Merge branch 'develop' of https://github.com/LLNL/spack into packages/swift_durham

14 files changed, 260 insertions, 42 deletions

diff --git a/var/spack/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 260dcbe851..9e0452ba6f 100644
--- a/var/spack/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -1,15 +1,18 @@
 import os
 
 from spack import *
+
+
 class Adios(Package):
-    """The Adaptable IO System (ADIOS) provides a simple, 
-        flexible way for scientists to describe the 
-        data in their code that may need to be written, 
-        read, or processed outside of the running simulation
     """
-    
+    The Adaptable IO System (ADIOS) provides a simple,
+    flexible way for scientists to describe the
+    data in their code that may need to be written,
+    read, or processed outside of the running simulation
+    """
+
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url      = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+    url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
 
     version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
 
@@ -22,13 +25,13 @@ class Adios(Package):
     depends_on('mxml')
 
     def install(self, spec, prefix):
-        configure_args = ["--prefix=%s" % prefix, 
-                          "--with-mxml=%s" % spec['mxml'].prefix, 
+        configure_args = ["--prefix=%s" % prefix,
+                          "--with-mxml=%s" % spec['mxml'].prefix,
                           "--with-hdf5=%s" % spec['hdf5'].prefix,
                           "--with-netcdf=%s" % os.environ["NETCDF_DIR"],
                           "--with-infiniband=no",
-                          "MPICC=cc","MPICXX=CC","MPIFC=ftn",
-                          "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"] 
+                          "MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
+                          "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
 
         if spec.satisfies('%gcc'):
             configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index e3de6ee5a1..79570205fa 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Curl(Package):
     """cURL is an open source command line tool and library for
     transferring data with URL syntax"""
@@ -31,6 +32,7 @@ class Curl(Package):
     homepage = "http://curl.haxx.se"
     url      = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
 
+    version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
     version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
     version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148')
     version('7.45.0', '62c1a352b28558f25ba6209214beadc8')
diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index 4b05864a1e..a9ebd6d42f 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -23,23 +23,44 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import llnl.util.tty as tty
+
 
 class Emacs(Package):
     """The Emacs programmable text editor."""
+
     homepage = "https://www.gnu.org/software/emacs"
     url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
 
     version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
 
+    variant('X', default=True, description="Enable a X toolkit (GTK+)")
+    variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)")
+
     depends_on('ncurses')
-    # Emacs also depends on:
-    #     GTK or other widget library
-    #     libtiff, png, etc.
-    # For now, we assume the system provides all that stuff.
-    # For Ubuntu 14.04 LTS:
-    #     sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev
+    depends_on('libtiff', when='+X')
+    depends_on('libpng', when='+X')
+    depends_on('libxpm', when='+X')
+    depends_on('giflib', when='+X')
+    depends_on('gtkplus', when='+X+gtkplus')
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
+        args = []
+        if '+X' in spec:
+            if '+gtkplus' in spec:
+                toolkit = 'gtk{0}'.format(spec['gtkplus'].version.up_to(1))
+            else:
+                toolkit = 'no'
+            args = [
+                '--with-x',
+                '--with-x-toolkit={0}'.format(toolkit)
+            ]
+        else:
+            args = ['--without-x']
+            if '+gtkplus' in spec:
+                tty.warn('The variant +gtkplus is ignored if ~X is selected.')
+
+        configure('--prefix={0}'.format(prefix), *args)
+
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py
new file mode 100644
index 0000000000..7082384b9b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/giflib/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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 Giflib(Package):
+    """The GIFLIB project maintains the giflib service library, which has
+    been pulling images out of GIFs since 1989."""
+
+    homepage = "http://giflib.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
+
+    version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/glib/g_date_strftime.patch b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch
new file mode 100644
index 0000000000..532c743277
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch
@@ -0,0 +1,34 @@
+From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001
+From: coypu <coypu@sdf.org>
+Date: Wed, 2 Mar 2016 19:43:10 +0200
+Subject: [PATCH 2/2] gdate: Suppress string format literal warning
+
+Newer versions of GCC emit an error here, but we know it's safe.
+https://bugzilla.gnome.org/761550
+---
+ glib/gdate.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/glib/gdate.c b/glib/gdate.c
+index 4aece02..92c34d2 100644
+--- a/glib/gdate.c
++++ b/glib/gdate.c
+@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate     *d,
+  *
+  * Returns: number of characters written to the buffer, or 0 the buffer was too small
+  */
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wformat-nonliteral"
++
+ gsize     
+ g_date_strftime (gchar       *s, 
+                  gsize        slen, 
+@@ -2549,3 +2552,5 @@ g_date_strftime (gchar       *s,
+   return retval;
+ #endif
+ }
++
++#pragma GCC diagnostic pop
+-- 
+2.7.1
+
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index b146ea63d8..342a61a6a1 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -25,20 +25,24 @@
 from spack import *
 import sys
 
+
 class Glib(Package):
     """The GLib package contains a low-level libraries useful for
        providing data structure handling for C, portability wrappers
        and interfaces for such runtime functionality as an event loop,
        threads, dynamic loading and an object system."""
     homepage = "https://developer.gnome.org/glib/"
-    url      = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
+    url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
 
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
     depends_on("libffi")
     depends_on("zlib")
     depends_on("pkg-config")
-    depends_on('gettext', sys.platform=='darwin')
+    depends_on('gettext', sys.platform == 'darwin')
+
+    # The following patch is needed for gcc-6.1
+    patch('g_date_strftime.patch')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 69b52130e9..99d138dcff 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -22,8 +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
 ##############################################################################
+
 from spack import *
-import os
+
 
 class Julia(Package):
     """The Julia Language: A fresh approach to technical computing"""
@@ -32,10 +33,14 @@ class Julia(Package):
 
     version('master',
             git='https://github.com/JuliaLang/julia.git', branch='master')
+    version('release-0.4',
+            git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
+    version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
     version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
 
-    patch('gc.patch')
+    patch('gc.patch', when='@0.4:0.4.5')
+    patch('gc.patch', when='@release-0.4')
     patch('openblas.patch', when='@0.4:0.4.5')
 
     # Build-time dependencies:
@@ -92,25 +97,21 @@ class Julia(Package):
     depends_on("mpi")
 
     def install(self, spec, prefix):
-        if '@master' in spec:
-            # Julia needs to know the offset from a specific commit
-            git = which('git')
-            git('fetch', '--unshallow')
-
         # Explicitly setting CC, CXX, or FC breaks building libuv, one
         # of Julia's dependencies. This might be a Darwin-specific
         # problem. Given how Spack sets up compilers, Julia should
         # still use Spack's compilers, even if we don't specify them
         # explicitly.
-        options = [#"CC=cc",
-                   #"CXX=c++",
-                   #"FC=fc",
-                   #"USE_SYSTEM_ARPACK=1",
-                   #"USE_SYSTEM_FFTW=1",
-                   #"USE_SYSTEM_GMP=1",
-                   #"USE_SYSTEM_MPFR=1",
-                   #TODO "USE_SYSTEM_PCRE=1",
-                   "prefix=%s" % prefix]
+        options = [
+            # "CC=cc",
+            # "CXX=c++",
+            # "FC=fc",
+            # "USE_SYSTEM_ARPACK=1",
+            # "USE_SYSTEM_FFTW=1",
+            # "USE_SYSTEM_GMP=1",
+            # "USE_SYSTEM_MPFR=1",
+            # "USE_SYSTEM_PCRE=1",
+            "prefix=%s" % prefix]
         with open('Make.user', 'w') as f:
             f.write('\n'.join(options) + '\n')
         make()
diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py
new file mode 100644
index 0000000000..10ca8158c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxpm/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 Libxpm(Package):
+    """Xpm file format library"""
+
+    homepage = "https://www.x.org/"
+    url      = "https://www.x.org/archive//individual/lib/libXpm-3.5.11.tar.gz"
+
+    version('3.5.11', '7c67c878ee048206b070bc0b24154f04')
+    version('3.5.10', 'a70507638d74541bf30a771f1e5938bb')
+    version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6')
+    version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897')
+    version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index ea1844aea0..90670ee517 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -50,6 +50,11 @@ class Mpich(Package):
     provides('mpi@:1.3', when='@1:')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('MPICH_CC', spack_cc)
         spack_env.set('MPICH_CXX', spack_cxx)
         spack_env.set('MPICH_F77', spack_f77)
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 34bace10d6..da386445bb 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -191,6 +191,11 @@ class Mvapich2(Package):
             run_env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('MPICH_CC', spack_cc)
         spack_env.set('MPICH_CXX', spack_cxx)
         spack_env.set('MPICH_F77', spack_f77)
diff --git a/var/spack/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index f79251d312..254a5f1595 100644
--- a/var/spack/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -1,14 +1,15 @@
-import os
 from spack import *
 
+
 class Mxml(Package):
-    """Mini-XML is a small XML library that you can use to read and write XML 
-       and XML-like data files in your application without requiring large 
-       non-standard libraries
+    """
+    Mini-XML is a small XML library that you can use to read and write XML
+    and XML-like data files in your application without requiring large
+    non-standard libraries
     """
 
     homepage = "http://www.msweet.org"
-    url      = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
+    url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
 
     version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19')
     version('2.8', 'd85ee6d30de053581242c4a86e79a5d2')
@@ -16,11 +17,11 @@ class Mxml(Package):
     version('2.6', '68977789ae64985dddbd1a1a1652642e')
     version('2.5', 'f706377fba630b39fa02fd63642b17e5')
 
-    # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use) 
+    # module swap PrgEnv-intel PrgEnv-$COMP
+    # (Can use whatever compiler you want to use)
     # Case statement to change CC and CXX flags
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static')
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 3d1951ceee..e52ff1af87 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -24,12 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class NetcdfFortran(Package):
     """Fortran interface for NetCDF4"""
 
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
 
+    version('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72')
     version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
 
     depends_on('netcdf')
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 588d862d96..15c8eefe96 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -109,6 +109,11 @@ class Openmpi(Package):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)  # NOQA: ignore=E501
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
         spack_env.set('OMPI_CC', spack_cc)
         spack_env.set('OMPI_CXX', spack_cxx)
         spack_env.set('OMPI_FC', spack_fc)
diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py
new file mode 100644
index 0000000000..da3a65c22e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-protobuf/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 PyProtobuf(Package):
+    """Protocol buffers are Google's language-neutral, platform-neutral,
+    extensible mechanism for serializing structured data - think XML, but
+    smaller, faster, and simpler. You define how you want your data to be
+    structured once, then you can use special generated source code to easily
+    write and read your structured data to and from a variety of data streams
+    and using a variety of languages."""
+
+    homepage = 'https://developers.google.com/protocol-buffers/'
+    url      = 'https://pypi.python.org/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
+
+    version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
+    version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
+    version('2.5.0', '338813f3629d59e9579fed9035ecd457')
+    version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a')
+    version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
+
+    extends('python')
+
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))