Merge pull request #1053 from davydden/pkg/dealii_suite_update

update Petsc, Slepc, Trilinos, Superlu-dist and deal.II

5 files changed, 85 insertions, 65 deletions

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 54b6426d36..23ec74abed 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -80,8 +80,8 @@ class Dealii(Package):
     depends_on("netcdf-cxx",       when='+netcdf+mpi')
     depends_on("oce",              when='+oce')
     depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi",        when='+petsc+mpi')
-    depends_on("slepc",            when='+slepc+petsc+mpi')
+    depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi')  # FIXME: update after 3.7 is supported upstream.  # NOQA: ignore=E501
+    depends_on("slepc@:3.6.3",     when='+slepc+petsc+mpi')
     depends_on("trilinos",         when='+trilinos+mpi')
 
     # developer dependnecies
@@ -108,12 +108,11 @@ class Dealii(Package):
             # 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' %
-                (spec['lapack'].lapack_shared_lib,
-                 spec['blas'].blas_shared_lib),
+            '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
+                spec['lapack'].prefix.include, spec['blas'].prefix.include),
+            '-DLAPACK_LIBRARIES=%s;%s' % (
+                spec['lapack'].lapack_shared_lib,
+                spec['blas'].blas_shared_lib),
             '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
@@ -168,14 +167,14 @@ class Dealii(Package):
         if '+netcdf' in spec:
             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)),
-                '-DNETCDF_INCLUDE_DIRS=%s;%s' %
-                    (spec['netcdf-cxx'].prefix.include,
-                     spec['netcdf'].prefix.include),
+                '-DNETCDF_LIBRARIES=%s;%s' % (
+                    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),
             ])
         else:
             options.extend([
@@ -266,9 +265,9 @@ class Dealii(Package):
                 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;)',
+                filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  # NOQA: ignore=E501
                             (''), 'step-40.cc')
-                filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',
+                filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  # NOQA: ignore=E501
                             (''), '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')
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 6456a1aabf..8dd1d8d2b9 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -28,13 +28,16 @@ from spack import *
 
 class Petsc(Package):
     """
-    PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications
-    modeled by partial differential equations.
+    PETSc is a suite of data structures and routines for the scalable
+    (parallel) solution of scientific applications modeled by partial
+    differential equations.
     """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
     url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
 
+    version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34')
+    version('3.6.4', '7632da2375a3df35b8891c9526dbdde7')
     version('3.6.3', '91dd3522de5a5ef039ff8f50800db606')
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
@@ -69,10 +72,12 @@ class Petsc(Package):
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
     # Hypre does not support complex numbers.
-    # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers
-    # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
+    # Also PETSc prefer to build it without internal superlu, likely due to
+    # conflict in headers see
+    # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py  # NOQA: ignore=E501
     depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
-    depends_on('superlu-dist', when='+superlu-dist+mpi')
+    depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi')
+    depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi')
     depends_on('mumps+mpi', when='+mumps+mpi')
     depends_on('scalapack', when='+mumps+mpi')
 
@@ -80,17 +85,17 @@ class Petsc(Package):
         if '~mpi' in self.spec:
             compiler_opts = [
                 '--with-cc=%s' % os.environ['CC'],
-                '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),
-                '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),
+                '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),  # NOQA: ignore=E501
+                '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),  # NOQA: ignore=E501
                 '--with-mpi=0'
             ]
-            error_message_fmt = '\t{library} support requires "+mpi" to be activated'
+            error_message_fmt = '\t{library} support requires "+mpi" to be activated'  # NOQA: ignore=E501
 
-            # If mpi is disabled (~mpi), it's an error to have any of these enabled.
-            # This generates a list of any such errors.
+            # If mpi is disabled (~mpi), it's an error to have any of these
+            # enabled. This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
-                      if ('+'+x) in self.spec]
+                      for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist')  # NOQA: ignore=E501
+                      if ('+' + x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
@@ -105,26 +110,31 @@ class Petsc(Package):
         options = ['--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
-            '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
-            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
+            '--with-precision=%s' % ('double' if '+double' in spec else 'single'),  # NOQA: ignore=E501
+            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),  # NOQA: ignore=E501
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
             '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
+                        'mumps', 'scalapack'):
             options.append(
-                '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
+                '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))  # NOQA: ignore=E501
             )
             if library in spec:
                 options.append(
-                    '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
+                    '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)  # NOQA: ignore=E501
                 )
-        # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a
+        # PETSc does not pick up SuperluDist from the dir as they look for
+        # superlu_dist_4.1.a
         if 'superlu-dist' in spec:
             options.extend([
-                '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include,
-                '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'),
+                '--with-superlu_dist-include=%s' %
+                spec['superlu-dist'].prefix.include,
+                '--with-superlu_dist-lib=%s' %
+                join_path(spec['superlu-dist'].prefix.lib,
+                          'libsuperlu_dist.a'),
                 '--with-superlu_dist=1'
             ])
         else:
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index c148a579ec..d3739bf6a6 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -34,13 +34,16 @@ class Slepc(Package):
     homepage = "http://www.grycap.upv.es/slepc"
     url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
 
+    version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2')
+    version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876')
     version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
 
-    variant('arpack', default=False, description='Enables Arpack wrappers')
+    variant('arpack', default=True, description='Enables Arpack wrappers')
 
-    depends_on('petsc')
-    depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi')
-    depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi')
+    depends_on('petsc@3.7:', when='@3.7.1:')
+    depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3')
+    depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi')
+    depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi')
 
     def install(self, spec, prefix):
         # set SLEPC_DIR for installation
@@ -64,7 +67,7 @@ class Slepc(Package):
         configure('--prefix=%s' % prefix, *options)
 
         make('MAKE_NP=%s' % make_jobs, parallel=False)
-        #FIXME:
+        # FIXME:
         # make('test')
         make('install')
 
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 6c06b5497c..e51d7224d9 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -25,50 +25,54 @@
 from spack import *
 import glob
 
+
 class SuperluDist(Package):
-    """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
+    """A general purpose library for the direct solution of large, sparse,
+    nonsymmetric systems of linear equations on high performance machines."""
     homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
     url      = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
 
     version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
-    # default to version 4.3 since petsc and trilinos are not tested with 5.0.
-    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True)
+    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
     version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
     version('4.1', '4edee38cc29f687bd0c8eb361096a455')
     version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
 
-    depends_on ('mpi')
-    depends_on ('blas')
-    depends_on ('lapack')
-    depends_on ('parmetis')
-    depends_on ('metis@5:')
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('parmetis')
+    depends_on('metis@5:')
 
     def install(self, spec, prefix):
         makefile_inc = []
         makefile_inc.extend([
             'PLAT         = _mac_x',
-            'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix
+            'DSuperLUroot = %s' % self.stage.source_path,
             'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
             'BLASDEF      = -DUSE_VENDOR_BLAS',
-            'BLASLIB      = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names
+            'BLASLIB      = %s %s' %
+                (to_link_flags(spec['lapack'].lapack_shared_lib),
+                 to_link_flags(spec['blas'].blas_shared_lib)),
             'METISLIB     = -L%s -lmetis' % spec['metis'].prefix.lib,
             'PARMETISLIB  = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
             'FLIBS        =',
-            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',
+            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',  # NOQA: ignore=E501
             'ARCH         = ar',
             'ARCHFLAGS    = cr',
             'RANLIB       = true',
-            'CC           = mpicc', # FIXME avoid hardcoding MPI compiler names
-            'CFLAGS       = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include),
+            'CC           = %s' % spec['mpi'].mpicc,
+            'CFLAGS       = -fPIC -std=c99 -O2 -I%s -I%s' %
+                (spec['parmetis'].prefix.include,
+                 spec['metis'].prefix.include),
             'NOOPTS       = -fPIC -std=c99',
-            'FORTRAN      = mpif77',
+            'FORTRAN      = %s' % spec['mpi'].mpif77,
             'F90FLAGS     = -O2',
-            'LOADER       = mpif77',
+            'LOADER       = %s' % spec['mpi'].mpif77,
             'LOADOPTS     =',
             'CDEFS        = -DAdd_'
-            ])
+        ])
 
-        #with working_dir('src'):
         with open('make.inc', 'w') as fh:
             fh.write('\n'.join(makefile_inc))
 
@@ -83,9 +87,10 @@ class SuperluDist(Package):
         mkdirp(headers_location)
         mkdirp(prefix.lib)
 
-        headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
+        headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h'))
         for h in headers:
-            install(h,headers_location)
+            install(h, headers_location)
 
-        superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
-        install(superludist_lib,self.prefix.lib)
+        superludist_lib = join_path(self.stage.source_path,
+                                    'lib/libsuperlu_dist.a')
+        install(superludist_lib, self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 6913d79dcc..3a53ac5c01 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -45,6 +45,8 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e')
+    version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9')
     version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
     version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
     version('12.2.1', '6161926ea247863c690e927687f83be9')
@@ -89,7 +91,8 @@ class Trilinos(Package):
     # work at the end. But let's avoid all this by simply using shared libs
     depends_on('mumps@5.0:+mpi+shared', when='+mumps')
     depends_on('scalapack', when='+mumps')
-    depends_on('superlu-dist', when='+superlu-dist')
+    depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist')
+    depends_on('superlu-dist', when='@12.6.2:+superlu-dist')
     depends_on('hypre~internal-superlu', when='+hypre')
     depends_on('hdf5+mpi', when='+hdf5')
     depends_on('python', when='+python')