re-merged mainline develop

2016-05-27 13:13:19 -07:00
parent f49644cdea f6a0cd1bf8
commit 9dad7c2ace
27 changed files with 1241 additions and 802 deletions
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -25,8 +25,10 @@
 from spack import *
 import sys

+
 class Dealii(Package):
-    """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
+    """C++ software library providing well-documented tools to build finite
+    element codes for a broad variety of PDEs."""
    homepage = "https://www.dealii.org"
    url      = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"

@@ -36,7 +38,7 @@ class Dealii(Package):
    variant('mpi',      default=True,  description='Compile with MPI')
    variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
    variant('doc',      default=False, description='Compile with documentation')
-    variant('gsl' ,     default=True,  description='Compile with GSL')
+    variant('gsl',      default=True,  description='Compile with GSL')
    variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
    variant('metis',    default=True,  description='Compile with Metis')
    variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
@@ -47,38 +49,40 @@ class Dealii(Package):
    variant('trilinos', default=True,  description='Compile with Trilinos (only with MPI)')

    # required dependencies, light version
-    depends_on ("blas")
-    # Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
-    # require at least 1.59
-    depends_on ("boost@1.59.0:",     when='~mpi')
-    depends_on ("boost@1.59.0:+mpi", when='+mpi')
-    depends_on ("bzip2")
-    depends_on ("cmake")
-    depends_on ("lapack")
-    depends_on ("muparser")
-    depends_on ("suite-sparse")
-    depends_on ("tbb")
-    depends_on ("zlib")
+    depends_on("blas")
+    # Boost 1.58 is blacklisted, see
+    # https://github.com/dealii/dealii/issues/1591
+    # Require at least 1.59
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams",     when='~mpi')  # NOQA: ignore=E501
+    depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi')  # NOQA: ignore=E501
+    depends_on("bzip2")
+    depends_on("cmake")
+    depends_on("lapack")
+    depends_on("muparser")
+    depends_on("suite-sparse")
+    depends_on("tbb")
+    depends_on("zlib")

    # optional dependencies
-    depends_on ("mpi", when="+mpi")
-    depends_on ("arpack-ng+mpi", when='+arpack+mpi')
-    depends_on ("doxygen", when='+doc')
-    depends_on ("gsl", when='@8.5.0:+gsl')
-    depends_on ("gsl", when='@dev+gsl')
-    depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
-    depends_on ("metis@5:", when='+metis')
-    depends_on ("netcdf+mpi", when="+netcdf+mpi")
-    depends_on ("netcdf-cxx", when='+netcdf+mpi')
-    depends_on ("oce", when='+oce')
-    depends_on ("p4est", when='+p4est+mpi')
-    depends_on ("petsc+mpi", when='+petsc+mpi')
-    depends_on ("slepc", when='+slepc+petsc+mpi')
-    depends_on ("trilinos", when='+trilinos+mpi')
+    depends_on("mpi",              when="+mpi")
+    depends_on("arpack-ng+mpi",    when='+arpack+mpi')
+    depends_on("doxygen+graphviz", when='+doc')
+    depends_on("graphviz",         when='+doc')
+    depends_on("gsl",              when='@8.5.0:+gsl')
+    depends_on("gsl",              when='@dev+gsl')
+    depends_on("hdf5+mpi",         when='+hdf5+mpi')
+    depends_on("metis@5:",         when='+metis')
+    depends_on("netcdf+mpi",       when="+netcdf+mpi")
+    depends_on("netcdf-cxx",       when='+netcdf+mpi')
+    depends_on("oce",              when='+oce')
+    depends_on("p4est",            when='+p4est+mpi')
+    depends_on("petsc+mpi",        when='+petsc+mpi')
+    depends_on("slepc",            when='+slepc+petsc+mpi')
+    depends_on("trilinos",         when='+trilinos+mpi')

    # developer dependnecies
-    depends_on ("numdiff", when='@dev')
-    depends_on ("astyle@2.04", when='@dev')
+    depends_on("numdiff",     when='@dev')
+    depends_on("astyle@2.04", when='@dev')

    def install(self, spec, prefix):
        options = []
@@ -96,17 +100,17 @@ def install(self, spec, prefix):
            '-DDEAL_II_WITH_THREADS:BOOL=ON',
            '-DBOOST_DIR=%s' % spec['boost'].prefix,
            '-DBZIP2_DIR=%s' % spec['bzip2'].prefix,
-            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead of Spack's.
-            # Be more specific to avoid this.
-            # Note that both lapack and blas are provided in -DLAPACK_XYZ variables
+            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead
+            # of Spack's. Be more specific to avoid this.
+            # Note that both lapack and blas are provided in -DLAPACK_XYZ.
            '-DLAPACK_FOUND=true',
            '-DLAPACK_INCLUDE_DIRS=%s;%s' %
                (spec['lapack'].prefix.include,
                 spec['blas'].prefix.include),
            '-DLAPACK_LIBRARIES=%s;%s' %
-                (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
-                 join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)),    # FIXME don't hardcode names
-            '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
+                (spec['lapack'].lapack_shared_lib,
+                 spec['blas'].blas_shared_lib),
+            '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
            '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
            '-DTBB_DIR=%s' % spec['tbb'].prefix,
            '-DZLIB_DIR=%s' % spec['zlib'].prefix
@@ -116,33 +120,34 @@ def install(self, spec, prefix):
        if '+mpi' in spec:
            options.extend([
                '-DDEAL_II_WITH_MPI:BOOL=ON',
-                '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
-                '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-                '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
            ])
        else:
            options.extend([
                '-DDEAL_II_WITH_MPI:BOOL=OFF',
            ])

-        # Optional dependencies for which librariy names are the same as CMake variables
-        for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'):
+        # Optional dependencies for which librariy names are the same as CMake
+        # variables:
+        for library in ('gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'):  # NOQA: ignore=E501
            if library in spec:
                options.extend([
-                    '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
-                    '-DDEAL_II_WITH_{library}:BOOL=ON'.format(library=library.upper())
+                    '-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
+                    '-DDEAL_II_WITH_%s:BOOL=ON' % library.upper()
                ])
            else:
                options.extend([
-                    '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper())
+                    '-DDEAL_II_WITH_%s:BOOL=OFF' % library.upper()
                ])

        # doxygen
        options.extend([
-            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'),
+            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' %
+            ('ON' if '+doc' in spec else 'OFF'),
        ])

-
        # arpack
        if '+arpack' in spec:
            options.extend([
@@ -160,11 +165,13 @@ def install(self, spec, prefix):
            options.extend([
                '-DNETCDF_FOUND=true',
                '-DNETCDF_LIBRARIES=%s;%s' %
-                    (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
-                    join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
+                    (join_path(spec['netcdf-cxx'].prefix.lib,
+                               'libnetcdf_c++.%s' % dsuf),
+                     join_path(spec['netcdf'].prefix.lib,
+                               'libnetcdf.%s' % dsuf)),
                '-DNETCDF_INCLUDE_DIRS=%s;%s' %
                    (spec['netcdf-cxx'].prefix.include,
-                    spec['netcdf'].prefix.include),
+                     spec['netcdf'].prefix.include),
            ])
        else:
            options.extend([
@@ -200,7 +207,7 @@ def install(self, spec, prefix):
        with working_dir('examples/step-3'):
            cmake('.')
            make('release')
-            make('run',parallel=False)
+            make('run', parallel=False)

        # An example which uses Metis + PETSc
        # FIXME: switch step-18 to MPI
@@ -213,7 +220,7 @@ def install(self, spec, prefix):
            if '^petsc' in spec and '^metis' in spec:
                cmake('.')
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

        # take step-40 which can use both PETSc and Trilinos
        # FIXME: switch step-40 to MPI run
@@ -222,43 +229,49 @@ def install(self, spec, prefix):
            print('========== Step-40 PETSc ============')
            print('=====================================')
            # list the number of cycles to speed up
-            filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
+            filter_file(r'(const unsigned int n_cycles = 8;)',
+                        ('const unsigned int n_cycles = 2;'), 'step-40.cc')
            cmake('.')
            if '^petsc' in spec:
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

            print('=====================================')
            print('========= Step-40 Trilinos ==========')
            print('=====================================')
            # change Linear Algebra to Trilinos
-            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',  ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
+            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',
+                        ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
            if '^trilinos+hypre' in spec:
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

            print('=====================================')
            print('=== Step-40 Trilinos SuperluDist ====')
            print('=====================================')
            # change to direct solvers
-            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')
-            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',  (''), 'step-40.cc')
-            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  (''), 'step-40.cc')
-            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  (''), 'step-40.cc')
-            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
+            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')  # NOQA: ignore=E501
+            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
+                        (''), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',
+                        (''), 'step-40.cc')
+            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',
+                        (''), 'step-40.cc')
+            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')  # NOQA: ignore=E501
            filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
            if '^trilinos+superlu-dist' in spec:
                make('release')
-                make('run',paralle=False)
+                make('run', paralle=False)

            print('=====================================')
            print('====== Step-40 Trilinos MUMPS =======')
            print('=====================================')
            # switch to Mumps
-            filter_file(r'(Amesos_Superludist)',  ('Amesos_Mumps'), 'step-40.cc')
+            filter_file(r'(Amesos_Superludist)',
+                        ('Amesos_Mumps'), 'step-40.cc')
            if '^trilinos+mumps' in spec:
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

        print('=====================================')
        print('============ Step-36 ================')
@@ -267,7 +280,7 @@ def install(self, spec, prefix):
            if 'slepc' in spec:
                cmake('.')
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

        print('=====================================')
        print('============ Step-54 ================')
@@ -276,7 +289,7 @@ def install(self, spec, prefix):
            if 'oce' in spec:
                cmake('.')
                make('release')
-                make('run',parallel=False)
+                make('run', parallel=False)

    def setup_environment(self, spack_env, env):
        env.set('DEAL_II_DIR', self.prefix)
--- a/var/spack/repos/builtin/packages/launchmon/package.py
+++ b/var/spack/repos/builtin/packages/launchmon/package.py
@@ -24,29 +24,19 @@
 ##############################################################################
 from spack import *

+
 class Launchmon(Package):
    """Software infrastructure that enables HPC run-time tools to
       co-locate tool daemons with a parallel job."""
-    homepage = "http://sourceforge.net/projects/launchmon"
-    url      = "http://downloads.sourceforge.net/project/launchmon/launchmon/1.0.1%20release/launchmon-1.0.1.tar.gz"
+    homepage = "https://github.com/LLNL/LaunchMON"
+    url      = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz"  # NOQA: ignore=E501

-    version('1.0.1', '2f12465803409fd07f91174a4389eb2b')
-    version('1.0.1-2', git='https://github.com/llnl/launchmon.git', commit='ff7e22424b8f375318951eb1c9282fcbbfa8aadf')
+    version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a')

    depends_on('autoconf')
    depends_on('automake')
    depends_on('libtool')

-
-    def patch(self):
-        # This patch makes libgcrypt compile correctly with newer gcc versions.
-        mf = FileFilter('tools/libgcrypt/tests/Makefile.in')
-        mf.filter(r'(basic_LDADD\s*=\s*.*)',     r'\1 -lgpg-error')
-        mf.filter(r'(tsexp_LDADD\s*=\s*.*)',     r'\1 -lgpg-error')
-        mf.filter(r'(keygen_LDADD\s*=\s*.*)',    r'\1 -lgpg-error')
-        mf.filter(r'(benchmark_LDADD\s*=\s*.*)', r'\1 -lgpg-error')
-
-
    def install(self, spec, prefix):
        configure(
            "--prefix=" + prefix,
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, shutil
+import os, glob


 class Llvm(Package):
@@ -46,7 +46,9 @@ class Llvm(Package):
    variant('libcxx', default=True, description="Build the LLVM C++ standard library")
    variant('compiler-rt', default=True, description="Build the LLVM compiler runtime, including sanitizers")
    variant('gold', default=True, description="Add support for LTO with the gold linker plugin")
-
+    variant('shared_libs', default=False, description="Build all components as shared libraries, faster, less memory to build, less stable")
+    variant('link_dylib', default=False, description="Build and link the libLLVM shared library rather than static")
+    variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend")

    # Build dependency
    depends_on('cmake @2.8.12.2:')
@@ -257,6 +259,28 @@ def install(self, spec, prefix):
        if '+compiler-rt' not in spec:
            cmake_args.append('-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF')

+        if '+shared_libs' in spec:
+            cmake_args.append('-DBUILD_SHARED_LIBS:Bool=ON')
+
+        if '+link_dylib' in spec:
+            cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON')
+
+        if '+all_targets' not in spec: # all is default on cmake
+            targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+            if 'x86' in spec.architecture.lower():
+                targets.append('X86')
+            elif 'arm' in spec.architecture.lower():
+                targets.append('ARM')
+            elif 'aarch64' in spec.architecture.lower():
+                targets.append('AArch64')
+            elif 'sparc' in spec.architecture.lower():
+                targets.append('sparc')
+            elif ('ppc' in spec.architecture.lower() or
+                  'power' in spec.architecture.lower()):
+                targets.append('PowerPC')
+
+            cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
+
        if  '+clang' not in spec:
            if '+clang_extra' in spec:
                raise SpackException('The clang_extra variant requires the clang variant to be selected')
@@ -267,7 +291,5 @@ def install(self, spec, prefix):
            cmake(*cmake_args)
            make()
            make("install")
-            query_path = os.path.join('bin', 'clang-query')
-            # Manually install clang-query, because llvm doesn't...
-            if os.path.exists(query_path):
-                shutil.copy(query_path, os.path.join(prefix, 'bin'))
+            cp = which('cp')
+            cp('-a', 'bin/', prefix)
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,55 +24,61 @@
 ##############################################################################

 from spack import *
-import glob, sys, os
+import glob
+import sys
+import os
+

 class Metis(Package):
-    """
-    METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill
-    reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel
-    recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
-    """
+    """METIS is a set of serial programs for partitioning graphs, partitioning
+       finite element meshes, and producing fill reducing orderings for sparse
+       matrices. The algorithms implemented in METIS are based on the
+       multilevel recursive-bisection, multilevel k-way, and multi-constraint
+       partitioning schemes."""

-    homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
-    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
+    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
+    base_url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis"

-    version('5.1.0', '5465e67079419a69e0116de24fce58fe',
-            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
-    version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
-            url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
+    version('5.1.0', '5465e67079419a69e0116de24fce58fe')
+    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('idx64', default=False, description='Use int64_t as default index type')
-    variant('double', default=False, description='Use double precision floating point types')
+    variant('real64', default=False, description='Use double precision floating point types')

-    depends_on('cmake @2.8:', when='@5:')  # build-time dependency
-    depends_on('gdb', when='+gdb')
+    depends_on('cmake@2.8:', when='@5:')  # build-time dependency

    patch('install_gklib_defs_rename.patch', when='@5:')

+    def url_for_version(self, version):
+        verdir = 'OLD/' if version < Version('4.0.3') else ''
+        return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)

-    @when('@4:4.0.3')
+    @when('@:4')
    def install(self, spec, prefix):
-
-        if '+gdb' in spec:
-            raise InstallError('gdb support not implemented in METIS 4!')
-        if '+idx64' in spec:
-            raise InstallError('idx64 option not implemented in METIS 4!')
-        if '+double' in spec:
-            raise InstallError('double option not implemented for METIS 4!')
+        # 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)

        options = ['COPTIONS=-fPIC']
        if '+debug' in spec:
            options.append('OPTFLAGS=-g -O0')
        make(*options)

+        # Compile and install library files
+        ccompile = Executable(self.compiler.cc)
+
        mkdir(prefix.bin)
-        for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
-                  'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
-            install(x, prefix.bin)
+        binfiles = ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
+                    'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk')
+        for binfile in binfiles:
+            install(binfile, prefix.bin)

        mkdir(prefix.lib)
        install('libmetis.a', prefix.lib)
@@ -82,106 +88,120 @@ def install(self, spec, prefix):
            install(h, prefix.include)

        mkdir(prefix.share)
-        for f in (join_path(*p)
-                  for p in (('Programs', 'io.c'),
-                            ('Test','mtest.c'),
-                            ('Graphs','4elt.graph'),
-                            ('Graphs', 'metis.mesh'),
-                            ('Graphs', 'test.mgraph'))):
-            install(f, prefix.share)
+        sharefiles = (('Graphs', '4elt.graph'), ('Graphs', 'metis.mesh'),
+                      ('Graphs', 'test.mgraph'))
+        for sharefile in tuple(join_path(*sf) for sf in sharefiles):
+            install(sharefile, prefix.share)

        if '+shared' in spec:
+            shared_flags = ['-fPIC', '-shared']
            if sys.platform == 'darwin':
-                lib_dsuffix = 'dylib'
-                load_flag = '-Wl,-all_load'
-                no_load_flag = ''
+                shared_suffix = 'dylib'
+                shared_flags.extend(['-Wl,-all_load', 'libmetis.a'])
            else:
-                lib_dsuffix = 'so'
-                load_flag = '-Wl,-whole-archive'
-                no_load_flag = '-Wl,-no-whole-archive'
+                shared_suffix = 'so'
+                shared_flags.extend(['-Wl,-whole-archive', 'libmetis.a',
+                                     '-Wl,-no-whole-archive'])

-            os.system(spack_cc + ' -fPIC -shared ' + load_flag +
-                      ' libmetis.a ' + no_load_flag + ' -o libmetis.' +
-                      lib_dsuffix)
-            install('libmetis.' + lib_dsuffix, prefix.lib)
+            shared_out = '%s/libmetis.%s' % (prefix.lib, shared_suffix)
+            shared_flags.extend(['-o', shared_out])
+
+            ccompile(*shared_flags)

        # Set up and run tests on installation
-        symlink(join_path(prefix.share, 'io.c'), 'io.c')
-        symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
-        os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
-        os.system(spack_cc + ' -I%s' % prefix.include +
-                  ' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
-        _4eltgraph = join_path(prefix.share, '4elt.graph')
-        test_mgraph = join_path(prefix.share, 'test.mgraph')
-        metis_mesh = join_path(prefix.share, 'metis.mesh')
-        kmetis = join_path(prefix.bin, 'kmetis')
-        os.system('./mtest ' + _4eltgraph)
-        os.system(kmetis + ' ' + _4eltgraph + ' 40')
-        os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
-        os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
-        os.system(kmetis + ' ' + test_mgraph + ' 2')
-        os.system(kmetis + ' ' + test_mgraph + ' 5')
-        os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
-        os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
-        os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
+        ccompile('-I%s' % prefix.include, '-L%s' % prefix.lib,
+                 '-Wl,-rpath=%s' % (prefix.lib if '+shared' in spec else ''),
+                 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'))
+        """

    @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

-        options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
+        options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
        options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)

        if '+shared' in spec:
            options.append('-DSHARED:BOOL=ON')
-
        if '+debug' in spec:
            options.extend(['-DDEBUG:BOOL=ON',
                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
-
        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 '+double' in spec:
+        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
-        # Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
+        # 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'))
+            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:
-            for f in ["4elt", "copter2", "mdual"]:
-                graph = join_path(source_directory,'graphs','%s.graph' % f)
-                Executable(join_path(prefix.bin,'graphchk'))(graph)
-                Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
-                Executable(join_path(prefix.bin,'ndmetis'))(graph)
+            make('install')

-            graph = join_path(source_directory,'graphs','test.mgraph')
-            Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
-            graph = join_path(source_directory,'graphs','metis.mesh')
-            Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
+            # now run some tests:
+            for f in ['4elt', 'copter2', 'mdual']:
+                graph = join_path(source_directory, 'graphs', '%s.graph' % f)
+                Executable(join_path(prefix.bin, 'graphchk'))(graph)
+                Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
+                Executable(join_path(prefix.bin, 'ndmetis'))(graph)
+
+            graph = join_path(source_directory, 'graphs', 'test.mgraph')
+            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')
+            GKlib_dist = join_path(prefix.include, 'GKlib')
            mkdirp(GKlib_dist)
-            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
-            for f in fs:
-                install(f, GKlib_dist)
+            hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
+            for hfile in hfiles:
+                install(hfile, GKlib_dist)
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -23,6 +23,8 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import sys
+

 class Octave(Package):
    """GNU Octave is a high-level language, primarily intended for numerical
@@ -34,7 +36,8 @@ class Octave(Package):
    homepage = "https://www.gnu.org/software/octave/"
    url      = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz"

-    version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799')
+    version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687')
+    version('4.0.0', 'a69f8320a4f20a8480c1b278b1adb799')

    # Variants
    variant('readline',   default=True)
@@ -62,33 +65,35 @@ class Octave(Package):
    # Required dependencies
    depends_on('blas')
    depends_on('lapack')
+    # Octave does not configure with sed from darwin:
+    depends_on('sed', sys.platform == 'darwin')
    depends_on('pcre')
+    depends_on('pkg-config')

    # Strongly recommended dependencies
-    depends_on('readline',    when='+readline')
+    depends_on('readline',     when='+readline')

    # Optional dependencies
-    depends_on('arpack',      when='+arpack')
-    depends_on('curl',        when='+curl')
-    depends_on('fftw',      when='+fftw')
-    depends_on('fltk',        when='+fltk')
-    depends_on('fontconfig',  when='+fontconfig')
-    depends_on('freetype',    when='+freetype')
-    depends_on('glpk',        when='+glpk')
-    depends_on('gl2ps',       when='+gl2ps')
-    depends_on('gnuplot',     when='+gnuplot')
-    depends_on('ImageMagick', when='+magick')
-    depends_on('hdf5',        when='+hdf5')
-    depends_on('jdk',         when='+jdk')
-    depends_on('llvm',        when='+llvm')
-    #depends_on('opengl',      when='+opengl')    # TODO: add package
-    depends_on('qhull',       when='+qhull')
-    depends_on('qrupdate',    when='+qrupdate')
-    #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
-    depends_on('qt',          when='+qt')
-    depends_on('suite-sparse',when='+suitesparse')
-    depends_on('zlib',        when='+zlib')
-
+    depends_on('arpack',       when='+arpack')
+    depends_on('curl',         when='+curl')
+    depends_on('fftw',         when='+fftw')
+    depends_on('fltk',         when='+fltk')
+    depends_on('fontconfig',   when='+fontconfig')
+    depends_on('freetype',     when='+freetype')
+    depends_on('glpk',         when='+glpk')
+    depends_on('gl2ps',        when='+gl2ps')
+    depends_on('gnuplot',      when='+gnuplot')
+    depends_on('ImageMagick',  when='+magick')
+    depends_on('hdf5',         when='+hdf5')
+    depends_on('jdk',          when='+jdk')
+    depends_on('llvm',         when='+llvm')
+    # depends_on('opengl',      when='+opengl')    # TODO: add package
+    depends_on('qhull',        when='+qhull')
+    depends_on('qrupdate',     when='+qrupdate')
+    # depends_on('qscintilla',  when='+qscintilla) # TODO: add package
+    depends_on('qt',           when='+qt')
+    depends_on('suite-sparse', when='+suitesparse')
+    depends_on('zlib',         when='+zlib')

    def install(self, spec, prefix):
        config_args = [
@@ -154,7 +159,8 @@ def install(self, spec, prefix):
            config_args.append("--without-glpk")

        if '+magick' in spec:
-            config_args.append("--with-magick=%s" % spec['ImageMagick'].prefix.lib)
+            config_args.append("--with-magick=%s"
+                               % spec['ImageMagick'].prefix.lib)

        if '+hdf5' in spec:
            config_args.extend([
@@ -187,7 +193,8 @@ def install(self, spec, prefix):

        if '+qrupdate' in spec:
            config_args.extend([
-                "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include,
+                "--with-qrupdate-includedir=%s"
+                % spec['qrupdate'].prefix.include,
                "--with-qrupdate-libdir=%s"     % spec['qrupdate'].prefix.lib
            ])
        else:
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -27,6 +27,26 @@
 from spack import *


+def _verbs_dir():
+    """
+    Try to find the directory where the OpenFabrics verbs package is
+    installed. Return None if not found.
+    """
+    try:
+        # Try to locate Verbs by looking for a utility in the path
+        ibv_devices = which("ibv_devices")
+        # Run it (silently) to ensure it works
+        ibv_devices(output=str, error=str)
+        # Get path to executable
+        path = ibv_devices.exe[0]
+        # Remove executable name and "bin" directory
+        path = os.path.dirname(path)
+        path = os.path.dirname(path)
+        return path
+    except:
+        return None
+
+
 class Openmpi(Package):
    """Open MPI is a project combining technologies and resources from
       several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI)
@@ -54,7 +74,7 @@ class Openmpi(Package):
    variant('psm', default=False, description='Build support for the PSM library.')
    variant('psm2', default=False, description='Build support for the Intel PSM2 library.')
    variant('pmi', default=False, description='Build support for PMI-based launchers')
-    variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+    variant('verbs', default=_verbs_dir() is not None, description='Build support for OpenFabrics verbs.')
    variant('mxm', default=False, description='Build Mellanox Messaging support')

    variant('thread_multiple', default=False, description='Enable MPI_THREAD_MULTIPLE support')
@@ -113,7 +133,6 @@ def install(self, spec, prefix):
            # Fabrics
            '--with-psm' if '+psm' in spec else '--without-psm',
            '--with-psm2' if '+psm2' in spec else '--without-psm2',
-            ('--with-%s' % self.verbs) if '+verbs' in spec else ('--without-%s' % self.verbs),
            '--with-mxm' if '+mxm' in spec else '--without-mxm',
            # Other options
            '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple',
@@ -121,6 +140,14 @@ def install(self, spec, prefix):
            '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3',
            '--enable-vt' if '+vt' in spec else '--disable-vt'
        ])
+        if '+verbs' in spec:
+            path = _verbs_dir()
+            if path is not None:
+                config_args.append('--with-%s=%s' % (self.verbs, path))
+            else:
+                config_args.append('--with-%s' % self.verbs)
+        else:
+            config_args.append('--without-%s' % self.verbs)

        # TODO: use variants for this, e.g. +lanl, +llnl, etc.
        # use this for LANL builds, but for LLNL builds, we need:
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -26,33 +26,36 @@
 from spack import *
 import sys

+
 class Parmetis(Package):
-    """
-    ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured
-    graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
-    """
+    """ParMETIS is an MPI-based parallel library that implements a variety of
+       algorithms for partitioning unstructured graphs, meshes, and for
+       computing fill-reducing orderings of sparse matrices."""
+
    homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
-    url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
+    base_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis'

    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')

-    depends_on('cmake @2.8:')  # build dependency
+    depends_on('cmake@2.8:')  # build dependency
    depends_on('mpi')
-
-    patch('enable_external_metis.patch')
    depends_on('metis@5:')

+    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: ignore=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: ignore=E501
    patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')

-    depends_on('gdb', when='+gdb')
+    def url_for_version(self, version):
+        verdir = 'OLD/' if version < Version('3.2.0') else ''
+        return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)

    def install(self, spec, prefix):
        options = []
@@ -60,30 +63,27 @@ def install(self, spec, prefix):

        build_directory = join_path(self.stage.path, 'spack-build')
        source_directory = self.stage.source_path
-        metis_source = join_path(source_directory, 'metis')

-        # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
-        # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
-                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
-                        '-DCMAKE_C_COMPILER:STRING=mpicc',
-                        '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
+        options.extend([
+            '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
+            '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
+            '-DCMAKE_C_COMPILER:STRING=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER:STRING=%s' % spec['mpi'].mpicxx
+        ])

        if '+shared' in spec:
            options.append('-DSHARED:BOOL=ON')
-
        if '+debug' in spec:
            options.extend(['-DDEBUG:BOOL=ON',
                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
-
        if '+gdb' in spec:
            options.append('-DGDB:BOOL=ON')

        with working_dir(build_directory, create=True):
            cmake(source_directory, *options)
            make()
-            make("install")
+            make('install')

-            # The shared library is not installed correctly on Darwin; correct this
+            # The shared library is not installed correctly on Darwin; fix this
            if (sys.platform == 'darwin') and ('+shared' in spec):
                fix_darwin_install_name(prefix.lib)
--- a/var/spack/repos/builtin/packages/py-autopep8/package.py
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyAutopep8(Package):
+    """Automatic pep8 formatter"""
+    homepage = "https://github.com/hhatto/autopep8"
+    url      = "https://github.com/hhatto/autopep8/archive/ver1.2.2.tar.gz"
+
+    version('1.2.2', 'def3d023fc9dfd1b7113602e965ad8e1')
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('py-pep8')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
--- a/var/spack/repos/builtin/packages/py-pep8/package.py
+++ b/var/spack/repos/builtin/packages/py-pep8/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyPep8(Package):
+    """python pep8 format checker"""
+    homepage = "https://github.com/PyCQA/pycodestyle"
+    url      = "https://github.com/PyCQA/pycodestyle/archive/1.7.0.tar.gz"
+
+    version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
--- a/var/spack/repos/builtin/packages/rust-bindgen/package.py
+++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py
@@ -0,0 +1,18 @@
+from spack import *
+import os
+
+
+class RustBindgen(Package):
+    """The rust programming language toolchain"""
+    homepage = "http://www.rust-lang.org"
+    url = "https://github.com/crabtw/rust-bindgen"
+
+    version('0.16', tag='0.16', git='https://github.com/crabtw/rust-bindgen')
+
+    extends("rust")
+    depends_on("llvm")
+
+    def install(self, spec, prefix):
+        env = dict(os.environ)
+        env['LIBCLANG_PATH'] = os.path.join(spec['llvm'].prefix, 'lib')
+        cargo('install', '--root', prefix, env=env)
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -0,0 +1,63 @@
+from spack import *
+import os
+
+
+def get_submodules():
+    git = which('git')
+    git('submodule', 'update', '--init', '--recursive')
+
+class Rust(Package):
+    """The rust programming language toolchain"""
+    homepage = "http://www.rust-lang.org"
+    url = "https://github.com/rust-lang/rust"
+
+    version('1.8.0', tag='1.8.0', git="https://github.com/rust-lang/rust")
+
+    resource(name='cargo',
+             git="https://github.com/rust-lang/cargo.git",
+             tag='0.10.0',
+             destination='cargo')
+
+    extendable = True
+
+    # Rust
+    depends_on("llvm")
+    depends_on("curl")
+    depends_on("git")
+    depends_on("cmake")
+    depends_on("python@:2.8")
+
+    # Cargo
+    depends_on("openssl")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--llvm-root=' + spec['llvm'].prefix)
+
+        make()
+        make("install")
+
+        # Install cargo, rust package manager
+        with working_dir(os.path.join('cargo', 'cargo')):
+            get_submodules()
+            configure('--prefix=' + prefix,
+                      '--local-rust-root=' + prefix)
+
+            make()
+            make("install")
+
+    def setup_dependent_package(self, module, ext_spec):
+        """
+        Called before python modules' install() methods.
+
+        In most cases, extensions will only need to have one or two lines::
+
+            cargo('build')
+            cargo('install', '--root', prefix)
+
+        or
+
+            cargo('install', '--root', prefix)
+        """
+        # Rust extension builds can have a global cargo executable function
+        module.cargo = Executable(join_path(self.spec.prefix.bin, 'cargo'))
--- a/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
+++ b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
@@ -1,5 +0,0 @@
-esmumps				:	scotch
-					(cd esmumps ; $(MAKE) scotch && $(MAKE) install)
-
-ptesmumps			:	ptscotch
-					(cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall)
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import re
 from spack import *


@@ -32,7 +31,7 @@ class Scotch(Package):
       partitioning, graph clustering, and sparse matrix ordering."""

    homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
-    url      = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"
+    url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"
    base_url = "http://gforge.inria.fr/frs/download.php/latestfile/298"
    list_url = "http://gforge.inria.fr/frs/?group_id=248"

@@ -44,6 +43,7 @@ class Scotch(Package):
    variant('compression', default=True, description='Activate the posibility to use compressed files')
    variant('esmumps', default=False, description='Activate the compilation of esmumps needed by mumps')
    variant('shared', default=True, description='Build a shared version of the library')
+    variant('metis', default=True, description='Build metis and parmetis wrapper libraries')

    depends_on('flex')
    depends_on('bison')
@@ -56,37 +56,15 @@ class Scotch(Package):
    # from the Scotch hosting site.  These alternative archives include a
    # superset of the behavior in their default counterparts, so we choose to
    # always grab these versions for older Scotch versions for simplicity.
+    def url_for_version(self, version):
+        return super(Scotch, self).url_for_version(version)
+
    @when('@:6.0.0')
    def url_for_version(self, version):
        return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version)

-    @when('@6.0.1:')
-    def url_for_version(self, version):
-        return super(Scotch, self).url_for_version(version)
-
-    # NOTE: Several of the 'esmumps' enabled Scotch releases up to version
-    # 6.0.0 have broken build scripts that don't properly build 'esmumps' as a
-    # separate target, so we need a patch procedure to remove 'esmumps' from
-    # existing targets and to add it as a standalone target.
-    @when('@:6.0.0')
    def patch(self):
-        makefile_path = os.path.join('src', 'Makefile')
-        with open(makefile_path, 'r') as makefile:
-            esmumps_enabled = any(re.search(r'^esmumps(\s*):(.*)$', line)
-                                  for line in makefile.readlines())
-
-        if not esmumps_enabled:
-            mff = FileFilter(makefile_path)
-            mff.filter(r'^.*((esmumps)|(ptesmumps)).*(install).*$', '')
-
-            mfesmumps_dir = os.path.dirname(os.path.realpath(__file__))
-            mfesmumps_path = os.path.join(mfesmumps_dir, 'Makefile.esmumps')
-            with open(makefile_path, 'a') as makefile:
-                makefile.write('\ninclude %s\n' % mfesmumps_path)
-
-    @when('@6.0.1:')
-    def patch(self):
-        pass
+        self.configure()

    # NOTE: Configuration of Scotch is achieved by writing a 'Makefile.inc'
    # file that contains all of the configuration variables and their desired
@@ -103,13 +81,13 @@ def configure(self):
        ]

        # Library Build Type #
-
        if '+shared' in self.spec:
            makefile_inc.extend([
+                # todo change for Darwin systems
                'LIB       = .so',
                'CLIBFLAGS = -shared -fPIC',
                'RANLIB    = echo',
-                'AR	       = $(CC)',
+                'AR        = $(CC)',
                'ARFLAGS   = -shared $(LDFLAGS) -o'
            ])
            cflags.append('-fPIC')
@@ -118,7 +96,7 @@ def configure(self):
                'LIB       = .a',
                'CLIBFLAGS = ',
                'RANLIB    = ranlib',
-                'AR	       = ar',
+                'AR        = ar',
                'ARFLAGS   = -ruv '
            ])

@@ -171,20 +149,49 @@ def configure(self):
                fh.write('\n'.join(makefile_inc))

    def install(self, spec, prefix):
-        self.configure()
-
        targets = ['scotch']
        if '+mpi' in self.spec:
            targets.append('ptscotch')

-        if '+esmumps' in self.spec:
-            targets.append('esmumps')
-            if '+mpi' in self.spec:
-                targets.append('ptesmumps')
+        if self.spec.version >= Version('6.0.0'):
+            if '+esmumps' in self.spec:
+                targets.append('esmumps')
+                if '+mpi' in self.spec:
+                    targets.append('ptesmumps')

        with working_dir('src'):
            for target in targets:
-                make(target, parallel=(target != 'ptesmumps'))
+                # It seams that building ptesmumps in parallel fails, for
+                # version prior to 6.0.0 there is no separated targets force
+                # ptesmumps, this library is built by the ptscotch target. This
+                # should explain the test for the can_make_parallel variable
+                can_make_parallel = \
+                    not (target == 'ptesmumps' or
+                         (self.spec.version < Version('6.0.0') and
+                          target == 'ptscotch'))
+                make(target, parallel=can_make_parallel)
+
+        # todo change this to take into account darwin systems
+        lib_ext = '.so' if '+shared' in self.spec else '.a'
+        # It seams easier to remove metis wrappers from the folder that will be
+        # installed than to tweak the Makefiles
+        if '+metis' not in self.spec:
+            with working_dir('lib'):
+                lib_ext = '.so' if '+shared' in self.spec else '.a'
+                force_remove('libscotchmetis{0}'.format(lib_ext))
+                force_remove('libptscotchparmetis{0}'.format(lib_ext))
+
+            with working_dir('include'):
+                force_remove('metis.h')
+                force_remove('parmetis.h')
+
+        if '~esmumps' in self.spec and self.spec.version < Version('6.0.0'):
+            with working_dir('lib'):
+                force_remove('libesmumps{0}'.format(lib_ext))
+                force_remove('libptesmumps{0}'.format(lib_ext))
+
+            with working_dir('include'):
+                force_remove('esmumps.h')

        install_tree('bin', prefix.bin)
        install_tree('lib', prefix.lib)
--- a/var/spack/repos/builtin/packages/stream/package.py
+++ b/var/spack/repos/builtin/packages/stream/package.py
@@ -0,0 +1,62 @@
+##############################################################################
+# 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 Stream(Package):
+    """The STREAM benchmark is a simple synthetic benchmark program that
+    measures sustainable memory bandwidth (in MB/s) and the corresponding
+    computation rate for simple vector kernels."""
+
+    homepage = "https://www.cs.virginia.edu/stream/ref.html"
+
+    version('5.10', git='https://github.com/jeffhammond/STREAM.git')
+
+    variant('openmp', default=False, description='Build with OpenMP support')
+
+    def patch(self):
+        makefile = FileFilter('Makefile')
+
+        # Use the Spack compiler wrappers
+        makefile.filter('CC = .*', 'CC = cc')
+        makefile.filter('FC = .*', 'FC = f77')
+
+        cflags = '-O2'
+        fflags = '-O2'
+        if '+openmp' in self.spec:
+            cflags += ' ' + self.compiler.openmp_flag
+            fflags += ' ' + self.compiler.openmp_flag
+
+        # Set the appropriate flags for this compiler
+        makefile.filter('CFLAGS = .*', 'CFLAGS = {0}'.format(cflags))
+        makefile.filter('FFLAGS = .*', 'FFLAGS = {0}'.format(fflags))
+
+    def install(self, spec, prefix):
+        make()
+
+        # Manual installation
+        mkdir(prefix.bin)
+        install('stream_c.exe', prefix.bin)
+        install('stream_f.exe', prefix.bin)
--- a/var/spack/repos/builtin/packages/tbb/package.py
+++ b/var/spack/repos/builtin/packages/tbb/package.py
@@ -23,9 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
 import glob

+
 class Tbb(Package):
    """Widely used C++ template library for task parallelism.
    Intel Threading Building Blocks (Intel TBB) lets you easily write parallel
@@ -35,35 +35,39 @@ class Tbb(Package):
    homepage = "http://www.threadingbuildingblocks.org/"

    # Only version-specific URL's work for TBB
-    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')    # NOQA: ignore=E501
+    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')  # NOQA: ignore=E501

-    def coerce_to_spack(self,tbb_build_subdir):
-        for compiler in ["icc","gcc","clang"]:
-              fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler ))
-              for f in fs:
-                  lines = open(f).readlines()
-                  of = open(f,"w")
-                  for l in lines:
-                      if l.strip().startswith("CPLUS ="):
+    def coerce_to_spack(self, tbb_build_subdir):
+        for compiler in ["icc", "gcc", "clang"]:
+            fs = glob.glob(join_path(tbb_build_subdir,
+                                     "*.%s.inc" % compiler))
+            for f in fs:
+                lines = open(f).readlines()
+                of = open(f, "w")
+                for l in lines:
+                    if l.strip().startswith("CPLUS ="):
                        of.write("# coerced to spack\n")
                        of.write("CPLUS = $(CXX)\n")
-                      elif l.strip().startswith("CPLUS ="):
+                    elif l.strip().startswith("CPLUS ="):
                        of.write("# coerced to spack\n")
                        of.write("CONLY = $(CC)\n")
-                      else:
-                        of.write(l);
+                    else:
+                        of.write(l)

    def install(self, spec, prefix):
-        #
-        # we need to follow TBB's compiler selection logic to get the proper build + link flags
-        # but we still need to use spack's compiler wrappers
+        if spec.satisfies('%gcc@6.1:') and spec.satisfies('@:4.4.3'):
+            raise InstallError('Only TBB 4.4.4 and above build with GCC 6.1!')
+
+        # We need to follow TBB's compiler selection logic to get the proper
+        # build + link flags but we still need to use spack's compiler wrappers
        # to accomplish this, we do two things:
        #
-        # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile
+        # * Look at the spack spec to determine which compiler we should pass
+        #   to tbb's Makefile;
        #
        # * patch tbb's build system to use the compiler wrappers (CC, CXX) for
-        #    icc, gcc, clang
-        #    (see coerce_to_spack())
+        #   icc, gcc, clang (see coerce_to_spack());
        #
        self.coerce_to_spack("build")

@@ -74,7 +78,6 @@ def install(self, spec, prefix):
        else:
            tbb_compiler = "gcc"

-
        mkdirp(prefix)
        mkdirp(prefix.lib)

@@ -82,10 +85,10 @@ def install(self, spec, prefix):
        # tbb does not have a configure script or make install target
        # we simply call make, and try to put the pieces together
        #
-        make("compiler=%s"  %(tbb_compiler))
+        make("compiler=%s"  % (tbb_compiler))

        # install headers to {prefix}/include
-        install_tree('include',prefix.include)
+        install_tree('include', prefix.include)

        # install libs to {prefix}/lib
        tbb_lib_names = ["libtbb",
@@ -94,10 +97,10 @@ def install(self, spec, prefix):

        for lib_name in tbb_lib_names:
            # install release libs
-            fs = glob.glob(join_path("build","*release",lib_name + ".*"))
+            fs = glob.glob(join_path("build", "*release", lib_name + ".*"))
            for f in fs:
                install(f, prefix.lib)
            # install debug libs if they exist
-            fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*"))
+            fs = glob.glob(join_path("build", "*debug", lib_name + "_debug.*"))
            for f in fs:
                install(f, prefix.lib)