Merge pull request #993 from xjrc/packages/metis

Update Package : METIS/ParMETIS

2 files changed, 127 insertions, 107 deletions

diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 061179b78e..c4f2afaff2 100644
--- 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 @@ class Metis(Package):
             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])
 
-        # 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(*shared_flags)
 
+        # Set up and run tests on installation
+        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")
+            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)
+            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')
+            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)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 2dead4a76a..9b36f273e4 100644
--- 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 @@ class Parmetis(Package):
 
         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)