,13 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
     url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz"
 
+    version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
     version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
+    version('1.0.1u', '130bb19745db2a5a09f22ccbbf7e69d0')
     version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
     version('1.0.1r', '1abd905e079542ccae948af37e393d28')
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
-- 
cgit v1.2.3-70-g09d2


From df5e151049a6fd9ba14632516a70f3a81f1a2379 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 23 Sep 2016 19:06:18 +0200
Subject: hypre: fix a bug with blas/lapack names (#1841)

---
 var/spack/repos/builtin/packages/hypre/package.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 96ed8411dd..f22303a864 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -54,20 +54,15 @@ class Hypre(Package):
         os.environ['CXX'] = spec['mpi'].mpicxx
         os.environ['F77'] = spec['mpi'].mpif77
 
-        # Since +shared does not build on macOS and also Atlas does not have
-        # a single static lib to build against, link against shared libs with
-        # a hope that --whole-archive linker option (or alike) was used
-        # to command the linker to include whole static libs' content into the
-        # shared lib
         # Note: --with-(lapack|blas)_libs= needs space separated list of names
         lapack = spec['lapack'].lapack_libs
         blas = spec['blas'].blas_libs
 
         configure_args = [
             '--prefix=%s' % prefix,
-            '--with-lapack-libs=%s' % lapack.names,
+            '--with-lapack-libs=%s' % ' '.join(lapack.names),
             '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
-            '--with-blas-libs=%s' % blas.names,
+            '--with-blas-libs=%s' % ' '.join(blas.names),
             '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
-- 
cgit v1.2.3-70-g09d2


From 3d282b9239991ae95e1eea5090ae956e2e76c5f1 Mon Sep 17 00:00:00 2001
From: "Robert D. French" <robert@robertdfrench.me>
Date: Fri, 23 Sep 2016 16:26:27 -0400
Subject: Add libmesh, needed for some FEM applications (#1846)

---
 .../repos/builtin/packages/libmesh/package.py      | 42 ++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libmesh/package.py

diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py
new file mode 100644
index 0000000000..ea81f5da73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmesh/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libmesh(Package):
+    """The libMesh library provides a framework for the numerical simulation of
+       partial differential equations using arbitrary unstructured
+       discretizations on serial and parallel platforms."""
+
+    homepage = "http://libmesh.github.io/"
+    url      = "https://github.com/libMesh/libmesh/releases/download/v1.0.0/libmesh-1.0.0.tar.bz2"
+
+    version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From 8147a0948916e5b1eda2abca394638eb891be28c Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 23 Sep 2016 16:32:57 -0400
Subject: Update jemalloc to 4.2.1 (#1839)

---
 var/spack/repos/builtin/packages/jemalloc/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index f5a983b7a9..e13d4292f8 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -31,6 +31,8 @@ class Jemalloc(Package):
     homepage = "http://www.canonware.com/jemalloc/"
     url      = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2"
 
+    version('4.2.1', '094b0a7b8c77c464d0dc8f0643fd3901')
+    version('4.2.0', 'e6b5d5a1ea93a04207528d274efdd144')
     version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94')
     version('4.0.4', '687c5cc53b9a7ab711ccd680351ff988')
 
-- 
cgit v1.2.3-70-g09d2


From 73ec2a27d08feebcd11be657f2ac25a93fa41928 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 23 Sep 2016 16:35:12 -0400
Subject: Don't require git for Julia @0.5: (#1834)

---
 var/spack/repos/builtin/packages/julia/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index c7c701175e..033e27fb64 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -70,7 +70,8 @@ class Julia(Package):
     depends_on("binutils", when='+binutils')
     depends_on("cmake @2.8:")
     depends_on("curl")
-    depends_on("git")           # I think Julia @0.5: doesn't use git any more
+    depends_on("git", when='@:0.4')
+    depends_on("git", when='@release-0.4')
     depends_on("openssl")
     depends_on("python @2.7:2.999")
 
-- 
cgit v1.2.3-70-g09d2


From 98d54182d3c5bdea7febf1114bc83f4464f3097a Mon Sep 17 00:00:00 2001
From: Bruno Turcksin <bruno.turcksin@gmail.com>
Date: Fri, 23 Sep 2016 16:36:21 -0400
Subject: Add Trilinos 12.8.1 (#1843)

---
 var/spack/repos/builtin/packages/trilinos/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 716d8f8eb6..a50201c903 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -45,6 +45,7 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     base_url = "https://github.com/trilinos/Trilinos/archive"
 
+    version('12.8.1', '01c0026f1e2050842857db941060ecd5')
     version('12.6.4', 'c2ea7b5aa0d10bcabdb9b9a6e3bac3ea')
     version('12.6.3', '8de5cc00981a0ca0defea6199b2fe4c1')
     version('12.6.2', 'dc7f9924872778798149ecadd81605a5')
-- 
cgit v1.2.3-70-g09d2


From 6ef6428331db023cc8f7af2ca5ff86ab488ad777 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 23 Sep 2016 22:38:29 +0200
Subject: m4: fix compilation on Sierra with GCC (#1844)

* m4: fix compilation on Sierra with GCC

* m4: check macOS version
---
 var/spack/repos/builtin/packages/m4/package.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index b3bb5e61ce..f7150727fe 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import sys
 
 
 class M4(Package):
@@ -47,6 +48,11 @@ class M4(Package):
         else:
             configure_args.append('--without-libsigsegv-prefix')
 
+        # http://lists.gnu.org/archive/html/bug-m4/2016-09/msg00002.html
+        if (sys.platform == "darwin") and (spec.satisfies('%gcc')) and \
+           (spec.architecture.platform_os.version == "10.12"):
+            configure_args.append('ac_cv_type_struct_sched_param=yes')
+
         configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 64194a823af1e54951bb67d5d354b4a91d90bc86 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 23 Sep 2016 16:16:59 -0500
Subject: Remove duplicate ICU package (#1837)

* Remove duplicate ICU package

* Ignore deleted files during flake8 tests

* Rename Boost ICU variant
---
 share/spack/qa/changed_files                       |  6 +--
 var/spack/repos/builtin/packages/R/package.py      |  2 +-
 var/spack/repos/builtin/packages/boost/package.py  |  6 +--
 .../repos/builtin/packages/harfbuzz/package.py     |  2 +-
 var/spack/repos/builtin/packages/icu/package.py    | 48 ----------------------
 var/spack/repos/builtin/packages/icu4c/package.py  | 16 ++++----
 .../repos/builtin/packages/r-stringi/package.py    |  2 +-
 7 files changed, 17 insertions(+), 65 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/icu/package.py

diff --git a/share/spack/qa/changed_files b/share/spack/qa/changed_files
index 9c60b3b20b..c1fa55c053 100755
--- a/share/spack/qa/changed_files
+++ b/share/spack/qa/changed_files
@@ -18,11 +18,11 @@ SPACK_ROOT="$(dirname "$0")/../../.."
 cd "$SPACK_ROOT"
 
 # Add changed files that have been committed since branching off of develop
-changed=($(git diff --name-only --find-renames develop... -- "$@"))
+changed=($(git diff --name-only --diff-filter=ACMR develop... -- "$@"))
 # Add changed files that have been staged but not yet committed
-changed+=($(git diff --name-only --find-renames --cached -- "$@"))
+changed+=($(git diff --name-only --diff-filter=ACMR --cached -- "$@"))
 # Add changed files that are unstaged
-changed+=($(git diff --name-only --find-renames -- "$@"))
+changed+=($(git diff --name-only --diff-filter=ACMR -- "$@"))
 # Add new files that are untracked
 changed+=($(git ls-files --exclude-standard --other -- "$@"))
 
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index e880a3aa66..a0899084d0 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -58,7 +58,7 @@ class R(Package):
     # Concrete dependencies
     depends_on('readline')
     depends_on('ncurses')
-    depends_on('icu')
+    depends_on('icu4c')
     depends_on('glib')
     depends_on('zlib')
     depends_on('bzip2')
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 2b78dbd858..49fbd09775 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -111,12 +111,12 @@ class Boost(Package):
             description="Build multi-threaded versions of libraries")
     variant('singlethreaded', default=True,
             description="Build single-threaded versions of libraries")
-    variant('icu_support', default=False,
-            description="Include ICU support (for regex/locale libraries)")
+    variant('icu', default=False,
+            description="Build with Unicode and ICU suport")
     variant('graph', default=False,
             description="Build the Boost Graph library")
 
-    depends_on('icu', when='+icu_support')
+    depends_on('icu4c', when='+icu')
     depends_on('python', when='+python')
     depends_on('mpi', when='+mpi')
     depends_on('bzip2', when='+iostreams')
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index f8d73d651b..c8b4c7e645 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -33,7 +33,7 @@ class Harfbuzz(Package):
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
     depends_on("glib")
-    depends_on("icu")
+    depends_on("icu4c")
     depends_on("freetype")
     depends_on("cairo")
     depends_on("zlib")
diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/icu/package.py
deleted file mode 100644
index bf24067879..0000000000
--- a/var/spack/repos/builtin/packages/icu/package.py
+++ /dev/null
@@ -1,48 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Icu(Package):
-    """The International Components for Unicode (ICU) package is a
-       mature, widely used set of C/C++ libraries providing Unicode and
-       Globalization support for software applications. ICU is widely
-       portable and gives applications the same results on all
-       platforms."""
-
-    homepage = "http://site.icu-project.org/"
-    url      = "http://download.icu-project.org/files/icu4c/54.1/icu4c-54_1-src.tgz"
-
-    version('54.1', 'e844caed8f2ca24c088505b0d6271bc0')
-
-    def url_for_version(self, version):
-        return "http://download.icu-project.org/files/icu4c/%s/icu4c-%s-src.tgz" % (
-            version, str(version).replace('.', '_'))
-
-    def install(self, spec, prefix):
-        with working_dir("source"):
-            configure("--prefix=%s" % prefix)
-            make()
-            make("install")
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index 615c59f92d..848ebfdeac 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -27,8 +27,9 @@ from spack import *
 
 class Icu4c(Package):
     """ICU is a mature, widely used set of C/C++ and Java libraries providing
-       Unicode and Globalization support for software applications.
-    """
+    Unicode and Globalization support for software applications. ICU4C is the
+    C/C++ interface."""
+
     homepage = "http://site.icu-project.org/"
     url      = "http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz"
 
@@ -40,10 +41,9 @@ class Icu4c(Package):
             base_url, version, version.underscored)
 
     def install(self, spec, prefix):
-        cd('source')
-
-        configure('--prefix={0}'.format(prefix))
+        with working_dir('source'):
+            configure('--prefix={0}'.format(prefix))
 
-        make()
-        make('check')
-        make('install')
+            make()
+            make('check')
+            make('install')
diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
index 22774dedec..cc57caf8cd 100644
--- a/var/spack/repos/builtin/packages/r-stringi/package.py
+++ b/var/spack/repos/builtin/packages/r-stringi/package.py
@@ -44,7 +44,7 @@ class RStringi(Package):
 
     extends('R')
 
-    depends_on('icu')
+    depends_on('icu4c')
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
-- 
cgit v1.2.3-70-g09d2


From ec91152a36eaa48527a9adf308a83d93aac34b89 Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Thu, 22 Sep 2016 15:34:58 -0500
Subject: a few package used in HEP including ROOT6

---
 .../builtin/packages/clhep/darwin/CLHEP.patch      |  11 ++
 var/spack/repos/builtin/packages/clhep/package.py  |  81 +++++++++++++++
 var/spack/repos/builtin/packages/geant4/package.py |  85 +++++++++++++++
 var/spack/repos/builtin/packages/gmake/package.py  |  42 ++++++++
 var/spack/repos/builtin/packages/hepmc/package.py  |  55 ++++++++++
 var/spack/repos/builtin/packages/heppdt/package.py |  48 +++++++++
 .../repos/builtin/packages/root/math_uint.patch    | 115 +++++++++++++++++++++
 var/spack/repos/builtin/packages/root/package.py   |  89 ++++++++++++++++
 .../packages/root/root6-60606-mathmore.patch       |  29 ++++++
 var/spack/repos/builtin/packages/xrootd/package.py |  52 ++++++++++
 10 files changed, 607 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch
 create mode 100644 var/spack/repos/builtin/packages/clhep/package.py
 create mode 100644 var/spack/repos/builtin/packages/geant4/package.py
 create mode 100644 var/spack/repos/builtin/packages/gmake/package.py
 create mode 100644 var/spack/repos/builtin/packages/hepmc/package.py
 create mode 100644 var/spack/repos/builtin/packages/heppdt/package.py
 create mode 100644 var/spack/repos/builtin/packages/root/math_uint.patch
 create mode 100644 var/spack/repos/builtin/packages/root/package.py
 create mode 100644 var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch
 create mode 100644 var/spack/repos/builtin/packages/xrootd/package.py

diff --git a/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch b/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch
new file mode 100644
index 0000000000..ca1d96574a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clhep/darwin/CLHEP.patch
@@ -0,0 +1,11 @@
+--- CLHEP/CMakeLists.txt	2016-06-20 14:41:12.000000000 -0500
++++ CLHEP/CMakeLists.txt	2016-06-20 14:40:57.000000000 -0500
+@@ -37,7 +37,7 @@
+ # If Policy CMP0042 exists, use OLD to prefer the use of install names
+ # instead of the new @rpath default. 
+ if(POLICY CMP0042)
+-  cmake_policy(SET CMP0042 NEW)
++  cmake_policy(SET CMP0042 OLD)
+ endif()
+ 
+ set(CMAKE_MODULE_PATH 
diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py
new file mode 100644
index 0000000000..02a9da9e27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clhep/package.py
@@ -0,0 +1,81 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Clhep(Package):
+    """CLHEP is a C++ Class Library for High Energy Physics. """
+    homepage = "http://proj-clhep.web.cern.ch/proj-clhep/"
+    url      = "http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.2.0.5.tgz"
+    list_url = "https://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/"
+
+    version('2.3.2.2', '567b304b0fa017e1e9fbf199f456ebe9')
+    version('2.3.1.1', '16efca7641bc118c9d217cc96fe90bf5')
+    version('2.3.1.0', 'b084934fc26a4182a08c09c292e19161')
+    version('2.3.0.0', 'a00399a2ca867f2be902c22fc71d7e2e')
+    version('2.2.0.8', '5a23ed3af785ac100a25f6cb791846af')
+    version('2.2.0.5', '1584e8ce6ebf395821aed377df315c7c')
+    version('2.2.0.4', '71d2c7c2e39d86a0262e555148de01c1')
+
+    variant('debug', default=False, description="Switch to the debug version of CLHEP.")
+    variant('cxx11', default=True, description="Compile using c++11 dialect.")
+    variant('cxx14', default=False, description="Compile using c++14 dialect.")
+
+    depends_on('cmake@2.8.12.2:', when='@2.2.0.4:2.3.0.0', type='build')
+    depends_on('cmake@3.2:', when='@2.3.0.1:', type='build')
+
+    def patch(self):
+        filter_file('SET CMP0042 OLD',
+                    'SET CMP0042 NEW',
+                    '%s/%s/CLHEP/CMakeLists.txt'
+                    % (self.stage.path, self.spec.version))
+
+    def install(self, spec, prefix):
+        # Handle debug
+        # Pull out the BUILD_TYPE so we can change it (Release is default)
+        cmake_args = [arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg]
+        build_type = 'Debug' if '+debug' in spec else 'MinSizeRel'
+        cmake_args.extend(['-DCMAKE_BUILD_TYPE=' + build_type])
+
+        if '+cxx11' in spec:
+            env['CXXFLAGS'] = self.compiler.cxx11_flag
+            cmake_args.append('-DCLHEP_BUILD_CXXSTD=' +
+                              self.compiler.cxx11_flag)
+
+        if '+cxx14' in spec:
+            env['CXXFLAGS'] = self.compiler.cxx14_flag
+            cmake_args.append('-DCLHEP_BUILD_CXXSTD=' +
+                              self.compiler.cxx14_flag)
+
+        # Note that the tar file is unusual in that there's a
+        # CLHEP directory (addtional layer)
+        cmake_args.append("../CLHEP")
+
+        # Run cmake in a build directory
+        with working_dir('build', create=True):
+            cmake(*cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
new file mode 100644
index 0000000000..239ef6d586
--- /dev/null
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -0,0 +1,85 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Geant4(Package):
+    """Geant4 is a toolkit for the simulation of the passage of particles
+    through matter. Its areas of application include high energy, nuclear
+    and accelerator physics, as well as studies in medical and space
+    science."""
+
+    homepage = "http://geant4.cern.ch/"
+    url      = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz"
+
+    version('10.02.p01', 'b81f7082a15f6a34b720b6f15c6289cfe4ddbbbdcef0dc52719f71fac95f7f1c')
+    version('10.01.p03', '4fb4175cc0dabcd517443fbdccd97439')
+
+    variant('qt', default=False, description='Enable Qt support')
+
+    depends_on('cmake@3.5:', type='build')
+
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01")
+    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03")
+    depends_on("expat")
+    depends_on("zlib")
+    depends_on("xerces-c")
+    depends_on("qt@4.8:", when="+qt")
+
+    def install(self, spec, prefix):
+        cmake_args = list(std_cmake_args)
+        cmake_args.append('-DXERCESC_ROOT_DIR:STRING=%s' %
+                          spec['xerces-c'].prefix)
+        cmake_args.append('-DGEANT4_BUILD_CXXSTD=c++14')
+
+        cmake_args += ['-DGEANT4_USE_GDML=ON',
+                       '-DGEANT4_USE_SYSTEM_EXPAT=ON',
+                       '-DGEANT4_USE_SYSTEM_ZLIB=ON',
+                       '-DGEANT4_USE_SYSTEM_CLHEP=ON']
+
+        # fixme: turn off data for now and maybe each data set should
+        # go into a separate package to cut down on disk usage between
+        # different code versions using the same data versions.
+        cmake_args.append('-DGEANT4_INSTALL_DATA=OFF')
+
+        # http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/InstallationGuide/html/ch02s03.html
+        # fixme: likely things that need addressing:
+        # -DGEANT4_USE_OPENGL_X11=ON
+
+        if '+qt' in spec:
+            cmake_args.append('-DGEANT4_USE_QT=ON')
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *cmake_args)
+            make()
+            make("install")
+
+    def url_for_version(self, version):
+        """Handle Geant4's unusual version string."""
+        return "http://geant4.cern.ch/support/source/geant4.%s.tar.gz" % version
diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py
new file mode 100644
index 0000000000..ca296350a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gmake/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Gmake(Package):
+    """GNU Make."""
+
+    homepage = "http://gnu.org/gnu/make"
+    url      = "ftp://ftp.gnu.org/gnu/make/make-4.0.tar.gz"
+
+    version('4.0', 'b5e558f981326d9ca1bfdb841640721a')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
+        with working_dir(prefix.bin):
+            symlink('make', 'gmake')
diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py
new file mode 100644
index 0000000000..ab80dcf6ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hepmc/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Hepmc(Package):
+    """The HepMC package is an object oriented, C++ event record for
+       High Energy Physics Monte Carlo generators and simulation."""
+
+    homepage = "http://hepmc.web.cern.ch/hepmc/"
+    url      = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz"
+
+    version('2.06.09', 'c47627ced4255b40e731b8666848b087')
+    version('2.06.08', 'a2e889114cafc4f60742029d69abd907')
+    version('2.06.07', '11d7035dccb0650b331f51520c6172e7')
+    version('2.06.06', '102e5503537a3ecd6ea6f466aa5bc4ae')
+    version('2.06.05', '2a4a2a945adf26474b8bdccf4f881d9c')
+
+    depends_on("cmake", type='build')
+
+    def install(self, spec, prefix):
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        options = [source_directory]
+        options.append('-Dmomentum:STRING=GEV')
+        options.append('-Dlength:STRING=MM')
+        options.extend(std_cmake_args)
+
+        with working_dir(build_directory, create=True):
+            cmake(*options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py
new file mode 100644
index 0000000000..5fb7ec86d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/heppdt/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Heppdt(Package):
+    """ The HepPID library contains translation methods for particle ID's
+    to and from various Monte Carlo generators and the PDG standard
+    numbering scheme. We realize that the generators adhere closely
+    to the standard, but there are occasional differences."""
+    homepage = "http://lcgapp.cern.ch/project/simu/HepPDT/"
+    url      = "http://lcgapp.cern.ch/project/simu/HepPDT/download/HepPDT-2.06.01.tar.gz"
+
+    version('3.04.01', 'a8e93c7603d844266b62d6f189f0ac7e')
+    version('3.04.00', '2d2cd7552d3e9539148febacc6287db2')
+    version('3.03.02', '0b85f1809bb8b0b28a46f23c718b2773')
+    version('3.03.01', 'd411f3bfdf9c4350d802241ba2629cc2')
+    version('3.03.00', 'cd84d0a0454be982dcd8c285e060a7b3')
+    version('2.06.01', '5688b4bdbd84b48ed5dd2545a3dc33c0')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/root/math_uint.patch b/var/spack/repos/builtin/packages/root/math_uint.patch
new file mode 100644
index 0000000000..ff4a38b91c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/math_uint.patch
@@ -0,0 +1,115 @@
+From 5f3faffdd869bce5e254ae70f69290e4651a061d Mon Sep 17 00:00:00 2001
+From: Lorenzo Moneta <Lorenzo.Moneta@cern.ch>
+Date: Mon, 4 Jan 2016 15:38:23 +0100
+Subject: [PATCH] Fix ROOT-7886. Use unsigned int instead of uint
+
+---
+ math/mathcore/inc/Math/Delaunay2D.h |  2 +-
+ math/mathcore/src/Delaunay2D.cxx    | 30 +++++++++++++++---------------
+ 2 files changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/math/mathcore/inc/Math/Delaunay2D.h b/math/mathcore/inc/Math/Delaunay2D.h
+index 6255e78..472bded 100644
+--- a/math/mathcore/inc/Math/Delaunay2D.h
++++ b/math/mathcore/inc/Math/Delaunay2D.h
+@@ -273,7 +273,7 @@ class Delaunay2D  {
+    double fYCellStep; //! inverse denominator to calculate X cell = fNCells / (fYNmax - fYNmin)
+    std::set<UInt_t> fCells[(fNCells+1)*(fNCells+1)]; //! grid cells with containing triangles
+ 
+-   inline unsigned int Cell(uint x, uint y) const {
++   inline unsigned int Cell(UInt_t x, UInt_t y) const {
+ 	   return x*(fNCells+1) + y;
+    }
+ 
+diff --git a/math/mathcore/src/Delaunay2D.cxx b/math/mathcore/src/Delaunay2D.cxx
+index c4d4680..9a82858 100644
+--- a/math/mathcore/src/Delaunay2D.cxx
++++ b/math/mathcore/src/Delaunay2D.cxx
+@@ -190,7 +190,7 @@ void Delaunay2D::DoFindTriangles() {
+ 
+ 				Triangle tri;
+ 
+-				auto transform = [&] (const uint i) {
++				auto transform = [&] (const unsigned int i) {
+ 					tri.x[i] = face.vertex(i)->point().x();
+ 					tri.y[i] = face.vertex(i)->point().y();
+ 					tri.idx[i] = face.vertex(i)->info();
+@@ -326,7 +326,7 @@ void Delaunay2D::DoFindTriangles() {
+ 	for(int t = 0; t < out.numberoftriangles; ++t){
+ 		Triangle tri;
+ 
+-		auto transform = [&] (const uint v) {
++		auto transform = [&] (const unsigned int v) {
+ 			//each triangle as numberofcorners vertices ( = 3)
+ 			tri.idx[v] = out.trianglelist[t*out.numberofcorners + v];
+ 
+@@ -354,14 +354,14 @@ void Delaunay2D::DoFindTriangles() {
+ 		auto bx = std::minmax({tri.x[0], tri.x[1], tri.x[2]});
+ 		auto by = std::minmax({tri.y[0], tri.y[1], tri.y[2]});
+ 
+-		uint cellXmin = CellX(bx.first);
+-		uint cellXmax = CellX(bx.second);
++		unsigned int cellXmin = CellX(bx.first);
++		unsigned int cellXmax = CellX(bx.second);
+ 
+-		uint cellYmin = CellY(by.first);
+-		uint cellYmax = CellY(by.second);
++		unsigned int cellYmin = CellY(by.first);
++		unsigned int cellYmax = CellY(by.second);
+ 
+-		for(uint i = cellXmin; i <= cellXmax; ++i)
+-			for(uint j = cellYmin; j <= cellYmax; ++j){
++		for(unsigned int i = cellXmin; i <= cellXmax; ++i)
++			for(unsigned int j = cellYmin; j <= cellYmax; ++j){
+ 				//printf("(%u,%u) = %u\n", i, j, Cell(i,j));
+ 				fCells[Cell(i,j)].insert(t);
+ 			}
+@@ -382,7 +382,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+    ///  FindAllTriangles();
+ 
+     //see comment in header for CGAL fallback section
+-    auto bayCoords = [&] (const uint t) -> std::tuple<double, double, double> {
++    auto bayCoords = [&] (const unsigned int t) -> std::tuple<double, double, double> {
+     	double la = ( (fTriangles[t].y[1] - fTriangles[t].y[2])*(xx - fTriangles[t].x[2])
+     					 + (fTriangles[t].x[2] - fTriangles[t].x[1])*(yy - fTriangles[t].y[2]) ) * fTriangles[t].invDenom;
+     	double lb = ( (fTriangles[t].y[2] - fTriangles[t].y[0])*(xx - fTriangles[t].x[2])
+@@ -401,7 +401,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+ 	if(cX < 0 || cX > fNCells || cY < 0 || cY > fNCells)
+ 		return fZout; //TODO some more fancy interpolation here
+ 
+-    for(uint t : fCells[Cell(cX, cY)]){
++    for(unsigned int t : fCells[Cell(cX, cY)]){
+     	auto coords = bayCoords(t);
+ 
+     	if(inTriangle(coords)){
+@@ -415,7 +415,7 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+ 
+     //debugging
+ 
+-    /*for(uint t = 0; t < fNdt; ++t){
++    /*for(unsigned int t = 0; t < fNdt; ++t){
+     	auto coords = bayCoords(t);
+ 
+     	if(inTriangle(coords)){
+@@ -423,17 +423,17 @@ double Delaunay2D::DoInterpolateNormalized(double xx, double yy)
+     		//brute force found a triangle -> grid not
+     		printf("Found triangle %u for (%f,%f) -> (%u,%u)\n", t, xx,yy, cX, cY);
+     		printf("Triangles in grid cell: ");
+-    		for(uint x : fCells[Cell(cX, cY)])
++    		for(unsigned int x : fCells[Cell(cX, cY)])
+     			printf("%u ", x);
+     		printf("\n");
+ 
+     		printf("Triangle %u is in cells: ", t);
+-    		for(uint i = 0; i <= fNCells; ++i)
+-    			for(uint j = 0; j <= fNCells; ++j)
++    		for(unsigned int i = 0; i <= fNCells; ++i)
++    			for(unsigned int j = 0; j <= fNCells; ++j)
+     				if(fCells[Cell(i,j)].count(t))
+     					printf("(%u,%u) ", i, j);
+     		printf("\n");
+-    		for(uint i = 0; i < 3; ++i)
++    		for(unsigned int i = 0; i < 3; ++i)
+     			printf("\tpoint %u (%u): (%f,%f) -> (%u,%u)\n", i, fTriangles[t].idx[i], fTriangles[t].x[i], fTriangles[t].y[i], CellX(fTriangles[t].x[i]), CellY(fTriangles[t].y[i]));
+ 
+     		//we found the triangle -> interpolate using the barycentric interpolation
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
new file mode 100644
index 0000000000..0f66dcebaa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -0,0 +1,89 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+import sys
+
+
+class Root(Package):
+    """ROOT is a data analysis framework."""
+    homepage = "https://root.cern.ch"
+    url      = "https://root.cern.ch/download/root_v6.07.02.source.tar.gz"
+
+    version('6.06.06', '4308449892210c8d36e36924261fea26')
+    version('6.06.04', '55a2f98dd4cea79c9c4e32407c2d6d17')
+    version('6.06.02', 'e9b8b86838f65b0a78d8d02c66c2ec55')
+
+    if sys.platform == 'darwin':
+        patch('math_uint.patch', when='@6.06.02')
+        patch('root6-60606-mathmore.patch', when='@6.06.06')
+
+    variant('graphviz', default=False, description='Enable graphviz support')
+
+    depends_on("cmake", type='build')
+    depends_on("pcre")
+    depends_on("fftw")
+    depends_on("graphviz", when="+graphviz")
+    depends_on("python")
+    depends_on("gsl")
+    depends_on("libxml2+python")
+    depends_on("jpeg")
+    if sys.platform != 'darwin':
+        depends_on("libpng")
+        depends_on("openssl")
+        depends_on("freetype")
+
+    def install(self, spec, prefix):
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+        options = [source_directory]
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+        options.append('-Dcxx14=on')
+        options.append('-Dcocoa=off')
+        options.append('-Dbonjour=off')
+        options.append('-Dx11=on')
+        options.extend(std_cmake_args)
+        if sys.platform == 'darwin':
+            darwin_options = [
+                '-Dcastor=OFF',
+                '-Drfio=OFF',
+                '-Ddcache=OFF']
+            options.extend(darwin_options)
+        with working_dir(build_directory, create=True):
+            cmake(*options)
+            make()
+            make("install")
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_env.set('ROOTSYS', self.prefix)
+        spack_env.set('ROOT_VERSION', 'v6')
+        spack_env.prepend_path('PYTHONPATH', self.prefix.lib)
+
+    def url_for_version(self, version):
+        """Handle ROOT's unusual version string."""
+        return "https://root.cern.ch/download/root_v%s.source.tar.gz" % version
diff --git a/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch b/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch
new file mode 100644
index 0000000000..d009a5af0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/root/root6-60606-mathmore.patch
@@ -0,0 +1,29 @@
+diff --git a/math/mathmore/inc/Math/QuantFuncMathMore.h b/math/mathmore/inc/Math/QuantFuncMathMore.h
+index fd6679c..03ccc03 100644
+--- a/math/mathmore/inc/Math/QuantFuncMathMore.h
++++ b/math/mathmore/inc/Math/QuantFuncMathMore.h
+@@ -25,17 +25,6 @@
+   **********************************************************************/
+ 
+ 
+-#if defined(__CINT__) && !defined(__MAKECINT__)
+-// avoid to include header file when using CINT
+-#ifndef _WIN32
+-#include "../lib/libMathMore.so"
+-#else
+-#include "../bin/libMathMore.dll"
+-#endif
+-
+-#else
+-
+-
+ #ifndef ROOT_Math_QuantFuncMathMore
+ #define ROOT_Math_QuantFuncMathMore
+ 
+@@ -190,5 +179,3 @@ namespace MathMore {
+ 
+ 
+ #endif // ROOT_Math_QuantFuncMathMore
+-
+-#endif // if defined (__CINT__) && !defined(__MAKECINT__)
+
diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
new file mode 100644
index 0000000000..db076dbc56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Xrootd(Package):
+    """The XROOTD project aims at giving high performance, scalable fault
+       tolerant access to data repositories of many kinds."""
+    homepage = "http://xrootd.org"
+    url      = "http://xrootd.org/download/v4.3.0/xrootd-4.3.0.tar.gz"
+
+    version('4.3.0', '39c2fab9f632f35e12ff607ccaf9e16c')
+
+    depends_on('cmake', type='build')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        build_directory = join_path(self.stage.path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+
+        with working_dir(build_directory, create=True):
+            cmake(source_directory, *options)
+            make()
+            make("install")
-- 
cgit v1.2.3-70-g09d2


From cb36aadaf6cfb0373e28b435cb0a4ea3ea19aac4 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 23 Sep 2016 18:01:38 -0700
Subject: Fix doc bugs, widen columns in the package list

---
 lib/spack/docs/conf.py                             | 2 +-
 var/spack/repos/builtin/packages/heppdt/package.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index 43d37f1526..ed3e5811bc 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -65,7 +65,7 @@ spack_version =  subprocess.Popen(
 
 # Set an environment variable so that colify will print output like it would to
 # a terminal.
-os.environ['COLIFY_SIZE'] = '25x80'
+os.environ['COLIFY_SIZE'] = '25x120'
 
 #
 # Generate package list using spack command
diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py
index 5fb7ec86d5..54c846ae33 100644
--- a/var/spack/repos/builtin/packages/heppdt/package.py
+++ b/var/spack/repos/builtin/packages/heppdt/package.py
@@ -27,7 +27,7 @@ from spack import *
 
 
 class Heppdt(Package):
-    """ The HepPID library contains translation methods for particle ID's
+    """The HepPID library contains translation methods for particle ID's
     to and from various Monte Carlo generators and the PDG standard
     numbering scheme. We realize that the generators adhere closely
     to the standard, but there are occasional differences."""
-- 
cgit v1.2.3-70-g09d2


From 1e10309ff707a29fe91993d9a9b408182ffa77f1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 26 Sep 2016 19:37:23 +0200
Subject: some fixes to blas/lapack usage in packages (#1852)

* atlas: fix unit test

* openblas: remove symlinks; use lapack_libs.ld_flags in the test

* mkl: fix openmp variant of blas/lapack libs

* intel-parallel-studio: fix openmp variant of blas/lapack libs

* netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl)

* arpack-ng: fix blas/lapack for multilib case (e.g. mkl)

* petsc: explicitly specify blas/lapack

* minor

* cantera: fix blas/lapack usage

* ipopt: fix blas/lapack usage

* netlib-lapack: fix external blas usage

* mfem: fix lapack/blas usage

* superlu-mt: fix blas usage

* flake8 fixes
---
 .../repos/builtin/packages/arpack-ng/package.py    |  4 ++--
 var/spack/repos/builtin/packages/atlas/package.py  |  2 +-
 .../repos/builtin/packages/cantera/package.py      |  3 ++-
 .../packages/intel-parallel-studio/package.py      |  5 ++++-
 var/spack/repos/builtin/packages/ipopt/package.py  |  5 ++---
 var/spack/repos/builtin/packages/mfem/package.py   |  3 +--
 var/spack/repos/builtin/packages/mkl/package.py    |  5 +++--
 .../builtin/packages/netlib-lapack/package.py      |  5 +----
 .../builtin/packages/netlib-scalapack/package.py   |  4 ++--
 .../repos/builtin/packages/openblas/package.py     | 24 ++--------------------
 var/spack/repos/builtin/packages/petsc/package.py  | 10 +++++++--
 .../repos/builtin/packages/superlu-mt/package.py   |  2 +-
 12 files changed, 29 insertions(+), 43 deletions(-)

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 7f92bc1950..87ab2bbaac 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -88,8 +88,8 @@ class ArpackNg(Package):
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
         # Make sure we use Spack's blas/lapack:
-        lapack_libs = spec['lapack'].lapack_libs.joined()
-        blas_libs = spec['blas'].blas_libs.joined()
+        lapack_libs = spec['lapack'].lapack_libs.joined(';')
+        blas_libs = spec['blas'].blas_libs.joined(';')
 
         options.extend([
             '-DLAPACK_FOUND=true',
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index e1914aac98..b31e365336 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -142,7 +142,7 @@ class Atlas(Package):
                                  'test_cblas_dgemm.output')
 
         include_flags = ["-I%s" % self.spec.prefix.include]
-        link_flags = self.lapack_libs.ld_flags
+        link_flags = self.lapack_libs.ld_flags.split()
 
         output = compile_c_and_execute(source_file, include_flags, link_flags)
         compare_output_file(output, blessed_file)
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 9c9c035325..9a9bc5bdbd 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -85,8 +85,9 @@ class Cantera(Package):
 
         # BLAS/LAPACK support
         if '+lapack' in spec:
+            lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
             options.extend([
-                'blas_lapack_libs=lapack,blas',
+                'blas_lapack_libs={0}'.format(','.join(lapack_blas.names)),
                 'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib)
             ])
 
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 74bdba455f..5547bae71c 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -64,7 +64,10 @@ class IntelParallelStudio(IntelInstaller):
         shared = True if '+shared' in self.spec else False
         suffix = dso_suffix if '+shared' in self.spec else 'a'
         mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
-        mkl_threading = ['libmkl_intel_thread'] if '+openmp' in self.spec else ['libmkl_sequential']  # NOQA: ignore=E501
+        mkl_threading = ['libmkl_sequential']
+        if '+openmp' in self.spec:
+            mkl_threading = ['libmkl_intel_thread', 'libiomp5'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
         mkl_libs = find_libraries(
             mkl_integer + ['libmkl_core'] + mkl_threading,
             root=join_path(self.prefix.lib, 'intel64'),
diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py
index d5981e9975..bd1e5f36ef 100644
--- a/var/spack/repos/builtin/packages/ipopt/package.py
+++ b/var/spack/repos/builtin/packages/ipopt/package.py
@@ -53,9 +53,8 @@ class Ipopt(Package):
         mumps_flags = "-ldmumps -lmumps_common -lpord -lmpiseq"
         mumps_libcmd = "-L%s " % mumps_dir.lib + mumps_flags
 
-        # By convention, spack links blas & lapack libs to libblas & liblapack
-        blas_lib = "-L%s" % blas_dir.lib + " -lblas"
-        lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
+        blas_lib = spec['blas'].blas_libs.ld_flags
+        lapack_lib = spec['lapack'].lapack_libs.ld_flags
 
         configure_args = [
             "--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index fd91f705eb..cbf9059f65 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -89,8 +89,7 @@ class Mfem(Package):
         options = ['PREFIX=%s' % prefix]
 
         if '+lapack' in spec:
-            lapack_lib = '-L{0} -llapack -L{1} -lblas'.format(
-                spec['lapack'].prefix.lib, spec['blas'].prefix.lib)
+            lapack_lib = (spec['lapack'].lapack_libs + spec['blas'].blas_libs).ld_flags  # NOQA: ignore=E501
             options.extend([
                 'MFEM_USE_LAPACK=YES',
                 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index a7353d57c4..b674876393 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -39,8 +39,9 @@ class Mkl(IntelInstaller):
         suffix = dso_suffix if '+shared' in self.spec else 'a'
         mkl_integer = ['libmkl_intel_ilp64'] if '+ilp64' in self.spec else ['libmkl_intel_lp64']  # NOQA: ignore=E501
         mkl_threading = ['libmkl_sequential']
-        if '+openmp' in spec:
-            mkl_threading = ['libmkl_intel_thread'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        if '+openmp' in self.spec:
+            mkl_threading = ['libmkl_intel_thread', 'libiomp5'] if '%intel' in self.spec else ['libmkl_gnu_thread']  # NOQA: ignore=E501
+        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
         mkl_libs = find_libraries(
             mkl_integer + ['libmkl_core'] + mkl_threading,
             root=join_path(self.prefix.lib, 'intel64'),
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index b73fe850d7..874473ba9c 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -91,12 +91,9 @@ class NetlibLapack(Package):
             cmake_args.extend(['-DCBLAS=ON'])  # always build CBLAS
 
         if '+external-blas' in spec:
-            # TODO : mechanism to specify the library should be more general,
-            # TODO : but this allows to have an hook to an external blas
             cmake_args.extend([
                 '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
-                '-DBLAS_LIBRARIES:PATH=%s' % join_path(
-                    spec['blas'].prefix.lib, 'libblas.a')
+                '-DBLAS_LIBRARIES:PATH=%s' % spec['blas'].blas_libs.joined(';')
             ])
 
         cmake_args.extend(std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index fe9f1a3023..578d2d8988 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -79,8 +79,8 @@ class NetlibScalapack(Package):
         options.extend([
             '-DLAPACK_FOUND=true',
             '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
-            '-DLAPACK_LIBRARIES=%s' % (lapack.joined()),
-            '-DBLAS_LIBRARIES=%s' % (blas.joined())
+            '-DLAPACK_LIBRARIES=%s' % (lapack.joined(';')),
+            '-DBLAS_LIBRARIES=%s' % (blas.joined(';'))
         ])
 
         if '+fpic' in spec:
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 89c35fb991..1f6dd0e013 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -111,24 +111,6 @@ class Openblas(Package):
         # no quotes around prefix (spack doesn't use a shell)
         make('install', "PREFIX=%s" % prefix, *make_defs)
 
-        # TODO : the links below are mainly there because client
-        # TODO : packages are wrongly written. Check if they can be removed
-
-        # Blas virtual package should provide blas.a and libblas.a
-        with working_dir(prefix.lib):
-            symlink('libopenblas.a', 'blas.a')
-            symlink('libopenblas.a', 'libblas.a')
-            if '+shared' in spec:
-                symlink('libopenblas.%s' % dso_suffix,
-                        'libblas.%s' % dso_suffix)
-
-        # Lapack virtual package should provide liblapack.a
-        with working_dir(prefix.lib):
-            symlink('libopenblas.a', 'liblapack.a')
-            if '+shared' in spec:
-                symlink('libopenblas.%s' % dso_suffix,
-                        'liblapack.%s' % dso_suffix)
-
         # Openblas may pass its own test but still fail to compile Lapack
         # symbols. To make sure we get working Blas and Lapack, do a small
         # test.
@@ -141,10 +123,8 @@ class Openblas(Package):
                                  'test_cblas_dgemm.output')
 
         include_flags = ["-I%s" % join_path(spec.prefix, "include")]
-        link_flags = ["-L%s" % join_path(spec.prefix, "lib"),
-                      "-llapack",
-                      "-lblas",
-                      "-lpthread"]
+        link_flags = self.lapack_libs.ld_flags.split()
+        link_flags.extend(["-lpthread"])
         if '+openmp' in spec:
             link_flags.extend([self.compiler.openmp_flag])
 
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 1f1b9adffd..1ad1eb6752 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -129,9 +129,15 @@ class Petsc(Package):
             '--with-scalar-type=%s' % (
                 'complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
-            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
-            '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0')
         ])
+        # Make sure we use exactly the same Blas/Lapack libraries
+        # across the DAG. To that end list them explicitly
+        lapack_blas = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options.extend([
+            '--with-blas-lapack-lib=%s' % lapack_blas.joined()
+        ])
+
         # Activates library support if needed
         for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
                         'mumps', 'scalapack'):
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
index e849273e08..ea94c2d4c5 100644
--- a/var/spack/repos/builtin/packages/superlu-mt/package.py
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -86,7 +86,7 @@ class SuperluMt(Package):
         if '+blas' in spec:
             config.extend([
                 'BLASDEF    = -DUSE_VENDOR_BLAS',
-                'BLASLIB    = -L{0} -lblas'.format(spec['blas'].prefix.lib)
+                'BLASLIB    = {0}'.format(spec['blas'].blas_libs.ld_flags)
             ])
         else:
             config.append('BLASLIB    = ../lib/libblas$(PLAT).a')
-- 
cgit v1.2.3-70-g09d2


From 3282eaea8d58af201a0fb734ae545674ef4dec71 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 26 Sep 2016 13:37:40 -0400
Subject: Update OpenSSL (#1853)

---
 var/spack/repos/builtin/packages/openssl/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index e5dce49918..12b5ed9c52 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -36,6 +36,7 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
     url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz"
 
+    version('1.0.2j', '96322138f0b69e61b7212bc53d5e912b')
     version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
     version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
-- 
cgit v1.2.3-70-g09d2


From 88af9f783d956ecc05f494db8539c66f66ebfb26 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 26 Sep 2016 13:38:02 -0400
Subject: Make PETSc build on Darwin (#1835)

Don't set cpp when building on Darwin.
---
 var/spack/repos/builtin/packages/petsc/package.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 1ad1eb6752..7ee2d29f4d 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -22,7 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
 import os
+import sys
 from spack import *
 
 
@@ -90,8 +92,6 @@ class Petsc(Package):
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
             compiler_opts = [
-                '--with-cpp=cpp',
-                '--with-cxxcpp=cpp',
                 '--with-cc=%s' % os.environ['CC'],
                 '--with-cxx=%s' % (os.environ['CXX']
                                    if self.compiler.cxx is not None else '0'),
@@ -113,11 +113,14 @@ class Petsc(Package):
                 raise RuntimeError('\n'.join(errors))
         else:
             compiler_opts = [
-                '--with-cpp=cpp',
-                '--with-cxxcpp=cpp',
                 '--with-mpi=1',
                 '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
             ]
+        if sys.platform != "darwin":
+            compiler_opts.extend([
+                '--with-cpp=cpp',
+                '--with-cxxcpp=cpp',
+            ])
         return compiler_opts
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From 00b3aa77aec2490a4967bd0a080373316fbb7061 Mon Sep 17 00:00:00 2001
From: Michael Kuhn <suraia@ikkoku.de>
Date: Tue, 27 Sep 2016 16:56:04 +0200
Subject: Update cdo to 1.7.2 (#1858)

---
 var/spack/repos/builtin/packages/cdo/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index a2f04e5b35..0a5ee60f7c 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -30,9 +30,9 @@ class Cdo(Package):
     Climate and NWP model Data. """
 
     homepage = "https://code.zmaw.de/projects/cdo"
-    url      = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz"
 
-    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2')
+    version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
+    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2', url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
 
     variant('mpi', default=True)
 
-- 
cgit v1.2.3-70-g09d2


From 9b575dd976f066264cd7803c5299046101f6ebd4 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 27 Sep 2016 09:56:24 -0500
Subject: Various updates to scipy and numpy (#1856)

---
 var/spack/repos/builtin/packages/py-numpy/package.py |  6 +++++-
 var/spack/repos/builtin/packages/py-scipy/package.py | 12 +++++++++---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index f800b5e834..0d68a892f2 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -32,9 +32,12 @@ class PyNumpy(Package):
     sophisticated (broadcasting) functions, tools for integrating C/C++ and
     Fortran code, and useful linear algebra, Fourier transform, and random
     number capabilities"""
+
     homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
+    version('1.11.1', '2f44a895a8104ffac140c3a70edbd450',
+            url="https://pypi.python.org/packages/e0/4c/515d7c4ac424ff38cc919f7099bf293dd064ba9a600e1e3835b3edefdb18/numpy-1.11.1.tar.gz")
     version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
     version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
@@ -44,6 +47,7 @@ class PyNumpy(Package):
     variant('lapack', default=True)
 
     extends('python')
+    depends_on('python@2.6:2.8,3.2:')
     depends_on('py-nose', type='build')
     depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
@@ -79,4 +83,4 @@ class PyNumpy(Package):
                 f.write('library_dirs=%s\n' % ':'.join(library_dirs))
                 f.write('rpath=%s\n' % ':'.join(library_dirs))
 
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        setup_py('install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 68b2cb13e0..abb843f8ee 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -26,19 +26,25 @@ from spack import *
 
 
 class PyScipy(Package):
-    """Scientific Library for Python."""
+    """SciPy (pronounced "Sigh Pie") is a Scientific Library for Python.
+    It provides many user-friendly and efficient numerical routines such
+    as routines for numerical integration and optimization."""
+
     homepage = "http://www.scipy.org/"
     url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
+    version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327',
+            url="https://pypi.python.org/packages/22/41/b1538a75309ae4913cdbbdc8d1cc54cae6d37981d2759532c1aa37a41121/scipy-0.18.1.tar.gz")
     version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     extends('python')
+    depends_on('python@2.6:2.8,3.2:')
     depends_on('py-nose', type='build')
     # Known not to work with 2.23, 2.25
     depends_on('binutils@2.26:', type='build')
-    depends_on('py-numpy+blas+lapack', type=nolink)
+    depends_on('py-numpy@1.7.1:+blas+lapack', type=nolink)
 
     def install(self, spec, prefix):
         if 'atlas' in spec:
@@ -50,4 +56,4 @@ class PyScipy(Package):
             env['BLAS'] = spec['blas'].blas_libs.joined()
             env['LAPACK'] = spec['lapack'].lapack_libs.joined()
 
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        setup_py('install', '--prefix={0}'.format(prefix))
-- 
cgit v1.2.3-70-g09d2


From cd960caf8dfb5cc80b8dae9493e3a078e45c7713 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 27 Sep 2016 08:52:02 -0400
Subject: Clean up Exceptions in `spec.py`

---
 lib/spack/spack/spec.py          | 63 ++--------------------------------------
 lib/spack/spack/test/spec_dag.py |  6 ++--
 2 files changed, 6 insertions(+), 63 deletions(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index c92594da72..99fc2d3ea4 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -1569,7 +1569,7 @@ class Spec(object):
         # actually deps of this package.  Raise an error.
         extra = set(spec_deps.keys()).difference(visited)
         if extra:
-            raise InvalidDependencyException(
+            raise InvalidDependencyError(
                 self.name + " does not depend on " + comma_or(extra))
 
         # Mark the spec as normal once done.
@@ -2667,17 +2667,11 @@ def parse_anonymous_spec(spec_like, pkg_name):
 
 
 class SpecError(spack.error.SpackError):
-
     """Superclass for all errors that occur while constructing specs."""
 
-    def __init__(self, message):
-        super(SpecError, self).__init__(message)
-
 
 class SpecParseError(SpecError):
-
     """Wrapper for ParseError for when we're parsing specs."""
-
     def __init__(self, parse_error):
         super(SpecParseError, self).__init__(parse_error.message)
         self.string = parse_error.string
@@ -2685,79 +2679,49 @@ class SpecParseError(SpecError):
 
 
 class DuplicateDependencyError(SpecError):
-
     """Raised when the same dependency occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateDependencyError, self).__init__(message)
-
 
 class DuplicateVariantError(SpecError):
-
     """Raised when the same variant occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateVariantError, self).__init__(message)
-
 
 class DuplicateCompilerSpecError(SpecError):
-
     """Raised when the same compiler occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateCompilerSpecError, self).__init__(message)
-
 
 class UnsupportedCompilerError(SpecError):
-
     """Raised when the user asks for a compiler spack doesn't know about."""
-
     def __init__(self, compiler_name):
         super(UnsupportedCompilerError, self).__init__(
             "The '%s' compiler is not yet supported." % compiler_name)
 
 
 class UnknownVariantError(SpecError):
-
     """Raised when the same variant occurs in a spec twice."""
-
     def __init__(self, pkg, variant):
         super(UnknownVariantError, self).__init__(
             "Package %s has no variant %s!" % (pkg, variant))
 
 
 class DuplicateArchitectureError(SpecError):
-
     """Raised when the same architecture occurs in a spec twice."""
 
-    def __init__(self, message):
-        super(DuplicateArchitectureError, self).__init__(message)
-
 
 class InconsistentSpecError(SpecError):
-
     """Raised when two nodes in the same spec DAG have inconsistent
        constraints."""
 
-    def __init__(self, message):
-        super(InconsistentSpecError, self).__init__(message)
-
-
-class InvalidDependencyException(SpecError):
 
+class InvalidDependencyError(SpecError):
     """Raised when a dependency in a spec is not actually a dependency
        of the package."""
 
-    def __init__(self, message):
-        super(InvalidDependencyException, self).__init__(message)
-
 
 class NoProviderError(SpecError):
-
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
-
     def __init__(self, vpkg):
         super(NoProviderError, self).__init__(
             "No providers found for virtual package: '%s'" % vpkg)
@@ -2765,11 +2729,9 @@ class NoProviderError(SpecError):
 
 
 class MultipleProviderError(SpecError):
-
     """Raised when there is no package that provides a particular
        virtual dependency.
     """
-
     def __init__(self, vpkg, providers):
         """Takes the name of the vpkg"""
         super(MultipleProviderError, self).__init__(
@@ -2780,10 +2742,8 @@ class MultipleProviderError(SpecError):
 
 
 class UnsatisfiableSpecError(SpecError):
-
     """Raised when a spec conflicts with package constraints.
        Provide the requirement that was violated when raising."""
-
     def __init__(self, provided, required, constraint_type):
         super(UnsatisfiableSpecError, self).__init__(
             "%s does not satisfy %s" % (provided, required))
@@ -2793,89 +2753,72 @@ class UnsatisfiableSpecError(SpecError):
 
 
 class UnsatisfiableSpecNameError(UnsatisfiableSpecError):
-
     """Raised when two specs aren't even for the same package."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableSpecNameError, self).__init__(
             provided, required, "name")
 
 
 class UnsatisfiableVersionSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec version conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableVersionSpecError, self).__init__(
             provided, required, "version")
 
 
 class UnsatisfiableCompilerSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec comiler conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerSpecError, self).__init__(
             provided, required, "compiler")
 
 
 class UnsatisfiableVariantSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec variant conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableVariantSpecError, self).__init__(
             provided, required, "variant")
 
 
 class UnsatisfiableCompilerFlagSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec variant conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableCompilerFlagSpecError, self).__init__(
             provided, required, "compiler_flags")
 
 
 class UnsatisfiableArchitectureSpecError(UnsatisfiableSpecError):
-
     """Raised when a spec architecture conflicts with package constraints."""
-
     def __init__(self, provided, required):
         super(UnsatisfiableArchitectureSpecError, self).__init__(
             provided, required, "architecture")
 
 
 class UnsatisfiableProviderSpecError(UnsatisfiableSpecError):
-
     """Raised when a provider is supplied but constraints don't match
        a vpkg requirement"""
-
     def __init__(self, provided, required):
         super(UnsatisfiableProviderSpecError, self).__init__(
             provided, required, "provider")
 
+
 # TODO: get rid of this and be more specific about particular incompatible
 # dep constraints
 
 
 class UnsatisfiableDependencySpecError(UnsatisfiableSpecError):
-
     """Raised when some dependency of constrained specs are incompatible"""
-
     def __init__(self, provided, required):
         super(UnsatisfiableDependencySpecError, self).__init__(
             provided, required, "dependency")
 
 
 class SpackYAMLError(spack.error.SpackError):
-
     def __init__(self, msg, yaml_error):
         super(SpackYAMLError, self).__init__(msg, str(yaml_error))
 
 
 class AmbiguousHashError(SpecError):
-
     def __init__(self, msg, *specs):
         super(AmbiguousHashError, self).__init__(msg)
         for spec in specs:
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 5c2731041c..40cdb02966 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -241,15 +241,15 @@ class SpecDagTest(MockPackagesTest):
 
     def test_invalid_dep(self):
         spec = Spec('libelf ^mpich')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
         spec = Spec('libelf ^libdwarf')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
         spec = Spec('mpich ^dyninst ^libelf')
-        self.assertRaises(spack.spec.InvalidDependencyException,
+        self.assertRaises(spack.spec.InvalidDependencyError,
                           spec.normalize)
 
     def test_equal(self):
-- 
cgit v1.2.3-70-g09d2


From 43ca805248deb8fe2f87c0009ab44cc30458e39a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 27 Sep 2016 09:28:22 -0400
Subject: Factor out canonical_deptype function, cleanup spec.py

---
 lib/spack/spack/spec.py             | 87 +++++++++++++++++++++++++++++++------
 lib/spack/spack/test/spec_syntax.py | 54 +++++++++++------------
 2 files changed, 100 insertions(+), 41 deletions(-)

diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 99fc2d3ea4..108e771748 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -123,6 +123,39 @@ from spack.util.spack_yaml import syaml_dict
 from spack.version import *
 from spack.provider_index import ProviderIndex
 
+__all__ = [
+    'Spec',
+    'alldeps',
+    'nolink',
+    'nobuild',
+    'canonical_deptype',
+    'validate_deptype',
+    'parse',
+    'parse_anonymous_spec',
+    'SpecError',
+    'SpecParseError',
+    'DuplicateDependencyError',
+    'DuplicateVariantError',
+    'DuplicateCompilerSpecError',
+    'UnsupportedCompilerError',
+    'UnknownVariantError',
+    'DuplicateArchitectureError',
+    'InconsistentSpecError',
+    'InvalidDependencyError',
+    'InvalidDependencyTypeError',
+    'NoProviderError',
+    'MultipleProviderError',
+    'UnsatisfiableSpecError',
+    'UnsatisfiableSpecNameError',
+    'UnsatisfiableVersionSpecError',
+    'UnsatisfiableCompilerSpecError',
+    'UnsatisfiableVariantSpecError',
+    'UnsatisfiableCompilerFlagSpecError',
+    'UnsatisfiableArchitectureSpecError',
+    'UnsatisfiableProviderSpecError',
+    'UnsatisfiableDependencySpecError',
+    'SpackYAMLError',
+    'AmbiguousHashError']
 
 # Valid pattern for an identifier in Spack
 identifier_re = r'\w[\w-]*'
@@ -156,12 +189,45 @@ _any_version = VersionList([':'])
 
 # Special types of dependencies.
 alldeps = ('build', 'link', 'run')
-nolink = ('build', 'run')
+nolink  = ('build', 'run')
+nobuild = ('link', 'run')
+norun   = ('link', 'build')
 special_types = {
     'alldeps': alldeps,
     'nolink': nolink,
+    'nobuild': nobuild,
+    'norun': norun,
 }
 
+legal_deps = tuple(special_types) + alldeps
+
+
+def validate_deptype(deptype):
+    if isinstance(deptype, str):
+        if deptype not in legal_deps:
+            raise InvalidDependencyTypeError(
+                "Invalid dependency type: %s" % deptype)
+
+    elif isinstance(deptype, (list, tuple)):
+        for t in deptype:
+            validate_deptype(t)
+
+    elif deptype is None:
+        raise InvalidDependencyTypeError("deptype cannot be None!")
+
+
+def canonical_deptype(deptype):
+    if deptype is None:
+        return alldeps
+
+    elif isinstance(deptype, str):
+        return special_types.get(deptype, (deptype,))
+
+    elif isinstance(deptype, (tuple, list)):
+        return (sum((canonical_deptype(d) for d in deptype), ()))
+
+    return deptype
+
 
 def colorize_spec(spec):
     """Returns a spec colorized according to the colors specified in
@@ -542,17 +608,8 @@ class Spec(object):
         raise InvalidDependencyException(
             self.name + " does not depend on " + comma_or(name))
 
-    def _deptype_norm(self, deptype):
-        if deptype is None:
-            return alldeps
-        # Force deptype to be a set object so that we can do set intersections.
-        if isinstance(deptype, str):
-            # Support special deptypes.
-            return special_types.get(deptype, (deptype,))
-        return deptype
-
     def _find_deps(self, where, deptype):
-        deptype = self._deptype_norm(deptype)
+        deptype = canonical_deptype(deptype)
 
         return [dep.spec
                 for dep in where.values()
@@ -565,7 +622,7 @@ class Spec(object):
         return self._find_deps(self._dependents, deptype)
 
     def _find_deps_dict(self, where, deptype):
-        deptype = self._deptype_norm(deptype)
+        deptype = canonical_deptype(deptype)
 
         return dict((dep.spec.name, dep)
                     for dep in where.values()
@@ -2718,6 +2775,10 @@ class InvalidDependencyError(SpecError):
        of the package."""
 
 
+class InvalidDependencyTypeError(SpecError):
+    """Raised when a dependency type is not a legal Spack dep type."""
+
+
 class NoProviderError(SpecError):
     """Raised when there is no package that provides a particular
        virtual dependency.
@@ -2804,8 +2865,6 @@ class UnsatisfiableProviderSpecError(UnsatisfiableSpecError):
 
 # TODO: get rid of this and be more specific about particular incompatible
 # dep constraints
-
-
 class UnsatisfiableDependencySpecError(UnsatisfiableSpecError):
     """Raised when some dependency of constrained specs are incompatible"""
     def __init__(self, provided, required):
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 3079288c77..d4eb9e057f 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -24,34 +24,34 @@
 ##############################################################################
 import unittest
 
-import spack.spec
+import spack.spec as sp
 from spack.parse import Token
 from spack.spec import *
 
 # Sample output for a complex lexing.
-complex_lex = [Token(ID, 'mvapich_foo'),
-               Token(DEP),
-               Token(ID, '_openmpi'),
-               Token(AT),
-               Token(ID, '1.2'),
-               Token(COLON),
-               Token(ID, '1.4'),
-               Token(COMMA),
-               Token(ID, '1.6'),
-               Token(PCT),
-               Token(ID, 'intel'),
-               Token(AT),
-               Token(ID, '12.1'),
-               Token(COLON),
-               Token(ID, '12.6'),
-               Token(ON),
-               Token(ID, 'debug'),
-               Token(OFF),
-               Token(ID, 'qt_4'),
-               Token(DEP),
-               Token(ID, 'stackwalker'),
-               Token(AT),
-               Token(ID, '8.1_1e')]
+complex_lex = [Token(sp.ID, 'mvapich_foo'),
+               Token(sp.DEP),
+               Token(sp.ID, '_openmpi'),
+               Token(sp.AT),
+               Token(sp.ID, '1.2'),
+               Token(sp.COLON),
+               Token(sp.ID, '1.4'),
+               Token(sp.COMMA),
+               Token(sp.ID, '1.6'),
+               Token(sp.PCT),
+               Token(sp.ID, 'intel'),
+               Token(sp.AT),
+               Token(sp.ID, '12.1'),
+               Token(sp.COLON),
+               Token(sp.ID, '12.6'),
+               Token(sp.ON),
+               Token(sp.ID, 'debug'),
+               Token(sp.OFF),
+               Token(sp.ID, 'qt_4'),
+               Token(sp.DEP),
+               Token(sp.ID, 'stackwalker'),
+               Token(sp.AT),
+               Token(sp.ID, '8.1_1e')]
 
 
 class SpecSyntaxTest(unittest.TestCase):
@@ -74,16 +74,16 @@ class SpecSyntaxTest(unittest.TestCase):
         """
         if spec is None:
             spec = expected
-        output = spack.spec.parse(spec)
+        output = sp.parse(spec)
 
         parsed = (" ".join(str(spec) for spec in output))
         self.assertEqual(expected, parsed)
 
     def check_lex(self, tokens, spec):
         """Check that the provided spec parses to the provided token list."""
-        lex_output = SpecLexer().lex(spec)
+        lex_output = sp.SpecLexer().lex(spec)
         for tok, spec_tok in zip(tokens, lex_output):
-            if tok.type == ID:
+            if tok.type == sp.ID:
                 self.assertEqual(tok, spec_tok)
             else:
                 # Only check the type for non-identifiers.
-- 
cgit v1.2.3-70-g09d2


From 0d3d74e5c2f0ad76c818449f21f91d6c9ed4e74a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 27 Sep 2016 10:22:46 -0400
Subject: Improvements to the Spack graph command.

- Distinguish between static (package) and dynamic (spec) graphs.

  - static graphs ignore conditions and multiple instances (hashes) and
    plot raw dependencies among packages.

  - dynamic graphs include information from particular specs (instances of
    packages) and can have multiple instances with hashes.

- Allow graphing all packages in the install DB.

  - useful for debugging.
---
 lib/spack/spack/cmd/graph.py | 40 ++++++++++++++++++++---
 lib/spack/spack/graph.py     | 78 ++++++++++++++++++++++++++++++--------------
 lib/spack/spack/package.py   | 14 ++++++++
 3 files changed, 103 insertions(+), 29 deletions(-)

diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 8faabfbb7b..6de1ed974b 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -24,8 +24,11 @@
 ##############################################################################
 import argparse
 
+import llnl.util.tty as tty
+
 import spack
 import spack.cmd
+from spack.spec import *
 from spack.graph import *
 
 description = "Generate graphs of package dependency relationships."
@@ -43,8 +46,21 @@ def setup_parser(subparser):
         help="Generate graph in dot format and print to stdout.")
 
     subparser.add_argument(
-        '--concretize', action='store_true',
-        help="Concretize specs before graphing.")
+        '--normalize', action='store_true',
+        help="Skip concretization; only print normalized spec.")
+
+    subparser.add_argument(
+        '-s', '--static', action='store_true',
+        help="Use static information from packages, not dynamic spec info.")
+
+    subparser.add_argument(
+        '-i', '--installed', action='store_true',
+        help="Graph all installed specs in dot format (implies --dot).")
+
+    subparser.add_argument(
+        '-t', '--deptype', action='store',
+        help="Comma-separated list of deptypes to traverse. default=%s."
+        % ','.join(alldeps))
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER,
@@ -52,15 +68,29 @@ def setup_parser(subparser):
 
 
 def graph(parser, args):
-    specs = spack.cmd.parse_specs(
-        args.specs, normalize=True, concretize=args.concretize)
+    concretize = not args.normalize
+    if args.installed:
+        if args.specs:
+            tty.die("Can't specify specs with --installed")
+        args.dot = True
+        specs = spack.installed_db.query()
+
+    else:
+        specs = spack.cmd.parse_specs(
+            args.specs, normalize=True, concretize=concretize)
 
     if not specs:
         setup_parser.parser.print_help()
         return 1
 
+    deptype = alldeps
+    if args.deptype:
+        deptype = tuple(args.deptype.split(','))
+        validate_deptype(deptype)
+        deptype = canonical_deptype(deptype)
+
     if args.dot:  # Dot graph only if asked for.
-        graph_dot(*specs)
+        graph_dot(specs, static=args.static, deptype=deptype)
 
     elif specs:  # ascii is default: user doesn't need to provide it explicitly
         graph_ascii(specs[0], debug=spack.debug)
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index b875e9da99..330e08cc71 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -67,8 +67,7 @@ from heapq import *
 from llnl.util.lang import *
 from llnl.util.tty.color import *
 
-import spack
-from spack.spec import Spec
+from spack.spec import *
 
 __all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
 
@@ -501,7 +500,7 @@ def graph_ascii(spec, **kwargs):
     graph.write(spec, color=color, out=out)
 
 
-def graph_dot(*specs, **kwargs):
+def graph_dot(specs, deptype=None, static=False, out=None):
     """Generate a graph in dot format of all provided specs.
 
     Print out a dot formatted graph of all the dependencies between
@@ -510,42 +509,73 @@ def graph_dot(*specs, **kwargs):
         spack graph --dot qt | dot -Tpdf > spack-graph.pdf
 
     """
-    out = kwargs.pop('out', sys.stdout)
-    check_kwargs(kwargs, graph_dot)
+    if out is None:
+        out = sys.stdout
+
+    if deptype is None:
+        deptype = alldeps
 
     out.write('digraph G {\n')
-    out.write('  label = "Spack Dependencies"\n')
     out.write('  labelloc = "b"\n')
     out.write('  rankdir = "LR"\n')
     out.write('  ranksep = "5"\n')
+    out.write('node[\n')
+    out.write('     fontname=Monaco,\n')
+    out.write('     penwidth=2,\n')
+    out.write('     fontsize=12,\n')
+    out.write('     margin=.1,\n')
+    out.write('     shape=box,\n')
+    out.write('     fillcolor=lightblue,\n')
+    out.write('     style="rounded,filled"]\n')
+
     out.write('\n')
 
-    def quote(string):
+    def q(string):
         return '"%s"' % string
 
     if not specs:
-        specs = [p.name for p in spack.repo.all_packages()]
-    else:
-        roots = specs
-        specs = set()
-        for spec in roots:
-            specs.update(Spec(s.name) for s in spec.normalized().traverse())
+        raise ValueError("Must provide specs ot graph_dot")
+
+    # Static graph includes anything a package COULD depend on.
+    if static:
+        names = set.union(*[s.package.possible_dependencies() for s in specs])
+        specs = [Spec(name) for name in names]
+
+    labeled = set()
 
-    deps = []
+    def label(key, label):
+        if key not in labeled:
+            out.write('  "%s" [label="%s"]\n' % (key, label))
+            labeled.add(key)
+
+    deps = set()
     for spec in specs:
-        out.write('  %-30s [label="%s"]\n' % (quote(spec.name), spec.name))
+        if static:
+            out.write('  "%s" [label="%s"]\n' % (spec.name, spec.name))
+
+            # Skip virtual specs (we'll find out about them from concrete ones.
+            if spec.virtual:
+                continue
+
+            # Add edges for each depends_on in the package.
+            for dep_name, dep in spec.package.dependencies.iteritems():
+                deps.add((spec.name, dep_name))
 
-        # Skip virtual specs (we'll find out about them from concrete ones.
-        if spec.virtual:
-            continue
+            # If the package provides something, add an edge for that.
+            for provider in set(s.name for s in spec.package.provided):
+                deps.add((provider, spec.name))
+
+        else:
+            def key_label(s):
+                return s.dag_hash(), "%s-%s" % (s.name, s.dag_hash(7))
 
-        # Add edges for each depends_on in the package.
-        for dep_name, dep in spec.package.dependencies.iteritems():
-            deps.append((spec.name, dep_name))
+            for s in spec.traverse(deptype=deptype):
+                skey, slabel = key_label(s)
+                out.write('  "%s" [label="%s"]\n' % (skey, slabel))
 
-        # If the package provides something, add an edge for that.
-        for provider in set(s.name for s in spec.package.provided):
-            deps.append((provider, spec.name))
+                for d in s.dependencies(deptype=deptype):
+                    dkey, _ = key_label(d)
+                    deps.add((skey, dkey))
 
     out.write('\n')
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index fe19e5d400..cffc795586 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -411,6 +411,20 @@ class Package(object):
         if self.is_extension:
             spack.repo.get(self.extendee_spec)._check_extendable()
 
+    def possible_dependencies(self, visited=None):
+        """Return set of possible transitive dependencies of this package."""
+        if visited is None:
+            visited = set()
+
+        visited.add(self.name)
+        for name in self.dependencies:
+            if name not in visited and not spack.spec.Spec(name).virtual:
+                pkg = spack.repo.get(name)
+                for name in pkg.possible_dependencies(visited):
+                    visited.add(name)
+
+        return visited
+
     @property
     def package_dir(self):
         """Return the directory where the package.py file lives."""
-- 
cgit v1.2.3-70-g09d2


From f082d26dddcd63af21a6f72cacba54c643cf26ff Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 27 Sep 2016 23:28:51 -0400
Subject: Fixes #1098: spack graph crashes for large graphs.

- Fixed logic for collapsing backward edges

- Last collapse now depends on whether prior step in left collapse
  sequence alrady did the collapse.
---
 lib/spack/spack/graph.py | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index 330e08cc71..acb6ee50de 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -128,7 +128,7 @@ def find(seq, predicate):
     return -1
 
 
-# Names of different graph line states.  We Record previous line
+# Names of different graph line states.  We record previous line
 # states so that we can easily determine what to do when connecting.
 states = ('node', 'collapse', 'merge-right', 'expand-right', 'back-edge')
 NODE, COLLAPSE, MERGE_RIGHT, EXPAND_RIGHT, BACK_EDGE = states
@@ -161,6 +161,9 @@ class AsciiGraph(object):
 
     def _write_edge(self, string, index, sub=0):
         """Write a colored edge to the output stream."""
+        # Ignore empty frontier entries (they're just collapsed)
+        if not self._frontier[index]:
+            return
         name = self._frontier[index][sub]
         edge = "@%s{%s}" % (self._name_to_color[name], string)
         self._out.write(edge)
@@ -419,20 +422,26 @@ class AsciiGraph(object):
                 if back:
                     back.sort()
                     prev_ends = []
+                    collapse_l1 = False
                     for j, (b, d) in enumerate(back):
                         self._frontier[i].remove(d)
                         if i - b > 1:
-                            self._back_edge_line(prev_ends, b, i, False,
-                                                 'left-1')
+                            collapse_l1 = any(not e for e in self._frontier)
+                            self._back_edge_line(
+                                prev_ends, b, i, collapse_l1, 'left-1')
                             del prev_ends[:]
                         prev_ends.append(b)
 
                     # Check whether we did ALL the deps as back edges,
                     # in which case we're done.
-                    collapse = not self._frontier[i]
-                    if collapse:
+                    pop = not self._frontier[i]
+                    collapse_l2 = pop
+                    if collapse_l1:
+                        collapse_l2 = False
+                    if pop:
                         self._frontier.pop(i)
-                    self._back_edge_line(prev_ends, -1, -1, collapse, 'left-2')
+                    self._back_edge_line(
+                        prev_ends, -1, -1, collapse_l2, 'left-2')
 
                 elif len(self._frontier[i]) > 1:
                     # Expand forward after doing all back connections
-- 
cgit v1.2.3-70-g09d2


From 05d52752fff1a6435f9173a2e1a6c6ab45232c3c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 27 Sep 2016 23:32:18 -0400
Subject: Make graph_ascii support deptypes.

- fix deptype support
- by default, graph command omits build depedencies
- update docs to use deptype args
---
 .gitignore                         |  1 +
 lib/spack/docs/configuration.rst   |  2 +-
 lib/spack/docs/packaging_guide.rst | 19 ++++++++++++++++---
 lib/spack/spack/cmd/graph.py       |  4 ++--
 lib/spack/spack/graph.py           | 32 ++++++++++++++------------------
 lib/spack/spack/spec.py            |  6 +++---
 6 files changed, 37 insertions(+), 27 deletions(-)

diff --git a/.gitignore b/.gitignore
index 072bf30c07..e6200a0676 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+/db
 /var/spack/stage
 /var/spack/cache
 /var/spack/repos/*/index.yaml
diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst
index ba534d1e62..6de823c845 100644
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -207,7 +207,7 @@ supply ``-p`` to Spack on the command line, before any subcommands.
 
 ``spack --profile`` output looks like this:
 
-.. command-output:: spack --profile graph dyninst
+.. command-output:: spack --profile graph --deptype=nobuild dyninst
    :ellipsis: 25
 
 The bottom of the output shows the top most time consuming functions,
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 0294f32748..70cd58f6c1 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -2888,9 +2888,22 @@ dependency graph.  For example:
 
 .. command-output:: spack graph mpileaks
 
-At the top is the root package in the DAG, with dependency edges
-emerging from it.  On a color terminal, the edges are colored by which
-dependency they lead to.
+At the top is the root package in the DAG, with dependency edges emerging
+from it.  On a color terminal, the edges are colored by which dependency
+they lead to.
+
+.. command-output:: spack graph --deptype=all mpileaks
+
+The ``deptype`` argument tells Spack what types of dependencies to graph.
+By default it includes link and run dependencies but not build
+dependencies.  Supplying ``--deptype=all`` will show the build
+dependencies as well.  This is equivalent to
+``--deptype=build,link,run``.  Options for ``deptype`` include:
+
+* Any combination of ``build``, ``link``, and ``run`` separated by
+  commas.
+* ``nobuild``, ``nolink``, ``norun`` to omit one type.
+* ``all`` or ``alldeps`` for all types of dependencies.
 
 You can also use ``spack graph`` to generate graphs in the widely used
 `Dot <http://www.graphviz.org/doc/info/lang.html>`_ format.  For
diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 6de1ed974b..3f7ab8bc2f 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -83,7 +83,7 @@ def graph(parser, args):
         setup_parser.parser.print_help()
         return 1
 
-    deptype = alldeps
+    deptype = nobuild
     if args.deptype:
         deptype = tuple(args.deptype.split(','))
         validate_deptype(deptype)
@@ -93,7 +93,7 @@ def graph(parser, args):
         graph_dot(specs, static=args.static, deptype=deptype)
 
     elif specs:  # ascii is default: user doesn't need to provide it explicitly
-        graph_ascii(specs[0], debug=spack.debug)
+        graph_ascii(specs[0], debug=spack.debug, deptype=deptype)
         for spec in specs[1:]:
             print  # extra line bt/w independent graphs
             graph_ascii(spec, debug=spack.debug)
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index acb6ee50de..f474799275 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -72,16 +72,15 @@ from spack.spec import *
 __all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
 
 
-def topological_sort(spec, **kwargs):
+def topological_sort(spec, reverse=False, deptype=None):
     """Topological sort for specs.
 
     Return a list of dependency specs sorted topologically.  The spec
     argument is not modified in the process.
 
     """
-    reverse = kwargs.get('reverse', False)
-    # XXX(deptype): iterate over a certain kind of dependency. Maybe color
-    #               edges based on the type of dependency?
+    deptype = canonical_deptype(deptype)
+
     if not reverse:
         parents = lambda s: s.dependents()
         children = lambda s: s.dependencies()
@@ -90,7 +89,7 @@ def topological_sort(spec, **kwargs):
         children = lambda s: s.dependents()
 
     # Work on a copy so this is nondestructive.
-    spec = spec.copy()
+    spec = spec.copy(deps=deptype)
     nodes = spec.index()
 
     topo_order = []
@@ -142,6 +141,7 @@ class AsciiGraph(object):
         self.node_character = '*'
         self.debug = False
         self.indent = 0
+        self.deptype = alldeps
 
         # These are colors in the order they'll be used for edges.
         # See llnl.util.tty.color for details on color characters.
@@ -388,7 +388,7 @@ class AsciiGraph(object):
         self._out = ColorStream(sys.stdout, color=color)
 
         # We'll traverse the spec in topo order as we graph it.
-        topo_order = topological_sort(spec, reverse=True)
+        topo_order = topological_sort(spec, reverse=True, deptype=self.deptype)
 
         # Work on a copy to be nondestructive
         spec = spec.copy()
@@ -484,27 +484,23 @@ class AsciiGraph(object):
 
                 # Replace node with its dependencies
                 self._frontier.pop(i)
-                if node.dependencies():
-                    deps = sorted((d.name for d in node.dependencies()),
-                                  reverse=True)
+                deps = node.dependencies(self.deptype)
+                if deps:
+                    deps = sorted((d.name for d in deps), reverse=True)
                     self._connect_deps(i, deps, "new-deps")  # anywhere.
 
                 elif self._frontier:
                     self._collapse_line(i)
 
 
-def graph_ascii(spec, **kwargs):
-    node_character = kwargs.get('node', 'o')
-    out            = kwargs.pop('out', None)
-    debug          = kwargs.pop('debug', False)
-    indent         = kwargs.pop('indent', 0)
-    color          = kwargs.pop('color', None)
-    check_kwargs(kwargs, graph_ascii)
-
+def graph_ascii(spec, node='o', out=None, debug=False,
+                indent=0, color=None, deptype=None):
     graph = AsciiGraph()
     graph.debug = debug
     graph.indent = indent
-    graph.node_character = node_character
+    graph.node_character = node
+    if deptype:
+        graph.deptype = canonical_deptype(deptype)
 
     graph.write(spec, color=color, out=out)
 
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 108e771748..ba9cea876d 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -194,6 +194,7 @@ nobuild = ('link', 'run')
 norun   = ('link', 'build')
 special_types = {
     'alldeps': alldeps,
+    'all': alldeps,  # allow "all" as string but not symbol.
     'nolink': nolink,
     'nobuild': nobuild,
     'norun': norun,
@@ -1418,12 +1419,11 @@ class Spec(object):
             # parser doesn't allow it. Spack must be broken!
             raise InconsistentSpecError("Invalid Spec DAG: %s" % e.message)
 
-    def index(self):
+    def index(self, deptype=None):
         """Return DependencyMap that points to all the dependencies in this
            spec."""
         dm = DependencyMap()
-        # XXX(deptype): use a deptype kwarg.
-        for spec in self.traverse():
+        for spec in self.traverse(deptype=deptype):
             dm[spec.name] = spec
         return dm
 
-- 
cgit v1.2.3-70-g09d2


From 6df84a794b27d3c16f5d72fc2e11f7f61b109859 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 28 Sep 2016 11:09:31 -0500
Subject: Add single letter arg flags for spack graph (#1871)

---
 lib/spack/spack/cmd/graph.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 3f7ab8bc2f..ed3aed1946 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -39,14 +39,14 @@ def setup_parser(subparser):
 
     method = subparser.add_mutually_exclusive_group()
     method.add_argument(
-        '--ascii', action='store_true',
+        '-a', '--ascii', action='store_true',
         help="Draw graph as ascii to stdout (default).")
     method.add_argument(
-        '--dot', action='store_true',
+        '-d', '--dot', action='store_true',
         help="Generate graph in dot format and print to stdout.")
 
     subparser.add_argument(
-        '--normalize', action='store_true',
+        '-n', '--normalize', action='store_true',
         help="Skip concretization; only print normalized spec.")
 
     subparser.add_argument(
-- 
cgit v1.2.3-70-g09d2


From 9aa77178f33793103653da1c81a73dd6a9e250be Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Wed, 28 Sep 2016 12:36:25 -0400
Subject: Prohibit Python3 in Python version check. (#1872)

---
 bin/spack | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/spack b/bin/spack
index 17586cc1f6..dcc25c5c83 100755
--- a/bin/spack
+++ b/bin/spack
@@ -25,9 +25,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-if not sys.version_info[:2] >= (2, 6):
+if (sys.version_info[0] > 2) or (sys.version_info[:2] < (2, 6)):
     v_info = sys.version_info[:3]
-    sys.exit("Spack requires Python 2.6 or higher. "
+    sys.exit("Spack requires Python 2.6 or 2.7. "
              "This is Python %d.%d.%d." % v_info)
 
 import os
-- 
cgit v1.2.3-70-g09d2


From 66c2ac0bc9639888f98cd0bd54688ac721045781 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 28 Sep 2016 13:58:51 -0500
Subject: Tell Mercurial where to find CA certs (#1873)

---
 .../repos/builtin/packages/mercurial/package.py    | 35 ++++++++++++++++++----
 1 file changed, 30 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py
index e51069662f..ea77953f15 100644
--- a/var/spack/repos/builtin/packages/mercurial/package.py
+++ b/var/spack/repos/builtin/packages/mercurial/package.py
@@ -22,23 +22,48 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
+import llnl.util.tty as tty
+import os
 
 
 class Mercurial(Package):
     """Mercurial is a free, distributed source control management tool."""
+
     homepage = "https://www.mercurial-scm.org"
     url      = "https://www.mercurial-scm.org/release/mercurial-3.9.tar.gz"
 
-    version('3.9'  , 'e2b355da744e94747daae3a5339d28a0')
+    version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce')
+    version('3.9',   'e2b355da744e94747daae3a5339d28a0')
     version('3.8.4', 'cec2c3db688cb87142809089c6ae13e9')
     version('3.8.3', '97aced7018614eeccc9621a3dea35fda')
     version('3.8.2', 'c38daa0cbe264fc621dc3bb05933b0b3')
     version('3.8.1', '172a8c588adca12308c2aca16608d7f4')
 
-    depends_on("python @2.6:2.7.999")
-    depends_on("py-docutils", type="build")
+    extends('python')
+    depends_on('python@2.6:2.8')
+    depends_on('py-docutils', type='build')
 
     def install(self, spec, prefix):
-        make('PREFIX=%s' % prefix, 'install')
+        make('install', 'PREFIX={0}'.format(prefix))
+
+        # Configuration of HTTPS certificate authorities
+        # https://www.mercurial-scm.org/wiki/CACertificates
+        hgrc_filename = join_path(prefix.etc, 'mercurial', 'hgrc')
+        mkdirp(os.path.dirname(hgrc_filename))
+
+        with open(hgrc_filename, 'w') as hgrc:
+            if os.path.exists('/etc/ssl/certs/ca-certificates.crt'):
+                # Debian/Ubuntu/Gentoo/Arch Linux
+                hgrc.write('[web]\ncacerts = /etc/ssl/certs/ca-certificates.crt')  # noqa
+            elif os.path.exists('/etc/pki/tls/certs/ca-bundle.crt'):
+                # Fedora/RHEL/CentOS
+                hgrc.write('[web]\ncacerts = /etc/pki/tls/certs/ca-bundle.crt')
+            elif os.path.exists('/etc/ssl/ca-bundle.pem'):
+                # openSUSE/SLE
+                hgrc.write('[web]\ncacerts = /etc/ssl/ca-bundle.pem')
+            else:
+                tty.warn('CA certificate not found. You may not be able to '
+                         'connect to an HTTPS server. If your CA certificate '
+                         'is in a non-standard location, you should add it to '
+                         '{0}'.format(hgrc_filename))
-- 
cgit v1.2.3-70-g09d2


From cb229f084239a1a8686785d3f453af5572d5f676 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 28 Sep 2016 15:00:26 -0400
Subject: Fixes #1720: spack reindex fails with invalid ref count. (#1867)

* Fixes #1720: spack reindex fails with invalid ref count.

- Database graph wasn't being built properly; dependencies were set up
  incorrectly in the nodes that ended up in the graph on reindex.

- Reworked _add to increment ref count properly and to always build
  bottom-up to make the logic simpler to understand.

* Add checks to ensure DB is a valid merkle tree.
---
 lib/spack/spack/database.py      | 99 ++++++++++++++++++++++------------------
 lib/spack/spack/package.py       |  3 +-
 lib/spack/spack/test/database.py | 27 +++++++++--
 3 files changed, 80 insertions(+), 49 deletions(-)

diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index e450b4d424..1adad5e90b 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -50,7 +50,7 @@ from llnl.util.lock import *
 
 import spack.spec
 from spack.version import Version
-from spack.spec import Spec
+from spack.spec import *
 from spack.error import SpackError
 from spack.repository import UnknownPackageError
 import spack.util.spack_yaml as syaml
@@ -64,6 +64,9 @@ _db_version = Version('0.9.2')
 # Default timeout for spack database locks is 5 min.
 _db_lock_timeout = 60
 
+# Types of dependencies tracked by the database
+_tracked_deps = nobuild
+
 
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
@@ -232,8 +235,6 @@ class Database(object):
                                  spec.format('$_$#'), dname, dhash[:7]))
                     continue
 
-                # defensive copy (not sure everything handles extra
-                # parent links yet)
                 child = data[dhash].spec
                 spec._add_dependency(child, dtypes)
 
@@ -328,7 +329,7 @@ class Database(object):
         self._data = data
 
     def reindex(self, directory_layout):
-        """Build database index from scratch based from a directory layout.
+        """Build database index from scratch based on a directory layout.
 
         Locks the DB if it isn't locked already.
 
@@ -359,9 +360,6 @@ class Database(object):
 
                 # Ask the directory layout to traverse the filesystem.
                 for spec in directory_layout.all_specs():
-                    # Create a spec for each known package and add it.
-                    path = directory_layout.path_for_spec(spec)
-
                     # Try to recover explicit value from old DB, but
                     # default it to False if DB was corrupt.
                     explicit = False
@@ -370,7 +368,7 @@ class Database(object):
                         if old_info is not None:
                             explicit = old_info.explicit
 
-                    self._add(spec, path, directory_layout, explicit=explicit)
+                    self._add(spec, directory_layout, explicit=explicit)
 
                 self._check_ref_counts()
 
@@ -389,10 +387,7 @@ class Database(object):
         counts = {}
         for key, rec in self._data.items():
             counts.setdefault(key, 0)
-            # XXX(deptype): This checks all dependencies, but build
-            #               dependencies might be able to be dropped in the
-            #               future.
-            for dep in rec.spec.dependencies():
+            for dep in rec.spec.dependencies(_tracked_deps):
                 dep_key = dep.dag_hash()
                 counts.setdefault(dep_key, 0)
                 counts[dep_key] += 1
@@ -450,52 +445,62 @@ class Database(object):
             # reindex() takes its own write lock, so no lock here.
             self.reindex(spack.install_layout)
 
-    def _add(self, spec, path, directory_layout=None, explicit=False):
-        """Add an install record for spec at path to the database.
+    def _add(self, spec, directory_layout=None, explicit=False):
+        """Add an install record for this spec to the database.
 
-        This assumes that the spec is not already installed. It
-        updates the ref counts on dependencies of the spec in the DB.
+        Assumes spec is installed in ``layout.path_for_spec(spec)``.
 
-        This operation is in-memory, and does not lock the DB.
+        Also ensures dependencies are present and updated in the DB as
+        either intsalled or missing.
 
         """
-        key = spec.dag_hash()
-        if key in self._data:
-            rec = self._data[key]
-            rec.installed = True
+        if not spec.concrete:
+            raise NonConcreteSpecAddError(
+                "Specs added to DB must be concrete.")
 
-            # TODO: this overwrites a previous install path (when path !=
-            # self._data[key].path), and the old path still has a
-            # dependent in the DB. We could consider re-RPATH-ing the
-            # dependents.  This case is probably infrequent and may not be
-            # worth fixing, but this is where we can discover it.
-            rec.path = path
-
-        else:
-            self._data[key] = InstallRecord(spec, path, True,
-                                            explicit=explicit)
-            for dep in spec.dependencies(('link', 'run')):
-                self._increment_ref_count(dep, directory_layout)
+        for dep in spec.dependencies(_tracked_deps):
+            dkey = dep.dag_hash()
+            if dkey not in self._data:
+                self._add(dep, directory_layout, explicit=False)
 
-    def _increment_ref_count(self, spec, directory_layout=None):
-        """Recursively examine dependencies and update their DB entries."""
         key = spec.dag_hash()
         if key not in self._data:
             installed = False
             path = None
             if directory_layout:
                 path = directory_layout.path_for_spec(spec)
-                installed = os.path.isdir(path)
+                try:
+                    directory_layout.check_installed(spec)
+                    installed = True
+                except DirectoryLayoutError as e:
+                    tty.warn(
+                        'Dependency missing due to corrupt install directory:',
+                        path, str(e))
+
+            # Create a new install record with no deps initially.
+            new_spec = spec.copy(deps=False)
+            self._data[key] = InstallRecord(
+                new_spec, path, installed, ref_count=0, explicit=explicit)
+
+            # Connect dependencies from the DB to the new copy.
+            for name, dep in spec.dependencies_dict(_tracked_deps).iteritems():
+                dkey = dep.spec.dag_hash()
+                new_spec._add_dependency(self._data[dkey].spec, dep.deptypes)
+                self._data[dkey].ref_count += 1
+
+            # Mark concrete once everything is built, and preserve
+            # the original hash of concrete specs.
+            new_spec._mark_concrete()
+            new_spec._hash = key
 
-            self._data[key] = InstallRecord(spec.copy(), path, installed)
-
-            for dep in spec.dependencies(('link', 'run')):
-                self._increment_ref_count(dep)
+        else:
+            # If it is already there, mark it as installed.
+            self._data[key].installed = True
 
-        self._data[key].ref_count += 1
+        self._data[key].explicit = explicit
 
     @_autospec
-    def add(self, spec, path, explicit=False):
+    def add(self, spec, directory_layout, explicit=False):
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -504,7 +509,7 @@ class Database(object):
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, path, explicit=explicit)
+            self._add(spec, directory_layout, explicit=explicit)
 
     def _get_matching_spec_key(self, spec, **kwargs):
         """Get the exact spec OR get a single spec that matches."""
@@ -534,7 +539,7 @@ class Database(object):
 
         if rec.ref_count == 0 and not rec.installed:
             del self._data[key]
-            for dep in spec.dependencies('link'):
+            for dep in spec.dependencies(_tracked_deps):
                 self._decrement_ref_count(dep)
 
     def _remove(self, spec):
@@ -548,7 +553,7 @@ class Database(object):
             return rec.spec
 
         del self._data[key]
-        for dep in rec.spec.dependencies('link'):
+        for dep in rec.spec.dependencies(_tracked_deps):
             self._decrement_ref_count(dep)
 
         # Returns the concrete spec so we know it in the case where a
@@ -657,6 +662,10 @@ class CorruptDatabaseError(SpackError):
     """Raised when errors are found while reading the database."""
 
 
+class NonConcreteSpecAddError(SpackError):
+    """Raised when attemptint to add non-concrete spec to DB."""
+
+
 class InvalidDatabaseVersionError(SpackError):
 
     def __init__(self, expected, found):
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index cffc795586..cb7f6b3f39 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1053,7 +1053,8 @@ class Package(object):
 
         # note: PARENT of the build process adds the new package to
         # the database, so that we don't need to re-read from file.
-        spack.installed_db.add(self.spec, self.prefix, explicit=explicit)
+        spack.installed_db.add(
+            self.spec, spack.install_layout, explicit=explicit)
 
     def sanity_check_prefix(self):
         """This function checks whether install succeeded."""
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index b114bbacb8..4395f17f97 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -124,6 +124,19 @@ class DatabaseTest(MockDatabase):
             self.assertEqual(new_rec.path,      rec.path)
             self.assertEqual(new_rec.installed, rec.installed)
 
+    def _check_merkleiness(self):
+        """Ensure the spack database is a valid merkle graph."""
+        all_specs = spack.installed_db.query(installed=any)
+
+        seen = {}
+        for spec in all_specs:
+            for dep in spec.dependencies():
+                hash_key = dep.dag_hash()
+                if hash_key not in seen:
+                    seen[hash_key] = id(dep)
+                else:
+                    self.assertEqual(seen[hash_key], id(dep))
+
     def _check_db_sanity(self):
         """Utiilty function to check db against install layout."""
         expected = sorted(spack.install_layout.all_specs())
@@ -133,10 +146,17 @@ class DatabaseTest(MockDatabase):
         for e, a in zip(expected, actual):
             self.assertEqual(e, a)
 
+        self._check_merkleiness()
+
     def test_020_db_sanity(self):
         """Make sure query() returns what's actually in the db."""
         self._check_db_sanity()
 
+    def test_025_reindex(self):
+        """Make sure reindex works and ref counts are valid."""
+        spack.installed_db.reindex(spack.install_layout)
+        self._check_db_sanity()
+
     def test_030_db_sanity_from_another_process(self):
         def read_and_modify():
             self._check_db_sanity()  # check that other process can read DB
@@ -203,9 +223,10 @@ class DatabaseTest(MockDatabase):
         self.assertTrue(concrete_spec not in remaining)
 
         # add it back and make sure everything is ok.
-        self.installed_db.add(concrete_spec, "")
+        self.installed_db.add(concrete_spec, spack.install_layout)
         installed = self.installed_db.query()
-        self.assertEqual(len(installed), len(original))
+        self.assertTrue(concrete_spec in installed)
+        self.assertEqual(installed, original)
 
         # sanity check against direcory layout and check ref counts.
         self._check_db_sanity()
@@ -233,7 +254,7 @@ class DatabaseTest(MockDatabase):
         self.assertEqual(self.installed_db.get_record('mpich').ref_count, 1)
 
         # Put the spec back
-        self.installed_db.add(rec.spec, rec.path)
+        self.installed_db.add(rec.spec, spack.install_layout)
 
         # record is present again
         self.assertEqual(
-- 
cgit v1.2.3-70-g09d2


From fea0a74bec4b14c6dda0be01a6a5c78f3bec913b Mon Sep 17 00:00:00 2001
From: "Robert D. French" <robert@robertdfrench.me>
Date: Wed, 28 Sep 2016 15:17:15 -0400
Subject: vim8 is out! (#1753)

* depends on ncurses for 8.0 or higher
---
 var/spack/repos/builtin/packages/vim/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index 5f2e5e19d9..26aeb4aad9 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -38,6 +38,7 @@ class Vim(Package):
     url      = "ftp://ftp.vim.org/pub/vim/unix/vim-7.4.tar.bz2"
     list_url = "http://ftp.vim.org/pub/vim/unix/"
 
+    version('8.0',     '808d2ebdab521e18bc5e0eaede0db867')
     version('7.4',     '607e135c559be642f210094ad023dc65')
     version('7.3',     '5b9510a17074e2b37d8bb38ae09edbf2')
     version('7.2',     'f0901284b338e448bfd79ccca0041254')
@@ -66,6 +67,8 @@ class Vim(Package):
     variant('gui', default=False, description="build with gui (gvim)")
     # virtual dependency?
 
+    depends_on('ncurses', when="@8.0:")
+
     def install(self, spec, prefix):
         feature_set = None
         for fs in self.feature_sets:
-- 
cgit v1.2.3-70-g09d2


From 295742e2b56b8731ff4651354cb754b2176fb6c2 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 28 Sep 2016 15:18:52 -0400
Subject: Fixes #1860. Subversion builds sequentially due to race.

---
 lib/spack/spack/graph.py                               | 2 +-
 var/spack/repos/builtin/packages/subversion/package.py | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index f474799275..9753741c61 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -522,7 +522,7 @@ def graph_dot(specs, deptype=None, static=False, out=None):
 
     out.write('digraph G {\n')
     out.write('  labelloc = "b"\n')
-    out.write('  rankdir = "LR"\n')
+    out.write('  rankdir = "TB"\n')
     out.write('  ranksep = "5"\n')
     out.write('node[\n')
     out.write('     fontname=Monaco,\n')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 26d143e4aa..02b7d96378 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -46,6 +46,9 @@ class Subversion(Package):
     # depends_on('perl')
     # depends_on('ruby')
 
+    # Installation has race cases.
+    parallel = False
+
     def install(self, spec, prefix):
 
         # configure, build, install:
-- 
cgit v1.2.3-70-g09d2


From 40407925011d3dc10cdbca6f755aff5952b27e76 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Wed, 28 Sep 2016 15:22:02 -0400
Subject: Update Qthreads to 1.11 (#1863)

---
 var/spack/repos/builtin/packages/qthreads/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index c68d8dba6c..aa2f0ac67a 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -39,10 +39,11 @@ class Qthreads(Package):
     homepage = "http://www.cs.sandia.gov/qthreads/"
 
     url = "https://github.com/Qthreads/qthreads/releases/download/1.10/qthread-1.10.tar.bz2"
+    version("1.11", "68b5f9a41cfd1a2ac112cc4db0612326")
     version("1.10", "d1cf3cf3f30586921359f7840171e551")
 
-    patch("restrict.patch")
-    patch("trap.patch")
+    patch("restrict.patch", when="@:1.10")
+    patch("trap.patch", when="@:1.10")
 
     depends_on("hwloc")
 
-- 
cgit v1.2.3-70-g09d2


From 3352889d73ef247f75a8a2d76e19e55b956de968 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Wed, 28 Sep 2016 16:51:41 -0400
Subject: py-pil: Protect against building with Python3. (#1868)

* py-pil: Does not build with Python3.

* Set py-pillow to be the default pil provider

* Update package.py

* Change to comments requested by adamjstewart

* Remove version constraint from extends(), avoid a Spack bug.
---
 etc/spack/defaults/packages.yaml                   | 1 +
 var/spack/repos/builtin/packages/py-pil/package.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml
index 83f9eb7ece..a6b361d908 100644
--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -19,3 +19,4 @@ packages:
       mpi: [openmpi, mpich]
       blas: [openblas]
       lapack: [openblas]
+      pil: [py-pillow]
diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py
index 2b3cce26d3..29a86d1e85 100644
--- a/var/spack/repos/builtin/packages/py-pil/package.py
+++ b/var/spack/repos/builtin/packages/py-pil/package.py
@@ -37,7 +37,10 @@ class PyPil(Package):
 
     provides('pil')
 
+    # py-pil currently only works with Python2.
+    # If you are using Python 3, try using py-pillow instead.
     extends('python')
+    depends_on('python@1.5.2:2.8')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From a77b48f4918415b4b50514daab7c0ee750c5f946 Mon Sep 17 00:00:00 2001
From: "Robert D. French" <robert@robertdfrench.me>
Date: Wed, 28 Sep 2016 17:02:29 -0400
Subject: Library for manipulating grib1 and grib2 files (#1736)

Pro tips from @adamjstewart:
* line too long in package description
* name it grib-api instead of grib_api
* depend on netcdf without reference to unnecessary constraints
---
 .../repos/builtin/packages/grib-api/package.py     | 50 ++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/grib-api/package.py

diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
new file mode 100644
index 0000000000..50164a6144
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class GribApi(Package):
+    """The ECMWF GRIB API is an application program interface accessible from C,
+       FORTRAN and Python programs developed for encoding and decoding WMO
+       FM-92 GRIB edition 1 and edition 2 messages."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2"
+
+    version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
+
+    depends_on('netcdf')
+    depends_on('jasper')
+
+    def install(self, spec, prefix):
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            '--with-netcdf={0}'.format(spec['netcdf'].prefix),
+            '--with-jasper={0}'.format(spec['jasper'].prefix)
+        ]
+        configure(*configure_options)
+
+        make()
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From deb1cb4805a9f02330a2380ccd68b72a48c84f13 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 29 Sep 2016 14:35:10 -0500
Subject: Add libint package (#1264)

* Add libint package

* Add Intel optimization flags recommended by CP2K

* Add new version and Intel compiler optimization flags for libxc

* Add older version of libint

* Libint depends on GMP C++ library
---
 var/spack/repos/builtin/packages/gmp/package.py    |   9 +-
 var/spack/repos/builtin/packages/libint/package.py | 103 +++++++++++++++++++++
 var/spack/repos/builtin/packages/libxc/package.py  |  20 +++-
 3 files changed, 127 insertions(+), 5 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/libint/package.py

diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index d85330dd6e..3ce784c6c1 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -37,9 +37,12 @@ class Gmp(Package):
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
     version('6.0.0',  '6ef5869ae735db9995619135bd856b84')
 
-    depends_on("m4", type='build')
+    depends_on('m4', type='build')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure('--prefix={0}'.format(prefix),
+                  '--enable-cxx')
+
         make()
-        make("install")
+        make('check')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py
new file mode 100644
index 0000000000..1962d8cbec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libint/package.py
@@ -0,0 +1,103 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libint(Package):
+    """Libint is a high-performance library for computing
+    Gaussian integrals in quantum mechanics."""
+
+    homepage = "https://github.com/evaleev/libint"
+    url      = "https://github.com/evaleev/libint/archive/v2.1.0.tar.gz"
+
+    version('2.1.0', 'd0dcb985fe32ddebc78fe571ce37e2d6')
+    version('1.1.6', '990f67b55f49ecc18f32c58da9240684')
+    version('1.1.5', '379b7d0718ff398715d6898807adf628')
+
+    # Build dependencies
+    depends_on('autoconf@2.52:', type='build')
+    depends_on('automake',       type='build')
+    depends_on('libtool',        type='build')
+
+    # Libint 2 dependencies
+    depends_on('boost', when='@2:')
+    depends_on('gmp',   when='@2:')
+
+    def url_for_version(self, version):
+        base_url = "https://github.com/evaleev/libint/archive"
+        if version == Version('1.0.0'):
+            return "{0}/LIBINT_1_00.tar.gz".format(base_url)
+        elif version < Version('2.1.0'):
+            return "{0}/release-{1}.tar.gz".format(base_url, version.dashed)
+        else:
+            return "{0}/v{1}.tar.gz".format(base_url, version)
+
+    def install(self, spec, prefix):
+        # Generate configure
+        libtoolize()
+        aclocal('-I', 'lib/autoconf')
+        autoconf()
+
+        config_args = [
+            '--prefix={0}'.format(prefix)
+        ]
+
+        # Optimizations for the Intel compiler, suggested by CP2K
+        optflags = '-O2'
+        if self.compiler.name == 'intel':
+            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            if which('xiar'):
+                env['AR'] = 'xiar'
+
+        env['CFLAGS']   = optflags
+        env['CXXFLAGS'] = optflags
+
+        # Optimization flag names have changed in libint 2
+        if self.version < Version('2.0.0'):
+            config_args.extend([
+                '--with-cc-optflags={0}'.format(optflags),
+                '--with-cxx-optflags={0}'.format(optflags)
+            ])
+        else:
+            config_args.extend([
+                '--with-cxx-optflags={0}'.format(optflags),
+                '--with-cxxgen-optflags={0}'.format(optflags)
+            ])
+
+        # Options required by CP2K, removed in libint 2
+        if self.version < Version('2.0.0'):
+            config_args.extend([
+                '--with-libint-max-am=5',
+                '--with-libderiv-max-am1=4'
+            ])
+
+        configure(*config_args)
+        make()
+
+        # Testing suite was added in libint 2
+        if self.version >= Version('2.0.0'):
+            make('check')
+
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
index 9ea4d1c326..fe82613ce2 100644
--- a/var/spack/repos/builtin/packages/libxc/package.py
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -32,11 +32,27 @@ class Libxc(Package):
     homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
     url      = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
 
+    version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
     version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix,
+        # Optimizations for the Intel compiler, suggested by CP2K
+        optflags = '-O2'
+        if self.compiler.name == 'intel':
+            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            if which('xiar'):
+                env['AR'] = 'xiar'
+
+        env['CFLAGS']  = optflags
+        env['FCFLAGS'] = optflags
+
+        configure('--prefix={0}'.format(prefix),
                   '--enable-shared')
 
         make()
-        make("install")
+
+        # libxc provides a testsuite, but many tests fail
+        # http://www.tddft.org/pipermail/libxc/2013-February/000032.html
+        # make('check')
+
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From 86cad961e52e2a28a2e0314fb34c1aca165da3cd Mon Sep 17 00:00:00 2001
From: Mitchell Devlin <mitchell.r.devlin@gmail.com>
Date: Thu, 29 Sep 2016 15:36:37 -0400
Subject: added libxstream (#1454)

---
 .../repos/builtin/packages/libxstream/package.py   | 50 ++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libxstream/package.py

diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py
new file mode 100644
index 0000000000..3201b58620
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxstream/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libxstream(Package):
+    '''LIBXSTREAM is a library to work with streams, events, and code regions
+    that are able to run asynchronous while preserving the usual stream
+    conditions.'''
+
+    homepage = 'https://github.com/hfp/libxstream'
+    url      = 'https://github.com/hfp/libxstream.git'
+
+    version('0.9.0', git='https://github.com/hfp/libxstream.git')
+
+    def patch(self):
+        kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
+        makefile = FileFilter('Makefile.inc')
+
+        makefile.filter('CC =',  'CC ?=',  **kwargs)
+        makefile.filter('CXX =', 'CXX ?=', **kwargs)
+        makefile.filter('FC =',  'FC ?=',  **kwargs)
+
+    def install(self, spec, prefix):
+        make()
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('documentation', prefix.share + '/libxstream/doc/')
-- 
cgit v1.2.3-70-g09d2


From 6ec46ca802d4726b59b3e3fb16a7676afb24a2e2 Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>
Date: Thu, 29 Sep 2016 21:37:07 +0200
Subject: updated to latest available package and fixed installation issue (old
 packages are no longer available for download) (#1523)

---
 var/spack/repos/builtin/packages/extrae/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py
index 72bfbe6326..cb20a8109e 100644
--- a/var/spack/repos/builtin/packages/extrae/package.py
+++ b/var/spack/repos/builtin/packages/extrae/package.py
@@ -53,8 +53,8 @@ class Extrae(Package):
        programming models either alone or in conjunction with MPI :
        OpenMP, CUDA, OpenCL, pthread, OmpSs"""
     homepage = "http://www.bsc.es/computer-sciences/extrae"
-    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-3.0.1.tar.bz2"
-    version('3.0.1', 'a6a8ca96cd877723cd8cc5df6bdb922b')
+    url      = "http://www.bsc.es/ssl/apps/performanceTools/files/extrae-3.3.0.tar.bz2"
+    version('3.3.0', 'f46e3f1a6086b5b3ac41c9585b42952d')
 
     depends_on("mpi")
     depends_on("dyninst")
@@ -62,6 +62,9 @@ class Extrae(Package):
     depends_on("boost")
     depends_on("libdwarf")
     depends_on("papi")
+    depends_on("libelf")
+    depends_on("libxml2")
+    depends_on("binutils+libiberty")
 
     def install(self, spec, prefix):
         if 'openmpi' in spec:
@@ -80,6 +83,9 @@ class Extrae(Package):
                   "--with-papi=%s" % spec['papi'].prefix,
                   "--with-dyninst-headers=%s" % spec[
                       'dyninst'].prefix.include,
+                  "--with-elf=%s" % spec['libelf'].prefix,
+                  "--with-xml-prefix=%s" % spec['libxml2'].prefix,
+                  "--with-binutils=%s" % spec['binutils'].prefix,
                   "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib)
 
         make()
-- 
cgit v1.2.3-70-g09d2


From 6c627dbac92ee044884b0f6c32ced5cb510909cf Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>
Date: Thu, 29 Sep 2016 21:37:35 +0200
Subject: Add cube variant for building GUI component with qt, parallel built
 supported (#1525)

---
 var/spack/repos/builtin/packages/cube/package.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index 8c835b3886..9cea3c40e8 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -43,14 +43,19 @@ class Cube(Package):
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20',
             url="http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz")
 
-    # TODO : add variant that builds GUI on top of Qt
+    variant('gui', default=False, description='Build CUBE GUI')
 
     depends_on('zlib')
+    depends_on('qt@4.6:', when='+gui')
 
     def install(self, spec, prefix):
         configure_args = ["--prefix=%s" % prefix,
-                          "--without-paraver",
-                          "--without-gui"]
+                          "--without-paraver"]
+
+        # TODO : need to handle cross compiling build
+        if '+gui' not in spec:
+            configure_args.append('--without-gui')
+
         configure(*configure_args)
-        make(parallel=False)
+        make()
         make("install", parallel=False)
-- 
cgit v1.2.3-70-g09d2


From 8d1ec0df3d4af0f6385ccd017aaad41d82cf96ef Mon Sep 17 00:00:00 2001
From: Michael Kuhn <suraia@ikkoku.de>
Date: Fri, 30 Sep 2016 18:45:08 +0200
Subject: Fix read locks on read-only file systems (#1857)

---
 lib/spack/llnl/util/lock.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index aa8272d5fe..b5e3a3a8f8 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -70,7 +70,8 @@ class Lock(object):
         while (time.time() - start_time) < timeout:
             try:
                 if self._fd is None:
-                    self._fd = os.open(self._file_path, os.O_RDWR)
+                    mode = os.O_RDWR if op == fcntl.LOCK_EX else os.O_RDONLY
+                    self._fd = os.open(self._file_path, mode)
 
                 fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
                 if op == fcntl.LOCK_EX:
-- 
cgit v1.2.3-70-g09d2


From 4b34ba103587b8799f7dccb29f68c1c886c4cee1 Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>
Date: Fri, 30 Sep 2016 23:31:28 +0200
Subject: pdt url change to download full installer tarball (#1881)

---
 var/spack/repos/builtin/packages/pdt/package.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py
index 648b2fab98..bed01aeefb 100644
--- a/var/spack/repos/builtin/packages/pdt/package.py
+++ b/var/spack/repos/builtin/packages/pdt/package.py
@@ -35,13 +35,14 @@ class Pdt(Package):
 
     """
     homepage = "https://www.cs.uoregon.edu/research/pdt/home.php"
-    url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdt-3.22.1.tar.gz"
+    url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdtoolkit-3.22.1.tar.gz"
 
-    version('3.22.1', 'be6fac0b1edb3e3287b0cb78741a24b6')
-    version('3.22',   'e6c7879fc49ac5ff67a76ce31ef9e251')
-    version('3.21',   '8df94298b71703decf680709a4ddf68f')
-    version('3.19',   'ba5591994998771fdab216699e362228')
-    version('3.18.1', '05281b5c82a4754df936df99ad7eec0f')
+    version('3.22.1', 'b56b9b3e621161c7fd9e4908b944840d')
+    version('3.22',   '982d667617802962a1f7fe6c4c31184f')
+    version('3.21',   '3092ca0d8833b69992c17e63ae66c263')
+    version('3.20',   'c3edabe202926abe04552e33cd39672d')
+    version('3.19',   '5c5e1e6607086aa13bf4b1b9befc5864')
+    version('3.18.1', 'e401534f5c476c3e77f05b7f73b6c4f2')
 
     def install(self, spec, prefix):
         configure('-prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From c86d4c89203d6c97e012b338de850603f19ade76 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret <jppelteret@gmail.com>
Date: Mon, 3 Oct 2016 02:50:39 +0200
Subject: Added bash-completion package (#951)

---
 .../builtin/packages/bash-completion/package.py    | 64 ++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bash-completion/package.py

diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py
new file mode 100644
index 0000000000..666a1bef13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bash-completion/package.py
@@ -0,0 +1,64 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BashCompletion(Package):
+    """Programmable completion functions for bash."""
+    homepage = "https://github.com/scop/bash-completion"
+    url      = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+
+    version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292')
+    version('develop',  git='https://github.com/scop/bash-completion.git')
+
+    # Build dependencies
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool',  type='build')
+
+    # Other dependencies
+    depends_on('bash@4.1:', type='run')
+
+    def install(self, spec, prefix):
+        make_args = ['--prefix=%s' % prefix]
+
+        autoreconf('-i')
+        configure(*make_args)
+        make()
+        # make("check") # optional, requires dejagnu and tcllib
+        make("install",
+             parallel=False)
+
+        # Guidelines for individual user as provided by the author at
+        # https://github.com/scop/bash-completion
+        print('=====================================================')
+        print('Bash completion has been installed. To use it, please')
+        print('include the following lines in your ~/.bash_profile :')
+        print('')
+        print('# Use bash-completion, if available')
+        print('[[ $PS1 && -f %s/share/bash-completion/bash_completion ]] && \ ' % prefix)  # NOQA: ignore=E501
+        print('    . %s/share/bash-completion/bash_completion'  % prefix)
+        print('')
+        print('=====================================================')
-- 
cgit v1.2.3-70-g09d2


From e854e053e4977016e1561793942910f609f7a4bc Mon Sep 17 00:00:00 2001
From: Bruno Turcksin <bruno.turcksin@gmail.com>
Date: Sun, 2 Oct 2016 21:36:31 -0400
Subject: Add boost 1.62.0 (#1882)

---
 var/spack/repos/builtin/packages/boost/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 49fbd09775..22351a2c3a 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -41,6 +41,7 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
+    version('1.62.0', '5fb94629535c19e48703bdb2b2e9490f')
     version('1.61.0', '6095876341956f65f9d35939ccea1a9f')
     version('1.60.0', '65a840e1a0b13a558ff19eeb2c4f0cbe')
     version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
-- 
cgit v1.2.3-70-g09d2


From 051c5dbc27265f38e5ce79418163c3714d2fe8ef Mon Sep 17 00:00:00 2001
From: Kelly Thompson <KineticTheory@users.noreply.github.com>
Date: Sun, 2 Oct 2016 19:36:48 -0600
Subject: New package: libquo (#1880)

* New package: libquo

libquo is a high-level, easy to use programming interface tailored specifically
for MPI/MPI+X codes that may benefit from evolving process binding policies
during their execution. QUO allows for arbitrary process binding policies to
be enacted and reverted during the execution of an MPI/MPI+X application as
different computational phases are entered and exited, respectively.

https://github.com/losalamos/libquo

* Remove use of 'which' and fix style non-conformance.
---
 var/spack/repos/builtin/packages/libquo/package.py | 68 ++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libquo/package.py

diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py
new file mode 100644
index 0000000000..8856913bb2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libquo/package.py
@@ -0,0 +1,68 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Libquo(Package):
+    """A high-level, easy to use programming interface tailored specifically
+    for MPI/MPI+X codes that may benefit from evolving process binding
+    policies during their execution. QUO allows for arbitrary process binding
+    policies to be enacted and reverted during the execution of an MPI/MPI+X
+    application as different computational phases are entered and exited,
+    respectively."""
+
+    homepage = "https://github.com/losalamos/libquo"
+    url      = "https://github.com/losalamos/libquo/archive/v1.2.9.tar.gz"
+
+    version('1.2.9', 'ca82ab33f13e2b89983f81e7c02e98c2')
+
+    depends_on('mpi')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+
+    def install(self, spec, prefix):
+        autoreconf_options = [
+            '--install',
+            '--verbose',
+            '--force',
+            '-I', 'config',
+            '-I', os.path.join(spec['automake'].prefix,
+                               'share', 'aclocal'),
+            '-I', os.path.join(spec['libtool'].prefix,
+                               'share', 'aclocal')
+        ]
+        autoreconf(*autoreconf_options)
+
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            'CC=%s' % join_path(spec['mpi'].prefix.bin, "mpicc"),
+            'FC=%s' % join_path(spec['mpi'].prefix.bin, "mpif90")
+        ]
+        configure(*configure_options)
+
+        make()
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From b2ff9dbcd41996a4bef13f674d5e58941a8d822b Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 2 Oct 2016 21:37:17 -0400
Subject: Update tmux to 2.3.0 (#1879)

---
 var/spack/repos/builtin/packages/tmux/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 573ee38a79..89c9751486 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -35,9 +35,10 @@ class Tmux(Package):
     homepage = "http://tmux.github.io"
     url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz"
 
-    version('1.9a', 'b07601711f96f1d260b390513b509a2d')
-    version('2.1', '74a2855695bccb51b6e301383ad4818c')
+    version('2.3', 'fcfd1611d705d8b31df3c26ebc93bd3e')
     version('2.2', 'bd95ee7205e489c62c616bb7af040099')
+    version('2.1', '74a2855695bccb51b6e301383ad4818c')
+    version('1.9a', 'b07601711f96f1d260b390513b509a2d')
 
     depends_on('libevent')
     depends_on('ncurses')
-- 
cgit v1.2.3-70-g09d2


From 28b48f3e1a60bd77134951e1311f0e0877f9c66d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 2 Oct 2016 21:37:26 -0400
Subject: Update PAPI to 5.5.0 (#1878)

---
 var/spack/repos/builtin/packages/papi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 5c4abe1730..90a7490e75 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -41,6 +41,7 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.5.0', '5e1244a04ca031d4cc29b46ce3dd05b5')
     version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
-- 
cgit v1.2.3-70-g09d2


From b22956bab2646ae52e118c5791a58cf46003bef8 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 2 Oct 2016 21:37:45 -0400
Subject: git: Don't link against -lrt on Darwin (#1877)

There is no librt on Darwin, and it's not necessary either.
---
 var/spack/repos/builtin/packages/git/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index a687b2bb35..ac97ad392b 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -22,6 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import sys
 from spack import *
 
 
@@ -79,5 +80,8 @@ class Git(Package):
 
         which('autoreconf')('-i')
         configure(*configure_args)
+        if sys.platform == "darwin":
+            # Don't link with -lrt; the system has no (and needs no) librt
+            filter_file(r' -lrt$', '', 'Makefile')
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 1ea958221877d992ec733b8dfb3dea8e2466a159 Mon Sep 17 00:00:00 2001
From: Alfredo Adolfo Gimenez <alfredo.gimenez@gmail.com>
Date: Sun, 2 Oct 2016 18:49:30 -0700
Subject: Added hadoop, spark, and variant spark+hadoop (#1833)

* Added hadoop, spark, and variant spark+hadoop

* Docstrings, dependency types, urls, copyright

* Flake8 fixes, link dependency for hadoop

* Build type for spark, env problem setting JAVA_HOME
---
 var/spack/repos/builtin/packages/hadoop/package.py | 53 +++++++++++++++
 var/spack/repos/builtin/packages/spark/package.py  | 75 ++++++++++++++++++++++
 2 files changed, 128 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hadoop/package.py
 create mode 100644 var/spack/repos/builtin/packages/spark/package.py

diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py
new file mode 100644
index 0000000000..fdcac10335
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hadoop/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Alfredo Gimenez, gimenez1@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Hadoop(Package):
+    """The Apache Hadoop software library is a framework that
+    allows for the distributed processing of large data sets
+    across clusters of computers using simple programming models.
+    """
+
+    homepage = "http://hadoop.apache.org/"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-2.6.4/hadoop-2.6.4.tar.gz"
+
+    version('2.6.4', '37019f13d7dcd819727be158440b9442')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+
+        def install_dir(dirname):
+            install_tree(dirname, join_path(prefix, dirname))
+
+        install_dir('bin')
+        install_dir('etc')
+        install_dir('include')
+        install_dir('lib')
+        install_dir('libexec')
+        install_dir('sbin')
+        install_dir('share')
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
new file mode 100644
index 0000000000..10b0ebed7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Alfredo Gimenez, gimenez1@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+import shutil
+
+
+class Spark(Package):
+    """Apache Spark is a fast and general engine
+    for large-scale data processing.
+    """
+
+    homepage = "http://spark.apache.org"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/spark/spark-2.0.0/spark-2.0.0-bin-without-hadoop.tgz"
+
+    variant('hadoop', default=False,
+            description='Build with Hadoop')
+
+    depends_on('jdk', type=('build', 'run'))
+    depends_on('hadoop', when='+hadoop', type=('build', 'run'))
+
+    version('2.0.0', '8a5307d973da6949a385aefb6ff747bb')
+    version('1.6.2', '304394fbe2899211217f0cd9e9b2b5d9')
+    version('1.6.1', 'fcf4961649f15af1fea78c882e65b001')
+
+    def install(self, spec, prefix):
+
+        def install_dir(dirname):
+            install_tree(dirname, join_path(prefix, dirname))
+
+        install_dir('bin')
+        install_dir('conf')
+        install_dir('jars')
+        install_dir('python')
+        install_dir('R')
+        install_dir('sbin')
+        install_dir('yarn')
+
+        # required for spark to recognize binary distribution
+        shutil.copy('RELEASE', prefix)
+
+    @when('+hadoop')
+    def setup_environment(self, spack_env, run_env):
+
+        env['JAVA_HOME'] = self.spec['jdk'].prefix
+        # spack_env.set('JAVA_HOME', self.spec['jdk'].prefix)
+
+        hadoop_bin_path = join_path(self.spec['hadoop'].prefix.bin, 'hadoop')
+        hadoop_bin = Executable(hadoop_bin_path)
+        hadoop_classpath = hadoop_bin('classpath', return_output=True)
+
+        run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath)
-- 
cgit v1.2.3-70-g09d2


From 621a4d637de554d9a137bc17a15668db8f11b7b2 Mon Sep 17 00:00:00 2001
From: Kelly Thompson <KineticTheory@users.noreply.github.com>
Date: Sun, 2 Oct 2016 19:50:42 -0600
Subject: Provide newer versions of llvm (3.8.1, 3.9.0) (#1765)

* Provide new versions of llvm.

+ Provide file list and md5 hashes for 3.8.1 and 3.9.0.
+ Clean up indentation for the 'releases' data structure to improve
  consistency.

* Adding a block of code to the 'resources' structure for cfe.

* Merge cfe and clang resources into single entity.
---
 var/spack/repos/builtin/packages/llvm/package.py | 152 ++++++++++++++---------
 1 file changed, 91 insertions(+), 61 deletions(-)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 7582faeb92..06572ea312 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -33,8 +33,8 @@ class Llvm(Package):
        with traditional virtual machines, though it does provide helpful
        libraries that can be used to build them. The name "LLVM" itself
        is not an acronym; it is the full name of the project.
-
     """
+
     homepage = 'http://llvm.org/'
     url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
@@ -42,7 +42,7 @@ class Llvm(Package):
 
     # currently required by mesa package
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005',
-            url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')  # currently required by mesa package
+            url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')
 
     variant('debug', default=False,
             description="Build a debug version of LLVM, this increases "
@@ -114,7 +114,7 @@ class Llvm(Package):
             'destination': 'projects',
             'placement': 'libcxxabi',
         },
-        'clang': {
+        'cfe': {
             'url':  base_url % {'pkg': 'cfe'},
             'destination': 'tools',
             'placement': 'clang',
@@ -144,63 +144,93 @@ class Llvm(Package):
         {
             'version': 'trunk',
             'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk',
-                    'resources': {
-                        'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
-                        'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk',
-                        'polly': 'http://llvm.org/svn/llvm-project/polly/trunk',
-                        'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk',
-                        'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
-                        'clang': 'http://llvm.org/svn/llvm-project/cfe/trunk',
-                        'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
-                        'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
-                        'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
-                    }
-        },
-        {
-            'version': '3.8.0',
-            'md5': '07a7a74f3c6bd65de4702bf941b511a0',
-            'resources': {
-                'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025',
-                'openmp': '8fd7cc35d48051613cf1e750e9f22e40',
-                'polly': '1b3b20f52d34a4024e21a4ea7112caa7',
-                'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a',
-                'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7',
-                'clang': 'cc99e7019bb74e6459e80863606250c5',
-                'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
-                'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
-                        'llvm-libunwind': '162ade468607f153cca12be90b5194fa',
-            }
-        },
-        {
-            'version': '3.7.1',
-            'md5': 'bf8b3a2c79e61212c5409041dfdbd319',
-            'resources': {
-                'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01',
-                'openmp': 'b4ad08cda4e5c22e42b66062b140438e',
-                'polly': '3a2a7367002740881637f4d47bca4dc3',
-                'libcxx': 'f9c43fa552a10e14ff53b94d04bea140',
-                'libcxxabi': '52d925afac9f97e9dcac90745255c169',
-                'clang': '0acd026b5529164197563d135a8fd83e',
-                'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
-                'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
-                        'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
-            }
-        },
-        {
-            'version': '3.7.0',
-            'md5': 'b98b9495e5655a672d6cb83e1a180f8e',
             'resources': {
-                'compiler-rt': '383c10affd513026f08936b5525523f5',
-                'openmp': 'f482c86fdead50ba246a1a2b0bbf206f',
-                'polly': '32f93ffc9cc7e042df22089761558f8b',
-                'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd',
-                'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772',
-                'clang': '8f9d27335e7331cf0a4711e952f21f01',
-                'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
-                'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
-                        'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
-            }
-        },
+                'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                'polly': 'http://llvm.org/svn/llvm-project/polly/trunk',
+                'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                'cfe': 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                }
+            },
+            {
+                'version': '3.9.0',
+                'md5': 'f2093e98060532449eb7d2fcfd0bc6c6',
+                'resources': {
+                    'compiler-rt': 'b7ea34c9d744da16ffc0217b6990d095',
+                    'openmp': '5390164f2374e1444e82393541ecf6c7',
+                    'polly': '1cf328cbae25267749b68cfa6f113674',
+                    'libcxx': '0a11efefd864ce6f321194e441f7e569',
+                    'libcxxabi': 'd02642308e22e614af6b061b9b4fedfa',
+                    'cfe': '29e1d86bee422ab5345f5e9fb808d2dc',
+                    'clang-tools-extra': 'f4f663068c77fc742113211841e94d5e',
+                    'lldb': '968d053c3c3d7297983589164c6999e9',
+                    'llvm-libunwind': '3e5c87c723a456be599727a444b1c166',
+                    }
+                },
+            {
+                'version': '3.8.1',
+                'md5': '538467e6028bbc9259b1e6e015d25845',
+                'resources': {
+                    'compiler-rt': 'f140db073d2453f854fbe01cc46f3110',
+                    'openmp': '078b8d4c51ad437a4f8b5989f5ec4156',
+                    'polly': '8a40e697a4ba1c8b640b85d074bd6e25',
+                    'libcxx': '1bc60150302ff76a0d79d6f9db22332e',
+                    'libcxxabi': '3c63b03ba2f30a01279ca63384a67773',
+                    'cfe': '4ff2f8844a786edb0220f490f7896080',
+                    'clang-tools-extra': '6e49f285d0b366cc3cab782d8c92d382',
+                    'lldb': '9e4787b71be8e432fffd31e13ac87623',
+                    'llvm-libunwind': 'd66e2387e1d37a8a0c8fe6a0063a3bab',
+                    }
+                },
+            {
+                'version': '3.8.0',
+                'md5': '07a7a74f3c6bd65de4702bf941b511a0',
+                'resources': {
+                    'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                    'openmp': '8fd7cc35d48051613cf1e750e9f22e40',
+                    'polly': '1b3b20f52d34a4024e21a4ea7112caa7',
+                    'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                    'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7',
+                    'cfe': 'cc99e7019bb74e6459e80863606250c5',
+                    'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
+                    'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                    'llvm-libunwind': '162ade468607f153cca12be90b5194fa',
+                    }
+                },
+            {
+                'version': '3.7.1',
+                'md5': 'bf8b3a2c79e61212c5409041dfdbd319',
+                'resources': {
+                    'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01',
+                    'openmp': 'b4ad08cda4e5c22e42b66062b140438e',
+                    'polly': '3a2a7367002740881637f4d47bca4dc3',
+                    'libcxx': 'f9c43fa552a10e14ff53b94d04bea140',
+                    'libcxxabi': '52d925afac9f97e9dcac90745255c169',
+                    'cfe': '0acd026b5529164197563d135a8fd83e',
+                    'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
+                    'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
+                    'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
+                    }
+                },
+            {
+                'version': '3.7.0',
+                'md5': 'b98b9495e5655a672d6cb83e1a180f8e',
+                'resources': {
+                    'compiler-rt': '383c10affd513026f08936b5525523f5',
+                    'openmp': 'f482c86fdead50ba246a1a2b0bbf206f',
+                    'polly': '32f93ffc9cc7e042df22089761558f8b',
+                    'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd',
+                    'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772',
+                    'cfe': '8f9d27335e7331cf0a4711e952f21f01',
+                    'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
+                    'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
+                    'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
+                    }
+                },
         {
             'version': '3.6.2',
             'md5': '0c1ee3597d75280dee603bae9cbf5cc2',
@@ -209,7 +239,7 @@ class Llvm(Package):
                 'openmp': '65dd5863b9b270960a96817e9152b123',
                 'libcxx': '22214c90697636ef960a49aef7c1823a',
                 'libcxxabi': '17518e361e4e228f193dd91e8ef54ba2',
-                'clang': 'ff862793682f714bb7862325b9c06e20',
+                'cfe': 'ff862793682f714bb7862325b9c06e20',
                 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06',
                 'lldb': '51e5eb552f777b950bb0ff326e60d5f0',
             }
@@ -222,7 +252,7 @@ class Llvm(Package):
                 'openmp': '121ddb10167d7fc38b1f7e4b029cf059',
                 'libcxx': '406f09b1dab529f3f7879f4d548329d2',
                 'libcxxabi': 'b22c707e8d474a99865ad3c521c3d464',
-                'clang': '93f9532f8f7e6f1d8e5c1116907051cb',
+                'cfe': '93f9532f8f7e6f1d8e5c1116907051cb',
                 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246',
                 'lldb': 'cc5ea8a414c62c33e760517f8929a204',
             }
-- 
cgit v1.2.3-70-g09d2


From 2ce1b388c955d2b0648afcbab332d3f9801cacab Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sun, 2 Oct 2016 20:51:09 -0500
Subject: Run make clean to prevent warning messages (#1742)

* Run make clean to prevent warning messages

* Don't delete temporary files after completion
---
 share/spack/qa/run-doc-tests | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/share/spack/qa/run-doc-tests b/share/spack/qa/run-doc-tests
index 67701167aa..dbf46c71aa 100755
--- a/share/spack/qa/run-doc-tests
+++ b/share/spack/qa/run-doc-tests
@@ -9,7 +9,7 @@
 #     run-doc-tests
 #
 # Notes:
-#     Requires sphinx, git, mercurial, and subversion.
+#     Requires sphinx, graphviz, git, mercurial, and subversion.
 #
 
 QA_DIR="$(dirname "$0")"
@@ -36,9 +36,7 @@ export PATH="$SPACK_ROOT/bin:$PATH"
 # Allows script to be run from anywhere
 cd "$DOC_DIR"
 
-# Cleanup temporary files upon exit or when script is killed
-trap 'make clean --silent' EXIT SIGINT SIGTERM
-
 # Treat warnings as fatal errors
+make clean --silent
 make SPHINXOPTS=-W
 
-- 
cgit v1.2.3-70-g09d2


From 16f99bd0b2ed7f41655043ede36f4c5b4b68ff55 Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nrichart@users.noreply.github.com>
Date: Mon, 3 Oct 2016 03:51:34 +0200
Subject: Adding latest version of fenics (#1528)

* Adding last version of fenics and making trilinos not ambiguous on hdf5

* forcing fenics to ignore hdf5 cxx

* Adding deptypes and correcting the hdf5 patch

* flake8 corrections

* cleaning some useless code
---
 .../packages/fenics/hdf5~cxx-detection.patch       | 11 +++++++
 var/spack/repos/builtin/packages/fenics/package.py | 35 +++++++++++++++-------
 .../repos/builtin/packages/trilinos/package.py     |  9 ++++++
 3 files changed, 44 insertions(+), 11 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch

diff --git a/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch b/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch
new file mode 100644
index 0000000000..52e36ab00b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fenics/hdf5~cxx-detection.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2016-08-16 02:30:13.466078087 +0200
++++ b/CMakeLists.txt	2016-08-16 02:30:36.879586772 +0200
+@@ -553,7 +553,7 @@
+     set(ENV{HDF5_ROOT} "$ENV{HDF5_DIR}")
+   endif()
+   set(HDF5_PREFER_PARALLEL TRUE)
+-  find_package(HDF5)
++  find_package(HDF5 COMPONENTS C)
+   set_package_properties(HDF5 PROPERTIES TYPE OPTIONAL
+     DESCRIPTION "Hierarchical Data Format 5 (HDF5)"
+     URL "https://www.hdfgroup.org/HDF5")
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index eeeefc540d..fd9a37df1b 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -62,17 +62,15 @@ class Fenics(Package):
     # variant('slepc4py',     default=True,  description='Uses SLEPc4py')
     # variant('pastix',       default=True,  description='Compile with Pastix')
 
-    patch('petsc-3.7.patch', when='^petsc@3.7:')
+    patch('petsc-3.7.patch', when='@1.6.1^petsc@3.7:')
     patch('petsc-version-detection.patch', when='@:1.6.1')
+    patch('hdf5~cxx-detection.patch')
 
     extends('python')
 
-    depends_on('py-numpy')
-    depends_on('py-ply')
-    depends_on('py-six')
-    depends_on('py-sphinx@1.0.1:', when='+doc')
-    depends_on('eigen@3.2.0:')
-    depends_on('boost')
+    depends_on('eigen@3.2.0:', type='build')
+    depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
+
     depends_on('mpi', when='+mpi')
     depends_on('hdf5', when='+hdf5')
     depends_on('parmetis@4.0.2:^metis+real64', when='+parmetis')
@@ -85,12 +83,27 @@ class Fenics(Package):
     depends_on('suite-sparse', when='+suite-sparse')
     depends_on('qt', when='+qt')
 
-    # This are the build dependencies
-    depends_on('py-setuptools')
-    depends_on('cmake@2.8.12:')
-    depends_on('swig@3.0.3:')
+    depends_on('py-ply', type=nolink)
+    depends_on('py-six', type=nolink)
+    depends_on('py-numpy', type=nolink)
+    depends_on('py-sympy', type=nolink)
+    depends_on('swig@3.0.3:', type=nolink)
+    depends_on('cmake@2.8.12:', type=nolink)
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-sphinx@1.0.1:', when='+doc', type='build')
 
     releases = [
+        {
+            'version': '2016.1.0',
+            'md5': '92e8d00f6487a575987201f0b0d19173',
+            'resources': {
+                'ffc': '35457ae164e481ba5c9189ebae060a47',
+                'fiat': 'ac0c49942831ee434301228842bcc280',
+                'instant': '0e3dbb464c4d90d691f31f0fdd63d4f6',
+                'ufl': '37433336e5c9b58d1d5ab4acca9104a7',
+            }
+        },
         {
             'version': '1.6.0',
             'md5': '35cb4baf7ab4152a40fb7310b34d5800',
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index a50201c903..203e1502d6 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -178,6 +178,15 @@ class Trilinos(Package):
         else:
             options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
         # Fortran lib
         libgfortran = os.path.dirname(os.popen(
             '%s --print-file-name libgfortran.a' %
-- 
cgit v1.2.3-70-g09d2


From df79ba0dcfd933789f407caea977541aa8b4d1ff Mon Sep 17 00:00:00 2001
From: Geoffrey Oxberry <goxberry@gmail.com>
Date: Sun, 2 Oct 2016 18:54:43 -0700
Subject: gcc: fix darwin dispatch/object.h header issue (#1518)

Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that
are gcc-incompatible, but compile fine with clang. The fix is to copy
the offending system header from /usr/include/${REST_OF_HEADER_PATH} to
${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc-
compatible features with gcc-compatible equivalents.

See https://github.com/hashdist/hashstack/pull/771/files for
inspiration, and
http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/
for a description of the header issue.
---
 var/spack/repos/builtin/packages/gcc/package.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3be3948b59..d152ce61c7 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -3,6 +3,7 @@ from spack import *
 from contextlib import closing
 from glob import glob
 import sys
+from os.path import isfile
 
 
 class Gcc(Package):
@@ -68,6 +69,19 @@ class Gcc(Package):
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
+        # Fix a standard header file for OS X Yosemite that
+        # is GCC incompatible by replacing non-GCC compliant macros
+        if 'yosemite' in spec.architecture:
+            if isfile(r'/usr/include/dispatch/object.h'):
+                new_dispatch_dir = join_path(prefix, 'include', 'dispatch')
+                mkdirp(new_dispatch_dir)
+                cp = which('cp')
+                new_header = join_path(new_dispatch_dir, 'object.h')
+                cp(r'/usr/include/dispatch/object.h', new_header)
+                filter_file(r'typedef void \(\^dispatch_block_t\)\(void\)',
+                            'typedef void* dispatch_block_t',
+                            new_header)
+
         # Generic options to compile GCC
         options = ["--prefix=%s" % prefix, "--libdir=%s/lib64" % prefix,
                    "--disable-multilib",
-- 
cgit v1.2.3-70-g09d2


From 50fcade81b6e14b38ecd2f6bc53299f15e7e3c84 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Mon, 3 Oct 2016 17:25:36 +0200
Subject: cp2k : added support for libint,  fixed compilation issues on elpa
 (#1889)

---
 var/spack/repos/builtin/packages/cp2k/package.py   | 12 ++++++++----
 var/spack/repos/builtin/packages/elpa/package.py   | 12 ++++++++++++
 var/spack/repos/builtin/packages/libint/package.py |  3 ++-
 3 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 15606cd80a..3a175ea1a2 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -47,6 +47,7 @@ class Cp2k(Package):
     depends_on('lapack')
     depends_on('blas')
     depends_on('fftw')
+    depends_on('libint@:1.2', when='@3.0')
 
     depends_on('mpi', when='+mpi')
     depends_on('scalapack', when='+mpi')
@@ -56,10 +57,8 @@ class Cp2k(Package):
     depends_on('wannier90', when='+mpi')
     depends_on('elpa', when='+mpi')
 
-    # TODO : add dependency on libint
     # TODO : add dependency on libsmm, libxsmm
     # TODO : add dependency on CUDA
-    # TODO : add dependency on QUIP
 
     parallel = False
 
@@ -88,7 +87,7 @@ class Cp2k(Package):
             }
             cppflags = [
                 '-D__FFTW3',
-                '-D__LIBPEXSI',
+                '-D__LIBINT',
                 '-I' + spec['fftw'].prefix.include
             ]
             fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
@@ -97,7 +96,11 @@ class Cp2k(Package):
             ])
             fftw = find_libraries(['libfftw3'], root=spec['fftw'].prefix.lib)
             ldflags = [fftw.search_flags]
-            libs = []
+            libs = [
+                join_path(spec['libint'].prefix.lib, 'libint.so'),
+                join_path(spec['libint'].prefix.lib, 'libderiv.so'),
+                join_path(spec['libint'].prefix.lib, 'libr12.so')
+            ]
             if '+plumed' in self.spec:
                 # Include Plumed.inc in the Makefile
                 mkf.write('include {0}\n'.format(
@@ -145,6 +148,7 @@ class Cp2k(Package):
             if '+mpi' in self.spec:
                 cppflags.extend([
                     '-D__parallel',
+                    '-D__LIBPEXSI',
                     '-D__WANNIER90',
                     '-D__ELPA3',
                     '-D__SCALAPACK'
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index ae3f26b3ec..b433bf40b0 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -58,6 +58,18 @@ class Elpa(Package):
             'CC={0}'.format(self.spec['mpi'].mpicc),
             'FC={0}'.format(self.spec['mpi'].mpifc),
             'CXX={0}'.format(self.spec['mpi'].mpicxx),
+            'FCFLAGS={0}'.format(
+                spec['lapack'].lapack_libs.joined()
+            ),
+            'LDFLAGS={0}'.format(
+                spec['lapack'].lapack_libs.joined()
+            ),
+            'SCALAPACK_FCFLAGS={0}'.format(
+                spec['scalapack'].scalapack_libs.joined()
+            ),
+            'SCALAPACK_LDFLAGS={0}'.format(
+                spec['scalapack'].scalapack_libs.joined()
+            ),
             '--prefix={0}'.format(self.prefix)
         ]
 
diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py
index 1962d8cbec..2ad5e93191 100644
--- a/var/spack/repos/builtin/packages/libint/package.py
+++ b/var/spack/repos/builtin/packages/libint/package.py
@@ -61,7 +61,8 @@ class Libint(Package):
         autoconf()
 
         config_args = [
-            '--prefix={0}'.format(prefix)
+            '--prefix={0}'.format(prefix),
+            '--enable-shared'
         ]
 
         # Optimizations for the Intel compiler, suggested by CP2K
-- 
cgit v1.2.3-70-g09d2


From e546d6246f2cdb14c6ae01ecf322e75de78325de Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>
Date: Tue, 4 Oct 2016 10:02:50 +0200
Subject: Spack package for HPCToolkit  (#1892)

* Spack package for HPCToolkit (performance analysis tool)

* Correction for PR comments, make flake8 happy

* update note / comments
---
 .../packages/hpctoolkit-externals/package.py       | 39 +++++++++++++++
 .../repos/builtin/packages/hpctoolkit/package.py   | 55 ++++++++++++++++++++++
 2 files changed, 94 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
 create mode 100644 var/spack/repos/builtin/packages/hpctoolkit/package.py

diff --git a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
new file mode 100644
index 0000000000..64b5d17851
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
@@ -0,0 +1,39 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class HpctoolkitExternals(Package):
+    """HPCToolkit performance analysis tool has many prerequisites and
+    HpctoolkitExternals package provides all these prerequisites."""
+
+    homepage = "http://hpctoolkit.org"
+
+    # Note: No precise release tags/branches provided
+    version('5.4',
+            git='https://github.com/HPCToolkit/hpctoolkit-externals.git',
+            commit='3d2953623357bb06e9a4b51eca90a4b039c2710e')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   'CXX=%s' % self.compiler.cxx]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../configure')
+            configure('--prefix=%s' % prefix, *options)
+            make('install')
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
new file mode 100644
index 0000000000..aac22ef829
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -0,0 +1,55 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Hpctoolkit(Package):
+    """HPCToolkit is an integrated suite of tools for measurement and analysis
+    of program performance on computers ranging from multicore desktop systems
+    to the nation's largest supercomputers. By using statistical sampling of
+    timers and hardware performance counters, HPCToolkit collects accurate
+    measurements of a program's work, resource consumption, and inefficiency
+    and attributes them to the full calling context in which they occur."""
+
+    homepage = "http://hpctoolkit.org"
+
+    # Note: No precise release tags/branches provided
+    version('5.4', git='https://github.com/HPCToolkit/hpctoolkit.git',
+            commit='d9ca2112762e5a06ea31b5295d793e4a83272d19')
+
+    variant('mpi', default=True, description='Enable MPI supoort')
+    variant('papi', default=True, description='Enable PAPI counter support')
+
+    depends_on('hpctoolkit-externals')
+    depends_on('papi', when='+papi')
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   'CXX=%s' % self.compiler.cxx,
+                   '--with-externals=%s' % spec['hpctoolkit-externals'].prefix]
+
+        if '+mpi' in spec:
+            options.extend(['MPICXX=%s' % spec['mpi'].mpicxx])
+
+        if '+papi' in spec:
+            options.extend(['--with-papi=%s' % spec['papi'].prefix])
+
+        # TODO: BG-Q configure option
+        with working_dir('spack-build', create=True):
+            configure = Executable('../configure')
+            configure('--prefix=%s' % prefix, *options)
+            make('install')
-- 
cgit v1.2.3-70-g09d2


From 2c701d372e775f0b8f58bf33a9a477ff3ba02cb9 Mon Sep 17 00:00:00 2001
From: Ivo Jimenez <ivo.jimenez@gmail.com>
Date: Tue, 4 Oct 2016 01:28:23 -0700
Subject: Adds lulesh package (#1887)

---
 var/spack/repos/builtin/packages/lulesh/package.py | 55 ++++++++++++++++++++
 .../builtin/packages/lulesh/remove_defaults.patch  | 60 ++++++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/lulesh/package.py
 create mode 100644 var/spack/repos/builtin/packages/lulesh/remove_defaults.patch

diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py
new file mode 100644
index 0000000000..e880d4fa14
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lulesh/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Lulesh(Package):
+    """Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics (LULESH)
+    """
+
+    homepage = "https://codesign.llnl.gov/lulesh.php"
+    url      = "https://codesign.llnl.gov/lulesh/lulesh2.0.3.tgz"
+
+    version("2.0.3", "336644a8750f71c7c6b9d2960976e7aa")
+
+    patch("remove_defaults.patch")
+
+    variant('mpip', default=False)
+
+    depends_on("mpi", type="build")
+    depends_on("mpip", when="+mpip")
+
+    def install(self, spec, prefix):
+        if '+mpip' in spec:
+            os.environ["LDFLAGS"] = " -lmpiP -ldwarf -lelf"
+
+            if os.uname()[4] == "x86_64":
+                os.environ["LDFLAGS"] += " -lunwind"
+
+        os.environ["CXX"] = spec['mpi'].mpicxx + " -DUSE_MPI=1"
+        os.environ["PREFIX"] = prefix
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch b/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch
new file mode 100644
index 0000000000..36cce25ba1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lulesh/remove_defaults.patch
@@ -0,0 +1,60 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,17 +1,9 @@
+ #default build suggestion of MPI + OPENMP with gcc on Livermore machines you might have to change the compiler name
+ 
+-SHELL = /bin/sh
+ .SUFFIXES: .cc .o
+ 
+ LULESH_EXEC = lulesh2.0
+ 
+-MPI_INC = /opt/local/include/openmpi
+-MPI_LIB = /opt/local/lib
+-
+-SERCXX = g++ -DUSE_MPI=0
+-MPICXX = mpig++ -DUSE_MPI=1
+-CXX = $(MPICXX)
+-
+ SOURCES2.0 = \
+ 	lulesh.cc \
+ 	lulesh-comm.cc \
+@@ -20,28 +12,6 @@
+ 	lulesh-init.cc
+ OBJECTS2.0 = $(SOURCES2.0:.cc=.o)
+ 
+-#Default build suggestions with OpenMP for g++
+-CXXFLAGS = -g -O3 -fopenmp -I. -Wall
+-LDFLAGS = -g -O3 -fopenmp
+-
+-#Below are reasonable default flags for a serial build
+-#CXXFLAGS = -g -O3 -I. -Wall
+-#LDFLAGS = -g -O3 
+-
+-#common places you might find silo on the Livermore machines.
+-#SILO_INCDIR = /opt/local/include
+-#SILO_LIBDIR = /opt/local/lib
+-#SILO_INCDIR = ./silo/4.9/1.8.10.1/include
+-#SILO_LIBDIR = ./silo/4.9/1.8.10.1/lib
+-
+-#If you do not have silo and visit you can get them at:
+-#silo:  https://wci.llnl.gov/codes/silo/downloads.html
+-#visit: https://wci.llnl.gov/codes/visit/download.html
+-
+-#below is and example of how to make with silo, hdf5 to get vizulization by default all this is turned off.  All paths are Livermore specific.
+-#CXXFLAGS = -g -DVIZ_MESH -I${SILO_INCDIR} -Wall -Wno-pragmas
+-#LDFLAGS = -g -L${SILO_LIBDIR} -Wl,-rpath -Wl,${SILO_LIBDIR} -lsiloh5 -lhdf5
+-
+ .cc.o: lulesh.h
+ 	@echo "Building $<"
+ 	$(CXX) -c $(CXXFLAGS) -o $@  $<
+@@ -56,6 +26,7 @@
+        /bin/rm -f *.o *~ $(OBJECTS) $(LULESH_EXEC)
+ 	/bin/rm -rf *.dSYM
+ 
+-tar: clean
+-	cd .. ; tar cvf lulesh-2.0.tar LULESH-2.0 ; mv lulesh-2.0.tar LULESH-2.0
+-
++install: lulesh2.0
++	@echo "Installing"
++	mkdir -p $(PREFIX)/bin
++	install --mode=755 lulesh2.0 $(PREFIX)/bin/
-- 
cgit v1.2.3-70-g09d2


From d36028cff4cc051eee0f40332ef3858b05411738 Mon Sep 17 00:00:00 2001
From: Ivo Jimenez <ivo.jimenez@gmail.com>
Date: Tue, 4 Oct 2016 01:30:52 -0700
Subject: Adds mpip package (#1886)

---
 var/spack/repos/builtin/packages/mpip/package.py | 44 ++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/mpip/package.py

diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py
new file mode 100644
index 0000000000..78e1dca68a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpip/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Mpip(Package):
+    """mpiP: Lightweight, Scalable MPI Profiling"""
+    homepage = "http://mpip.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/mpip/mpiP/mpiP-3.4.1/mpiP-3.4.1.tar.gz"
+
+    version("3.4.1", "1168adc83777ac31d6ebd385823aabbd")
+
+    depends_on("libelf", type="build")
+    depends_on("libdwarf", type="build")
+    depends_on('libunwind', when=os.uname()[4] == "x86_64", type="build")
+    depends_on("mpi", type="build")
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix, "--without-f77")
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From 36c79e9df61b8a3dbddc6a456a3a5ce3cc7a073c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 4 Oct 2016 01:49:07 -0700
Subject: Fixes #1893: missing import

---
 lib/spack/spack/database.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 1adad5e90b..f73d3765c8 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -49,6 +49,7 @@ from llnl.util.filesystem import *
 from llnl.util.lock import *
 
 import spack.spec
+from spack.directory_layout import DirectoryLayoutError
 from spack.version import Version
 from spack.spec import *
 from spack.error import SpackError
-- 
cgit v1.2.3-70-g09d2


From 1d981ebd50fe9b24826fae565f133494d2e49242 Mon Sep 17 00:00:00 2001
From: Sergey Kosukhin <skosukhin@gmail.com>
Date: Tue, 4 Oct 2016 17:29:22 +0100
Subject: A set of tools used in climate modeling and numerical weather
 prediction. (#1317)

* Update grib-api: switched to cmake building system.

* Update harfbuzz: added pkg-config dependency.

* Update pango: added pkg-config dependency.

* Add libemos package.

* Add Magics (from ECMWF) package.

* Revert "Variant for building cdo without mpi (#1638)":
CDO does not use MPI.

This reverts commit 079d063c6d94be84974f1ddd6eb880e902c95b4a.

* Update CDO package: full featured implementation.

* Update magics: added python as build dependency.

* Update cdo: added disabling configuration options.
---
 var/spack/repos/builtin/packages/cdo/package.py    |  81 ++++++++++++++-
 .../repos/builtin/packages/grib-api/package.py     |  58 ++++++++---
 .../repos/builtin/packages/harfbuzz/package.py     |   1 +
 .../repos/builtin/packages/libemos/package.py      |  52 ++++++++++
 .../packages/magics/no_hardcoded_python.patch      |   5 +
 var/spack/repos/builtin/packages/magics/package.py | 115 +++++++++++++++++++++
 .../packages/magics/resolve_isnan_ambiguity.patch  |  73 +++++++++++++
 var/spack/repos/builtin/packages/pango/package.py  |   1 +
 8 files changed, 367 insertions(+), 19 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/libemos/package.py
 create mode 100644 var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
 create mode 100644 var/spack/repos/builtin/packages/magics/package.py
 create mode 100644 var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch

diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index 0a5ee60f7c..775dc31cf3 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -34,13 +34,84 @@ class Cdo(Package):
     version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
     version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2', url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
 
-    variant('mpi', default=True)
+    variant('szip', default=True, description='Enable szip compression for GRIB1')
+    variant('hdf5', default=False, description='Enable HDF5 support')
+    variant('netcdf', default=True, description='Enable NetCDF support')
+    variant('udunits2', default=True, description='Enable UDUNITS2 support')
+    variant('grib', default=True, description='Enable GRIB_API support')
+    variant('libxml2', default=True, description='Enable libxml2 support')
+    variant('proj', default=True, description='Enable PROJ library for cartographic projections')
+    variant('curl', default=True, description='Enable curl support')
+    variant('fftw', default=True, description='Enable support for fftw3')
+    variant('magics', default=True, description='Enable Magics library support')
 
-    depends_on('netcdf')
-    depends_on('netcdf+mpi', when='+mpi')
-    depends_on('netcdf~mpi', when='~mpi')
+    depends_on('szip', when='+szip')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('hdf5+threadsafe', when='+hdf5')
+    depends_on('udunits2', when='+udunits2')
+    depends_on('grib-api', when='+grib')
+    depends_on('libxml2', when='+libxml2')
+    depends_on('proj', when='+proj')
+    depends_on('curl', when='+curl')
+    depends_on('fftw', when='+fftw')
+    depends_on('magics', when='+magics') 
 
     def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
+        config_args = ["--prefix=" + prefix,
+                       "--enable-shared",
+                       "--enable-static"]
+
+        if '+szip' in spec:
+            config_args.append('--with-szlib=' + spec['szip'].prefix)
+        else:
+            config_args.append('--without-szlib')
+
+        if '+hdf5' in spec:
+            config_args.append('--with-hdf5=' + spec['hdf5'].prefix)
+        else:
+            config_args.append('--without-hdf5')
+
+        if '+netcdf' in spec:
+            config_args.append('--with-netcdf=' + spec['netcdf'].prefix)
+        else:
+            config_args.append('--without-netcdf')
+
+        if '+udunits2' in spec:
+            config_args.append('--with-udunits2=' + spec['udunits2'].prefix)
+        else:
+            config_args.append('--without-udunits2')
+
+        if '+grib' in spec:
+            config_args.append('--with-grib_api=' + spec['grib-api'].prefix)
+        else:
+            config_args.append('--without-grib_api')
+
+        if '+libxml2' in spec:
+            config_args.append('--with-libxml2=' + spec['libxml2'].prefix)
+        else:
+            config_args.append('--without-libxml2')
+
+        if '+proj' in spec:
+            config_args.append('--with-proj=' + spec['proj'].prefix)
+        else:
+            config_args.append('--without-proj')
+
+        if '+curl' in spec:
+            config_args.append('--with-curl=' + spec['curl'].prefix)
+        else:
+            config_args.append('--without-curl')
+
+        if '+fftw' in spec:
+            config_args.append('--with-fftw3')
+        else:
+            config_args.append('--without-fftw3')
+
+        if '+magics' in spec:
+            config_args.append('--with-magics=' + spec['magics'].prefix)
+        else:
+            config_args.append('--without-magics')
+
+        configure(*config_args)
+
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
index 50164a6144..8b81e14a27 100644
--- a/var/spack/repos/builtin/packages/grib-api/package.py
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -26,25 +26,55 @@ from spack import *
 
 
 class GribApi(Package):
-    """The ECMWF GRIB API is an application program interface accessible from C,
-       FORTRAN and Python programs developed for encoding and decoding WMO
+    """The ECMWF GRIB API is an application program interface accessible from
+       C, FORTRAN and Python programs developed for encoding and decoding WMO
        FM-92 GRIB edition 1 and edition 2 messages."""
 
     homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz"
 
     version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
+    version('1.16.0', '8c7fdee03344e4379d400ae20976a460')
 
-    depends_on('netcdf')
-    depends_on('jasper')
+    variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library')
+    variant('jpeg', default=True, description='Enable jpeg 2000 for grib 2 decoding/encoding')
+    variant('png', default=False, description='Enable png for decoding/encoding')
+
+    depends_on('cmake', type='build')
+    depends_on('libpng', when='+png')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('jasper', when='+jpeg')
 
     def install(self, spec, prefix):
-        configure_options = [
-            '--prefix={0}'.format(prefix),
-            '--with-netcdf={0}'.format(spec['netcdf'].prefix),
-            '--with-jasper={0}'.format(spec['jasper'].prefix)
-        ]
-        configure(*configure_options)
-
-        make()
-        make('install')
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DBUILD_SHARED_LIBS=BOTH')
+
+        # We will add python support later.
+        options.append('-DENABLE_PYTHON=OFF')
+
+        # Disable FORTRAN interface if we don't have it.
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+jpeg' in spec:
+            options.append('-DENABLE_JPG=ON')
+            options.append('-DJASPER_PATH=%s' % spec['jasper'].prefix)
+        else:
+            options.append('-DENABLE_JPG=OFF')
+
+        if '+png' in spec:
+            options.append('-DENABLE_PNG=ON')
+        else:
+            options.append('-DENABLE_PNG=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index c8b4c7e645..7c98c2a96a 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -32,6 +32,7 @@ class Harfbuzz(Package):
 
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
+    depends_on("pkg-config", type="build")
     depends_on("glib")
     depends_on("icu4c")
     depends_on("freetype")
diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py
new file mode 100644
index 0000000000..0275c7ede9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libemos/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libemos(Package):
+    """The Interpolation library (EMOSLIB) includes Interpolation software and
+       BUFR & CREX encoding/decoding routines."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/EMOS/Emoslib"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz"
+
+    version('4.4.2', 'f15a9aff0f40861f3f046c9088197376')
+
+    depends_on('cmake', type='build')
+    depends_on('grib-api')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        options.append('-DGRIB_API_PATH=%s' % spec['grib_api'].prefix)
+
+        # To support long pathnames that spack generates
+        options.append('-DCMAKE_Fortran_FLAGS=-ffree-line-length-none')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
new file mode 100644
index 0000000000..e2e2a5d1ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
@@ -0,0 +1,5 @@
+--- a/tools/xml2mv.py	2016-06-27 17:49:27.000000000 +0200
++++ a/tools/xml2mv.py	2016-09-13 16:25:17.246960456 +0200
+@@ -1 +1 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
new file mode 100644
index 0000000000..cd793ae051
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -0,0 +1,115 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Magics(Package):
+    """Magics is the latest generation of the ECMWF's Meteorological plotting
+       software MAGICS. Although completely redesigned in C++, it is intended
+       to be as backwards-compatible as possible with the Fortran interface."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473464/Magics-2.29.0-Source.tar.gz"
+
+    # Maintainers of Magics do not keep tarballs of minor releases. Once the
+    # next minor released is published the previous one becomes unavailable.
+    # That is why the preferred version is the latest stable one.
+    version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
+    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
+
+    # The patch changes the hardcoded path to python in shebang to enable the
+    # usage of the first python installation that appears in $PATH
+    patch('no_hardcoded_python.patch')
+
+    # The patch reorders includes and adds namespaces where necessary to
+    # resolve ambiguity of invocations of isnan and isinf functions. The
+    # patch is not needed since the version 2.29.1
+    patch('resolve_isnan_ambiguity.patch', when='@2.29.0')
+
+    variant('bufr', default=False, description='Enable BUFR support')
+    variant('netcdf', default=False, description='Enable NetCDF support')
+    variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
+    variant('metview', default=False, description='Enable metview support')
+    variant('qt', default=False, description='Enable metview support with qt')
+
+    depends_on('cmake', type='build')
+    depends_on('pkg-config', type='build')
+
+    # Currently python is only necessary to run
+    # building preprocessing scripts.
+    depends_on('python', type='build')
+    depends_on('grib-api')
+    depends_on('proj')
+    depends_on('boost')
+    depends_on('expat')
+    depends_on('pango', when='+cairo')
+    depends_on('netcdf-cxx', when='+netcdf')
+    depends_on('libemos', when='+bufr')
+    depends_on('qt', when='+metview+qt')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DENABLE_ODB=OFF')
+        options.append('-DENABLE_PYTHON=OFF')
+        options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix)
+        options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+        options.append('-DENABLE_TESTS=OFF')
+
+        if '+bufr' in spec:
+            options.append('-DENABLE_BUFR=ON')
+            options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
+        else:
+            options.append('-DENABLE_BUFR=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf-cxx'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+cairo' in spec:
+            options.append('-DENABLE_CAIRO=ON')
+        else:
+            options.append('-DENABLE_CAIRO=OFF')
+
+        if '+metview' in spec:
+            if '+qt' in spec:
+                options.append('-DENABLE_METVIEW=ON')
+                if spec['qt'].version.up_to(1) == '5':
+                    options.append('-DENABLE_QT5=ON')
+            else:
+                options.append('-DENABLE_METVIEW_NO_QT=ON')
+        else:
+            options.append('-DENABLE_METVIEW=OFF')
+
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
new file mode 100644
index 0000000000..54b96ae88e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
@@ -0,0 +1,73 @@
+--- a/src/common/Polyline.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/common/Polyline.cc	2016-09-14 13:31:35.784617803 +0200
+@@ -31,2 +30,0 @@
+-#include "TeCoord2D.h"
+-#include "TeGeometryAlgorithms.h"
+--- a/src/decoders/GribRegularInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribRegularInterpretor.cc	2016-09-14 13:43:41.673614590 +0200
+@@ -2083,2 +2083,2 @@
+-                            if (isnan(val1)) {
+-                                if (isnan(val2)) {
++                            if (std::isnan(val1)) {
++                                if (std::isnan(val2)) {
+@@ -2090 +2090 @@
+-                                if (isnan(val2)) {
++                                if (std::isnan(val2)) {
+@@ -2101 +2101 @@
+-                            if (isnan(val) || isinf(val) || isinf(-val)) {
++                            if (std::isnan(val) || std::isinf(val) || std::isinf(-val)) {
+@@ -2105 +2105 @@
+-                        if (isnan(val))
++                        if (std::isnan(val))
+--- a/src/decoders/GribSatelliteInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribSatelliteInterpretor.cc	2016-09-14 13:48:55.243699910 +0200
+@@ -33,5 +32,0 @@
+-#include "TeProjection.h"
+-#include "TeDataTypes.h"
+-#include "TeRasterParams.h"
+-#include "TeDecoderMemory.h"
+-#include "TeRasterRemap.h"
+--- a/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-09-14 13:52:37.481201085 +0200
+@@ -93 +93 @@
+-				if ( !isnan(*d) ) {
++				if ( !std::isnan(*d) ) {
+--- a/src/decoders/NetcdfOrcaInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfOrcaInterpretor.cc	2016-09-14 13:51:16.248650570 +0200
+@@ -210,2 +210,2 @@
+-							if ( isnan(val1) ) {
+-								if ( isnan(val2) ) {
++							if ( std::isnan(val1) ) {
++								if ( std::isnan(val2) ) {
+@@ -218 +218 @@
+-								if ( isnan(val2) ) {
++								if ( std::isnan(val2) ) {
+@@ -226 +226 @@
+-							if (isnan(val) || isinf(val) || isinf(-val) ) {
++							if (std::isnan(val) || std::isinf(val) || std::isinf(-val) ) {
+@@ -230 +230 @@
+-						if (isnan(val) ) val = missing;
++						if (std::isnan(val) ) val = missing;
+@@ -296 +296 @@
+-           if (isnan(value) ) 
++           if (std::isnan(value) ) 
+--- a/src/terralib/kernel/TeCentroid.cpp	2016-04-28 14:38:09.000000000 +0200
++++ b/src/terralib/kernel/TeCentroid.cpp	2016-09-14 14:17:31.675996554 +0200
+@@ -23,0 +24,2 @@
++#include "TeGeometryAlgorithms.h"
++
+@@ -30 +31,0 @@
+-#include "TeGeometryAlgorithms.h"
+--- a/src/terralib/kernel/TeDatabase.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeDatabase.h	2016-09-14 14:20:01.041100590 +0200
+@@ -33,0 +34 @@
++#include "TeGeometry.h"
+@@ -38 +38,0 @@
+-#include "TeGeometry.h"
+--- a/src/terralib/kernel/TeOverlayUtils.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeOverlayUtils.h	2016-09-14 14:21:51.649920405 +0200
+@@ -37,0 +38,2 @@
++#include "TeGeometry.h"
++
+@@ -44 +45,0 @@
+-#include "TeGeometry.h"
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 2da20e9dc2..75c4ac807d 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -38,6 +38,7 @@ class Pango(Package):
     version('1.36.8', '217a9a753006275215fa9fa127760ece')
     version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb')
 
+    depends_on("pkg-config", type="build")
     depends_on("harfbuzz")
     depends_on("cairo")
 
-- 
cgit v1.2.3-70-g09d2


From e9d4780bbc307f37e6385fc80c8fea1abaab5782 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 4 Oct 2016 09:40:28 -0700
Subject: Rework build environment and cc to use smaller RPATHs. (#1894)

- Fixed up dependency management so that:
  - build deps go in PATH and -I
  - link deps go in -L args
  - only *immediate* link deps are RPATH'd

The latter reduces the number of libraries that need to be added to
DT_NEEDED / LC_RPATH.  This removes redundant RPATHs to transitive
dependencies.
---
 lib/spack/env/cc                     | 32 ++++++++++++-----
 lib/spack/spack/build_environment.py | 23 ++++++++++---
 lib/spack/spack/test/cc.py           | 66 ++++++++++++++++++++++++++++++++++++
 3 files changed, 108 insertions(+), 13 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6bb50d261..4b8922178a 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -266,22 +266,38 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
-            args=("-L$dep/lib" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib" "${args[@]}")
+            fi
         elif [[ $mode == ld ]]; then
-            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
-            args=("-L$dep/lib" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib" "${args[@]}")
+            fi
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode == ccld ]]; then
-            $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
-            args=("-L$dep/lib64" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib64" "${args[@]}")
+            fi
         elif [[ $mode == ld ]]; then
-            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
-            args=("-L$dep/lib64" "${args[@]}")
+            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            fi
+            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                args=("-L$dep/lib64" "${args[@]}")
+            fi
         fi
     fi
 done
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 9b5ed367d1..c3fa7418e8 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -77,6 +77,8 @@ SPACK_NO_PARALLEL_MAKE = 'SPACK_NO_PARALLEL_MAKE'
 #
 SPACK_ENV_PATH = 'SPACK_ENV_PATH'
 SPACK_DEPENDENCIES = 'SPACK_DEPENDENCIES'
+SPACK_RPATH_DEPS = 'SPACK_RPATH_DEPS'
+SPACK_LINK_DEPS = 'SPACK_LINK_DEPS'
 SPACK_PREFIX = 'SPACK_PREFIX'
 SPACK_INSTALL = 'SPACK_INSTALL'
 SPACK_DEBUG = 'SPACK_DEBUG'
@@ -254,9 +256,15 @@ def set_build_environment_variables(pkg, env, dirty=False):
     env.set_path(SPACK_ENV_PATH, env_paths)
 
     # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
-    dep_prefixes = [d.prefix
-                    for d in pkg.spec.traverse(root=False, deptype='build')]
+    dep_prefixes = [d.prefix for d in
+                    pkg.spec.traverse(root=False, deptype=('build', 'link'))]
     env.set_path(SPACK_DEPENDENCIES, dep_prefixes)
+
+    # These variables control compiler wrapper behavior
+    env.set_path(SPACK_RPATH_DEPS, [d.prefix for d in get_rpath_deps(pkg)])
+    env.set_path(SPACK_LINK_DEPS, [
+        d.prefix for d in pkg.spec.traverse(root=False, deptype=('link'))])
+
     # Add dependencies to CMAKE_PREFIX_PATH
     env.set_path('CMAKE_PREFIX_PATH', dep_prefixes)
 
@@ -288,8 +296,8 @@ def set_build_environment_variables(pkg, env, dirty=False):
                 env.remove_path('PATH', p)
 
     # Add bin directories from dependencies to the PATH for the build.
-    bin_dirs = reversed(
-        filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+    bin_dirs = reversed(filter(os.path.isdir, [
+        '%s/bin' % d.prefix for d in pkg.spec.dependencies(deptype='build')]))
     for item in bin_dirs:
         env.prepend_path('PATH', item)
 
@@ -382,10 +390,15 @@ def set_module_variables_for_package(pkg, module):
     m.dso_suffix = dso_suffix
 
 
+def get_rpath_deps(pkg):
+    """We only need to RPATH immediate dependencies."""
+    return pkg.spec.dependencies(deptype='link')
+
+
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""
     rpaths = [pkg.prefix.lib, pkg.prefix.lib64]
-    deps = pkg.spec.dependencies(deptype='link')
+    deps = get_rpath_deps(pkg)
     rpaths.extend(d.prefix.lib for d in deps
                   if os.path.isdir(d.prefix.lib))
     rpaths.extend(d.prefix.lib64 for d in deps
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3e4bb31d2..73c711724c 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -223,6 +223,8 @@ class CompilerTest(unittest.TestCase):
     def test_dep_include(self):
         """Ensure a single dependency include directory is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
         self.check_cc('dump-args', test_command,
                       self.realcc + ' ' +
                       '-Wl,-rpath,' + self.prefix + '/lib ' +
@@ -233,6 +235,8 @@ class CompilerTest(unittest.TestCase):
     def test_dep_lib(self):
         """Ensure a single dependency RPATH is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
         self.check_cc('dump-args', test_command,
                       self.realcc + ' ' +
                       '-Wl,-rpath,' + self.prefix + '/lib ' +
@@ -241,10 +245,34 @@ class CompilerTest(unittest.TestCase):
                       '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
                       ' '.join(test_command))
 
+    def test_dep_lib_no_rpath(self):
+        """Ensure a single dependency link flag is added with no dep RPATH."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
+    def test_dep_lib_no_lib(self):
+        """Ensure a single dependency RPATH is added with no -L."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
+
     def test_all_deps(self):
         """Ensure includes and RPATHs for all deps are added. """
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
             self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         # This is probably more constrained than it needs to be; it
         # checks order within prepended args and doesn't strictly have
@@ -273,6 +301,8 @@ class CompilerTest(unittest.TestCase):
         """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
             self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         self.check_ld('dump-args', test_command,
                       'ld ' +
@@ -290,10 +320,46 @@ class CompilerTest(unittest.TestCase):
 
                       ' '.join(test_command))
 
+    def test_ld_deps_no_rpath(self):
+        """Ensure SPACK_RPATH_DEPS controls RPATHs for ld."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-L' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+
+    def test_ld_deps_no_link(self):
+        """Ensure SPACK_LINK_DEPS controls -L for ld."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-rpath ' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+
     def test_ld_deps_reentrant(self):
         """Make sure ld -r is handled correctly on OS's where it doesn't
            support rpaths."""
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([self.dep1])
+        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
 
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
         reentrant_test_command = ['-r'] + test_command
-- 
cgit v1.2.3-70-g09d2


From 7806fded3e7e90aeb0d864ab76545cc57fbe2b03 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 4 Oct 2016 13:47:25 -0500
Subject: Update documentation URL after switch to readthedocs (#1901)

---
 var/spack/repos/builtin/packages/cuda/package.py         |  2 +-
 var/spack/repos/builtin/packages/daal/package.py         |  2 +-
 .../builtin/packages/intel-parallel-studio/package.py    |  2 +-
 var/spack/repos/builtin/packages/intel/package.py        |  2 +-
 var/spack/repos/builtin/packages/ipp/package.py          |  2 +-
 var/spack/repos/builtin/packages/mkl/package.py          |  2 +-
 var/spack/repos/builtin/packages/pgi/package.py          |  2 +-
 var/spack/repos/builtin/packages/turbomole/package.py    | 16 ++++++++--------
 8 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 558535bec6..36cf3058d7 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -39,7 +39,7 @@ class Cuda(Package):
     Type, select runfile and click Download. Spack will search your
     current directory for this file. Alternatively, add this file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html.
 
     Note: This package does not currently install the drivers necessary
     to run CUDA. These will need to be installed manually. See:
diff --git a/var/spack/repos/builtin/packages/daal/package.py b/var/spack/repos/builtin/packages/daal/package.py
index e13dd80e19..35cb6cbce8 100644
--- a/var/spack/repos/builtin/packages/daal/package.py
+++ b/var/spack/repos/builtin/packages/daal/package.py
@@ -9,7 +9,7 @@ class Daal(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/daal"
 
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 5547bae71c..efa30f9305 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -11,7 +11,7 @@ class IntelParallelStudio(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index 26134a12ae..5b9c26df0e 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -77,7 +77,7 @@ class Intel(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
diff --git a/var/spack/repos/builtin/packages/ipp/package.py b/var/spack/repos/builtin/packages/ipp/package.py
index 2bd931d5bd..93c5284695 100644
--- a/var/spack/repos/builtin/packages/ipp/package.py
+++ b/var/spack/repos/builtin/packages/ipp/package.py
@@ -9,7 +9,7 @@ class Ipp(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "https://software.intel.com/en-us/intel-ipp"
 
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index b674876393..8a31858bf5 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -9,7 +9,7 @@ class Mkl(IntelInstaller):
 
     Note: You will have to add the download file to a
     mirror so that Spack can find it. For instructions on how to set up a
-    mirror, see http://software.llnl.gov/spack/mirrors.html.
+    mirror, see http://spack.readthedocs.io/en/latest/mirrors.html.
 
     To set the threading layer at run time set MKL_THREADING_LAYER
     variable to one of the following values: INTEL (default), SEQUENTIAL, PGI.
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index c58d563682..6fa8457dc9 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -36,7 +36,7 @@ class Pgi(Package):
     architecture) to the format: pgi-<version>.tar.gz. Spack will search your
     current directory for a file of this format. Alternatively, add this
     file to a mirror so that Spack can find it. For instructions on how to
-    set up a mirror, see http://software.llnl.gov/spack/mirrors.html"""
+    set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://www.pgroup.com/"
     url = "file://%s/pgi-16.3.tar.gz" % os.getcwd()
diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py
index 6ccce23f97..b2d7e90057 100644
--- a/var/spack/repos/builtin/packages/turbomole/package.py
+++ b/var/spack/repos/builtin/packages/turbomole/package.py
@@ -29,14 +29,14 @@ import subprocess
 
 class Turbomole(Package):
     """TURBOMOLE: Program Package for ab initio Electronic Structure
-       Calculations. NB: Requires a license to download."""
-
-    # NOTE: Turbomole requires purchase of a license to download. Go to the
-    # NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details.
-    # NOTE: Spack will search the current directory for this file. It is
-    # NOTE: probably best to add this file to a Spack mirror so that it can be
-    # NOTE: found from anywhere.  For information on setting up a Spack mirror
-    # NOTE: see http://software.llnl.gov/spack/mirrors.html
+    Calculations.
+
+    Note: Turbomole requires purchase of a license to download. Go to the
+    Turbomole home page, http://www.turbomole-gmbh.com, for details.
+    Spack will search the current directory for this file. It is
+    probably best to add this file to a Spack mirror so that it can be
+    found from anywhere.  For information on setting up a Spack mirror
+    see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://www.turbomole-gmbh.com/"
 
-- 
cgit v1.2.3-70-g09d2


From 544fa3eddb2e0e3830439204888a58a9c0e186e2 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 4 Oct 2016 12:37:57 -0700
Subject: Fix some documentation build warnings. (#1902)

- Fix issue with package_list.py regeneration confusing Sphinx.
- Add -E option to avoid caching and make Sphinx happy.
---
 lib/spack/docs/Makefile         |  2 +-
 lib/spack/docs/command_index.in |  3 +--
 lib/spack/docs/conf.py          | 23 +++++++++++------------
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/lib/spack/docs/Makefile b/lib/spack/docs/Makefile
index bdbdab7e8b..1b56959aad 100644
--- a/lib/spack/docs/Makefile
+++ b/lib/spack/docs/Makefile
@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -E
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
diff --git a/lib/spack/docs/command_index.in b/lib/spack/docs/command_index.in
index 94cdf38109..8c5c97dd9c 100644
--- a/lib/spack/docs/command_index.in
+++ b/lib/spack/docs/command_index.in
@@ -1,5 +1,4 @@
-.. _command_index:
-
+=================
 Command index
 =================
 
diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index ed3e5811bc..57469964ee 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -1,10 +1,7 @@
 # flake8: noqa
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov.
 # LLNL-CODE-647188
 #
 # For details, see https://github.com/llnl/spack
@@ -70,9 +67,10 @@ os.environ['COLIFY_SIZE'] = '25x120'
 #
 # Generate package list using spack command
 #
-with open('package_list.rst', 'w') as plist_file:
-    subprocess.Popen(
-        [spack_root + '/bin/spack', 'package-list'], stdout=plist_file)
+if not os.path.exists('package_list.rst'):
+    with open('package_list.rst', 'w') as plist_file:
+        subprocess.Popen(
+            [spack_root + '/bin/spack', 'package-list'], stdout=plist_file)
 
 #
 # Find all the `spack-*` references and add them to a command index
@@ -85,11 +83,12 @@ for filename in glob('*rst'):
             if match:
                 command_names.append(match.group(1).strip())
 
-shutil.copy('command_index.in', 'command_index.rst')
-with open('command_index.rst', 'a') as index:
-    index.write('\n')
-    for cmd in sorted(command_names):
-        index.write('   * :ref:`%s`\n' % cmd)
+if not os.path.exists('command_index.rst'):
+    shutil.copy('command_index.in', 'command_index.rst')
+    with open('command_index.rst', 'a') as index:
+        index.write('\n')
+        for cmd in sorted(command_names):
+            index.write('   * :ref:`%s`\n' % cmd)
 
 
 # Run sphinx-apidoc
-- 
cgit v1.2.3-70-g09d2


From 9daafc32f127b0ce22dba40cbdfc8c139c2acf58 Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.s.kumbhar@gmail.com>
Date: Tue, 4 Oct 2016 23:40:35 +0200
Subject: Packages for Darshan I/O performance characterization tool from ANL
 (#1900)

---
 .../builtin/packages/darshan-runtime/package.py    | 65 ++++++++++++++++++++++
 .../repos/builtin/packages/darshan-util/package.py | 41 ++++++++++++++
 2 files changed, 106 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/darshan-runtime/package.py
 create mode 100644 var/spack/repos/builtin/packages/darshan-util/package.py

diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py
new file mode 100644
index 0000000000..640573fdc1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py
@@ -0,0 +1,65 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class DarshanRuntime(Package):
+    """Darshan (runtime) is a scalable HPC I/O characterization tool
+    designed to capture an accurate picture of application I/O behavior,
+    including properties such as patterns of access within files, with
+    minimum overhead. DarshanRuntime package should be installed on
+    systems where you intend to instrument MPI applications."""
+
+    homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
+    url = "ftp://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
+
+    version('3.1.0', '439d717323e6265b2612ed127886ae52')
+    version('3.0.0', '732577fe94238936268d74d7d74ebd08')
+
+    depends_on('mpi')
+    depends_on('zlib')
+
+    variant('slurm', default=False, description='Use Slurm Job ID')
+    variant('cobalt', default=False, description='Use Coblat Job Id')
+    variant('pbs', default=False, description='Use PBS Job Id')
+
+    def install(self, spec, prefix):
+
+        job_id = 'NONE'
+        if '+slurm' in spec:
+            job_id = 'SLURM_JOBID'
+        if '+cobalt' in spec:
+            job_id = 'COBALT_JOBID'
+        if '+pbs' in spec:
+            job_id = 'PBS_JOBID'
+
+        # TODO: BG-Q and other platform configure options
+        options = ['CC=%s' % spec['mpi'].mpicc,
+                   '--with-mem-align=8',
+                   '--with-log-path-by-env=DARSHAN_LOG_DIR_PATH',
+                   '--with-jobid-env=%s' % job_id,
+                   '--with-zlib=%s' % spec['zlib'].prefix]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../darshan-runtime/configure')
+            configure('--prefix=%s' % prefix, *options)
+            make()
+            make('install')
+
+    def setup_environment(self, spack_env, run_env):
+        # default path for log file, could be user or site specific setting
+        darshan_log_dir = '%s' % os.environ['HOME']
+        run_env.set('DARSHAN_LOG_DIR_PATH', darshan_log_dir)
diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py
new file mode 100644
index 0000000000..3446104a83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/darshan-util/package.py
@@ -0,0 +1,41 @@
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class DarshanUtil(Package):
+    """Darshan (util) is collection of tools for parsing and summarizing log
+    files produced by Darshan (runtime) instrumentation. This package is
+    typically installed on systems (front-end) where you intend to analyze
+    log files produced by Darshan (runtime)."""
+
+    homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
+    url = "ftp://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
+
+    version('3.1.0', '439d717323e6265b2612ed127886ae52')
+    version('3.0.0', '732577fe94238936268d74d7d74ebd08')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+
+        options = ['CC=%s' % self.compiler.cc,
+                   '--with-zlib=%s' % spec['zlib'].prefix]
+
+        with working_dir('spack-build', create=True):
+            configure = Executable('../darshan-util/configure')
+            configure('--prefix=%s' % prefix, *options)
+            make()
+            make('install')
-- 
cgit v1.2.3-70-g09d2


From bff1656a1a842b4de217129cc8cba732a30928a7 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 4 Oct 2016 15:36:37 -0700
Subject: Read-only locks should close fd before opening for write. (#1906)

- Fixes bad file descriptor error in lock acquire, #1904
- Fix bug introduced in previous PR #1857
- Backported fix from soon-to-be merged fine-grained DB locking branch.
---
 lib/spack/llnl/util/lock.py  |  8 ++++++++
 lib/spack/spack/test/lock.py | 29 +++++++++++++++++++++++++++++
 2 files changed, 37 insertions(+)

diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index b5e3a3a8f8..f5f53101ae 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -69,6 +69,14 @@ class Lock(object):
         start_time = time.time()
         while (time.time() - start_time) < timeout:
             try:
+                # If this is already open read-only and we want to
+                # upgrade to an exclusive write lock, close first.
+                if self._fd is not None:
+                    flags = fcntl.fcntl(self._fd, fcntl.F_GETFL)
+                    if op == fcntl.LOCK_EX and flags | os.O_RDONLY:
+                        os.close(self._fd)
+                        self._fd = None
+
                 if self._fd is None:
                     mode = os.O_RDWR if op == fcntl.LOCK_EX else os.O_RDONLY
                     self._fd = os.open(self._file_path, mode)
diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py
index fb96539897..32cbe13ce1 100644
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -157,6 +157,35 @@ class LockTest(unittest.TestCase):
             self.acquire_read, self.acquire_read, self.acquire_read,
             self.timeout_write, self.timeout_write)
 
+    #
+    # Test that read can be upgraded to write.
+    #
+    def test_upgrade_read_to_write(self):
+        # ensure lock file exists the first time, so we open it read-only
+        # to begin wtih.
+        touch(self.lock_path)
+
+        lock = Lock(self.lock_path)
+        self.assertTrue(lock._reads == 0)
+        self.assertTrue(lock._writes == 0)
+
+        lock.acquire_read()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 0)
+
+        lock.acquire_write()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 1)
+
+        lock.release_write()
+        self.assertTrue(lock._reads == 1)
+        self.assertTrue(lock._writes == 0)
+
+        lock.release_read()
+        self.assertTrue(lock._reads == 0)
+        self.assertTrue(lock._writes == 0)
+        self.assertTrue(lock._fd is None)
+
     #
     # Longer test case that ensures locks are reusable. Ordering is
     # enforced by barriers throughout -- steps are shown with numbers.
-- 
cgit v1.2.3-70-g09d2