Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases

Conflicts:
	lib/spack/spack/package.py

20 files changed, 371 insertions, 94 deletions

diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 9e0452ba6f..59e0a451a9 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -12,9 +12,9 @@ class Adios(Package):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+    url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
 
-    version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
+    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
new file mode 100644
index 0000000000..7400c3a56c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cdo/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 Cdo(Package):
+    """CDO is a collection of command line Operators to manipulate and analyse
+    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')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index b39b086396..bfb8764feb 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.6.0',    'aa40fbecf49d99c083415c2411d12db9')
     version('3.5.2',    '701386a1b5ec95f8d1075ecf96383e02')
     version('3.5.1',    'ca051f4a66375c89d1a524e726da0296')
     version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')
diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index 800e4b9d96..9b173bb0dd 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -35,6 +35,7 @@ class Flex(Package):
     version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
 
     depends_on("bison", type='build')
+    depends_on("m4", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index f87dae9f4e..65fef57559 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -23,7 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys
+import os
+import sys
+
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -37,7 +39,7 @@ class Hypre(Package):
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
     # hypre does not know how to build shared libraries on Darwin
-    variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
+    variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
     variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
@@ -46,21 +48,26 @@ class Hypre(Package):
     depends_on("lapack")
 
     def install(self, spec, prefix):
-        blas_dir = spec['blas'].prefix
-        lapack_dir = spec['lapack'].prefix
-        mpi_dir = spec['mpi'].prefix
-
-        os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
-        os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
-        os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
-
+        os.environ['CC'] = spec['mpi'].mpicc
+        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
         configure_args = [
-                "--prefix=%s" % prefix,
-                "--with-lapack-libs=lapack",
-                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
-                "--with-blas-libs=blas",
-                "--with-blas-lib-dirs=%s/lib" % blas_dir]
+            '--prefix=%s' % prefix,
+            '--with-lapack-libs=%s' % to_lib_name(
+                spec['lapack'].lapack_shared_lib),
+            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
+            '--with-blas-libs=%s' % to_lib_name(
+                spec['blas'].blas_shared_lib),
+            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+        ]
+
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
@@ -76,4 +83,12 @@ class Hypre(Package):
             configure(*configure_args)
 
             make()
+            if self.run_tests:
+                make("check")
+                make("test")
+                Executable(join_path('test', 'ij'))()
+                sstruct = Executable(join_path('test', 'struct'))
+                sstruct()
+                sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
+                        '-rhsone')
             make("install")
diff --git a/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch b/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch
new file mode 100644
index 0000000000..cbf79ff971
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch
@@ -0,0 +1,25 @@
+diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c
+index fa72a0e..1f4845f 100644
+--- a/src/libjasper/jpc/jpc_dec.c
++++ b/src/libjasper/jpc/jpc_dec.c
+@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile)
+	/* Apply an inverse intercomponent transform if necessary. */
+	switch (tile->cp->mctid) {
+	case JPC_MCT_RCT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;
+	case JPC_MCT_ICT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;
diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py
new file mode 100644
index 0000000000..f450c7d155
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jasper/package.py
@@ -0,0 +1,63 @@
+##############################################################################
+# 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 Jasper(Package):
+    """Library for manipulating JPEG-2000 images"""
+
+    homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
+    url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
+
+    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
+
+    variant('shared', default=True,
+            description='Builds shared versions of the libraries')
+    variant('debug', default=False,
+            description='Builds debug versions of the libraries')
+
+    depends_on('libjpeg-turbo')
+
+    # Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
+    # when certain JPEG-2000 files with an alpha channel are processed
+    # see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
+    patch('fix_alpha_channel_assert_fail.patch')
+
+    def install(self, spec, prefix):
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            '--mandir={0}'.format(spec.prefix.man),
+        ]
+
+        if '+shared' in spec:
+            configure_options.append('--enable-shared')
+
+        if '+debug' not in spec:
+            configure_options.append('--disable-debug')
+
+        configure(*configure_options)
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index 454e78d29c..6ea64f5313 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -9,7 +9,13 @@ 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://software.llnl.gov/spack/mirrors.html.
+
+    To set the threading layer at run time set MKL_THREADING_LAYER
+    variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+    To set interface layer at run time, use set the MKL_INTERFACE_LAYER
+    variable to LP64 or ILP64.
+    """
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
 
@@ -18,6 +24,11 @@ class Mkl(IntelInstaller):
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
 
+    # virtual dependency
+    provides('blas')
+    provides('lapack')
+    # TODO: MKL also provides implementation of Scalapack.
+
     def install(self, spec, prefix):
 
         self.intel_prefix = os.path.join(prefix, "pkg")
@@ -26,3 +37,28 @@ class Mkl(IntelInstaller):
         mkl_dir = os.path.join(self.intel_prefix, "mkl")
         for f in os.listdir(mkl_dir):
             os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, 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)
+
+        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)
+
+    def setup_environment(self, spack_env, env):
+        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 92c45c9b95..b85a6d2b94 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -23,7 +23,10 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys, glob
+import os
+import sys
+import glob
+
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -44,13 +47,11 @@ class Mumps(Package):
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
-
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
     depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
-    depends_on('lapack')
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
@@ -60,42 +61,52 @@ class Mumps(Package):
     # end before install
     # def patch(self):
     def write_makefile_inc(self):
-        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
-            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
+        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:  # NOQA: ignore=E501
+            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')  # NOQA: ignore=E501
 
-        makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
+        makefile_conf = ["LIBBLAS = %s" % to_link_flags(
+            self.spec['blas'].blas_shared_lib)
+        ]
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
-            makefile_conf.extend(
-                ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
-                 "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
-                                          join_lib,
-                                          join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
+            makefile_conf.extend([
+                "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
+                "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
+                                         join_lib,
+                                         join_lib.join(['esmumps',
+                                                        'scotch',
+                                                        'scotcherr']))
+            ])
+
             orderings.append('-Dscotch')
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
         if '+parmetis' in self.spec and '+metis' in self.spec:
-            libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
-            makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+            makefile_conf.extend([
+                "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                "LMETIS = -L%s -l%s -L%s -l%s" % (
+                    self.spec['parmetis'].prefix.lib, 'parmetis',
+                    self.spec['metis'].prefix.lib, 'metis')
+            ])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
-            makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
+            makefile_conf.extend([
+                "IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')
+            ])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
         # when building shared libs need -fPIC, otherwise
-        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1'
+        # can not be used when making a shared object; recompile with -fPIC
         fpic = '-fPIC' if '+shared' in self.spec else ''
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
@@ -104,7 +115,7 @@ class Mumps(Package):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # NOQA: ignore=E501
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -113,7 +124,6 @@ class Mumps(Package):
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O ' % fpic])
 
-
         if '+mpi' in self.spec:
             makefile_conf.extend(
                 ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
@@ -134,16 +144,17 @@ class Mumps(Package):
 
         if '+shared' in self.spec:
             if sys.platform == 'darwin':
-                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                # Building dylibs with mpif90 causes segfaults on 10.8 and
+                # 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # NOQA: ignore=E501
                     'RANLIB=echo'
                 ])
             else:
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # NOQA: ignore=E501
                     'RANLIB=echo'
                 ])
         else:
@@ -153,9 +164,8 @@ class Mumps(Package):
                 'RANLIB = ranlib'
             ])
 
-
-        makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
-                                          'Makefile.inc')
+        makefile_inc_template = join_path(
+            os.path.dirname(self.module.__file__), 'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
 
@@ -164,8 +174,6 @@ class Mumps(Package):
                 makefile_inc = '\n'.join(makefile_conf)
                 fh.write(makefile_inc)
 
-
-
     def install(self, spec, prefix):
         make_libs = []
 
@@ -189,15 +197,15 @@ class Mumps(Package):
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
 
-        if '~mpi' in spec:            
+        if '~mpi' in spec:
             lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
             lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
             install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
-            for f in glob.glob(join_path('libseq','*.h')):
+            for f in glob.glob(join_path('libseq', '*.h')):
                 install(f, prefix.include)
 
-        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
-        # FIXME: use something like numdiff to compare blessed output with the current
+        # FIXME: extend the tests to mpirun -np 2 when build with MPI
+        # FIXME: use something like numdiff to compare output files
         with working_dir('examples'):
             if '+float' in spec:
                 os.system('./ssimpletest < input_simpletest_real')
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 063d38e4f9..ad4ee59640 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -33,6 +33,7 @@ class Netcdf(Package):
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
 
+    version('4.4.1', '7843e35b661c99e1d49e60791d5072d8')
     version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
@@ -47,8 +48,10 @@ class Netcdf(Package):
 
     # Required for NetCDF-4 support
     depends_on("zlib")
-    depends_on("hdf5+mpi", when='+mpi')
-    depends_on("hdf5~mpi", when='~mpi')
+    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')
 
     def install(self, spec, prefix):
         # Environment variables
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index a8250a38de..f7733249cf 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -25,8 +25,10 @@
 from spack import *
 import sys
 
+
 class NetlibScalapack(Package):
-    """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
+    """ScaLAPACK is a library of high-performance linear algebra routines for
+    parallel distributed memory machines"""
 
     homepage = "http://www.netlib.org/scalapack/"
     url      = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
@@ -48,10 +50,22 @@ class NetlibScalapack(Package):
 
     def install(self, spec, prefix):
         options = [
-            "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
-            "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
-            "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK)
-            ]
+            "-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",
+        ]
+
+        # 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),
+        ])
 
         if '+fpic' in spec:
             options.extend([
@@ -66,16 +80,15 @@ class NetlibScalapack(Package):
             make()
             make("install")
 
-        # The shared libraries are not installed correctly on Darwin; correct this
+        # 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_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
-        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
+        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)]
+        spec.libraries = [join_path(spec.prefix.lib,
+                                    'libscalapack.%s' % lib_suffix)]
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index c1950a91ac..f96cb9b4cd 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -46,6 +46,7 @@ class PyH5py(Package):
     depends_on('hdf5@1.8.4:')
     depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', when='+mpi')
 
     # Build and runtime dependencies
     depends_on('py-numpy@1.6.1:', type=nolink)
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 6bc11a5e48..2febdac658 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -44,6 +44,7 @@ class PyNumpy(Package):
 
     extends('python')
     depends_on('py-nose', type='build')
+    depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 516b5c6cfe..bbb1e9c13a 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -53,6 +53,7 @@ class Python(Package):
 
     extendable = True
 
+    variant('tk',   default=False, description='Provide support for Tkinter')
     variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
     # From https://docs.python.org/2/c-api/unicode.html: Python's default
     # builds use a 16-bit type for Py_UNICODE and store Unicode values
@@ -68,6 +69,8 @@ class Python(Package):
     depends_on("ncurses")
     depends_on("sqlite")
     depends_on("zlib")
+    depends_on("tk",  when="+tk")
+    depends_on("tcl", when="+tk")
 
     def install(self, spec, prefix):
         # Need this to allow python build to find the Python installation.
@@ -77,24 +80,32 @@ class Python(Package):
         # Rest of install is pretty standard except setup.py needs to
         # be able to read the CPPFLAGS and LDFLAGS as it scans for the
         # library and headers to build
-        cppflags = ' -I'.join([
+        include_dirs = [
             spec['openssl'].prefix.include,  spec['bzip2'].prefix.include,
             spec['readline'].prefix.include, spec['ncurses'].prefix.include,
             spec['sqlite'].prefix.include,   spec['zlib'].prefix.include
-        ])
+        ]
 
-        ldflags = ' -L'.join([
+        library_dirs = [
             spec['openssl'].prefix.lib,  spec['bzip2'].prefix.lib,
             spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
             spec['sqlite'].prefix.lib,   spec['zlib'].prefix.lib
-        ])
+        ]
+
+        if '+tk' in spec:
+            include_dirs.extend([
+                spec['tk'].prefix.include, spec['tcl'].prefix.include
+            ])
+            library_dirs.extend([
+                spec['tk'].prefix.lib, spec['tcl'].prefix.lib
+            ])
 
         config_args = [
             "--prefix={0}".format(prefix),
             "--with-threads",
             "--enable-shared",
-            "CPPFLAGS=-I{0}".format(cppflags),
-            "LDFLAGS=-L{0}".format(ldflags)
+            "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)),
+            "LDFLAGS=-L{0}".format(" -L".join(library_dirs))
         ]
 
         if '+ucs4' in spec:
@@ -116,6 +127,25 @@ class Python(Package):
 
         self.filter_compilers(spec, prefix)
 
+    # TODO: Once better testing support is integrated, add the following tests
+    # https://wiki.python.org/moin/TkInter
+    #
+    #    if '+tk' in spec:
+    #        env['TK_LIBRARY']  = join_path(spec['tk'].prefix.lib,
+    #            'tk{0}'.format(spec['tk'].version.up_to(2)))
+    #        env['TCL_LIBRARY'] = join_path(spec['tcl'].prefix.lib,
+    #            'tcl{0}'.format(spec['tcl'].version.up_to(2)))
+    #
+    #        $ python
+    #        >>> import _tkinter
+    #
+    #        if spec.satisfies('@3:')
+    #            >>> import tkinter
+    #            >>> tkinter._test()
+    #        else:
+    #            >>> import Tkinter
+    #            >>> Tkinter._test()
+
     def filter_compilers(self, spec, prefix):
         """Run after install to tell the configuration files and Makefiles
         to use the compilers that Spack built the package with.
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 2cc89b843f..a71bfd8bd4 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -32,21 +32,20 @@ class SuiteSparse(Package):
     homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
     url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
 
-    version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
     version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
+    version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
 
-    # FIXME: (see below)
-    # variant('tbb', default=True, description='Build with Intel TBB')
+    variant('tbb', default=True, description='Build with Intel TBB')
 
     depends_on('blas')
     depends_on('lapack')
 
     depends_on('metis@5.1.0', when='@4.5.1:')
-    # FIXME:
     # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
     # flags does not seem to be used, which leads to linking errors on Linux.
-    # Try re-enabling in future versions.
-    # depends_on('tbb', when='+tbb')
+    depends_on('tbb', when='@4.5.3:+tbb')
+
+    patch('tbb_453.patch', when='@4.5.3')
 
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned.
@@ -73,20 +72,24 @@ class SuiteSparse(Package):
         ])
 
         # Intel TBB in SuiteSparseQR
-        if '+tbb' in spec:
+        if 'tbb' in spec:
             make_args.extend([
                 'SPQR_CONFIG=-DHAVE_TBB',
                 'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
             ])
 
-        # BLAS arguments require path to libraries
-        # FIXME: (blas/lapack always provide libblas and liblapack as aliases)
+        # 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)
         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
-            make_args.extend([
-                'BLAS=-lblas -lstdc++',
-                'LAPACK=-llapack'
-            ])
+            blas += ' -lstdc++'
+
+        make_args.extend([
+            'BLAS=%s' % blas,
+            'LAPACK=%s' % lapack
+        ])
 
         make('install', *make_args)
diff --git a/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch b/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch
new file mode 100644
index 0000000000..70241ed017
--- /dev/null
+++ b/var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch
@@ -0,0 +1,13 @@
+diff --git a/SPQR/Lib/Makefile b/SPQR/Lib/Makefile
+index eaade58..d0de852 100644
+--- a/SPQR/Lib/Makefile
++++ b/SPQR/Lib/Makefile
+@@ -13,7 +13,7 @@ ccode: all
+ include ../../SuiteSparse_config/SuiteSparse_config.mk
+ 
+ # SPQR depends on CHOLMOD, AMD, COLAMD, LAPACK, the BLAS and SuiteSparse_config
+-LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(LAPACK) $(BLAS)
++LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(TBB) $(LAPACK) $(BLAS)
+ 
+ # compile and install in SuiteSparse/lib
+ library:
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index a4d8b515bb..ef922314d8 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Tcl(Package):
     """Tcl (Tool Command Language) is a very powerful but easy to
        learn dynamic programming language, suitable for a very wide
@@ -34,9 +35,6 @@ class Tcl(Package):
        extensible."""
     homepage = "http://www.tcl.tk"
 
-    def url_for_version(self, version):
-        return 'http://prdownloads.sourceforge.net/tcl/tcl%s-src.tar.gz' % version
-
     version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
     version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304')
     version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f')
@@ -44,8 +42,18 @@ class Tcl(Package):
 
     depends_on('zlib')
 
+    def url_for_version(self, version):
+        base_url = 'http://prdownloads.sourceforge.net/tcl'
+        return '{0}/tcl{1}-src.tar.gz'.format(base_url, version)
+
+    def setup_environment(self, spack_env, env):
+        # When using Tkinter from within spack provided python+tk, python
+        # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
+        env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
+                self.spec.version.up_to(2))))
+
     def install(self, spec, prefix):
         with working_dir('unix'):
-            configure("--prefix=%s" % prefix)
+            configure("--prefix={0}".format(prefix))
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
index 988619df30..c98e964efa 100644
--- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py
+++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
@@ -24,11 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class TheSilverSearcher(Package):
     """Fast recursive grep alternative"""
     homepage = "http://geoff.greer.fm/ag/"
-    url      = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.30.0.tar.gz"
+    url      = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz"
 
+    version('0.32.0', '3fdfd5836924246073d5344257a06823')
     version('0.30.0', '95e2e7859fab1156c835aff7413481db')
 
     depends_on('pcre')
diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py
index 330e1c77f5..894d3af6cc 100644
--- a/var/spack/repos/builtin/packages/tk/package.py
+++ b/var/spack/repos/builtin/packages/tk/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Tk(Package):
     """Tk is a graphical user interface toolkit that takes developing
        desktop applications to a higher level than conventional
@@ -33,16 +34,24 @@ class Tk(Package):
        and more."""
     homepage = "http://www.tcl.tk"
 
-    def url_for_version(self, version):
-        return "http://prdownloads.sourceforge.net/tcl/tk%s-src.tar.gz" % version
-
+    version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
     version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221')
 
     depends_on("tcl")
 
+    def url_for_version(self, version):
+        base_url = "http://prdownloads.sourceforge.net/tcl"
+        return "{0}/tk{1}-src.tar.gz".format(base_url, version)
+
+    def setup_environment(self, spack_env, env):
+        # When using Tkinter from within spack provided python+tk, python
+        # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
+        env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format(
+                self.spec.version.up_to(2))))
+
     def install(self, spec, prefix):
         with working_dir('unix'):
-            configure("--prefix=%s" % prefix,
-                      "--with-tcl=%s" % spec['tcl'].prefix.lib)
+            configure("--prefix={0}".format(prefix),
+                      "--with-tcl={0}".format(spec['tcl'].prefix.lib))
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 56499af8d9..77589bb8f9 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -118,6 +118,7 @@ class Trilinos(Package):
         options.extend(std_cmake_args)
 
         mpi_bin = spec['mpi'].prefix.bin
+        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
         options.extend([
             '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@@ -131,10 +132,12 @@ class Trilinos(Package):
             '-DTPL_ENABLE_MPI:BOOL=ON',
             '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
             '-DTPL_ENABLE_BLAS=ON',
-            '-DBLAS_LIBRARY_NAMES=blas',  # FIXME: don't hardcode names
+            '-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
+                spec['blas'].blas_shared_lib),
             '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
             '-DTPL_ENABLE_LAPACK=ON',
-            '-DLAPACK_LIBRARY_NAMES=lapack',
+            '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
+                spec['lapack'].lapack_shared_lib),
             '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',