Check in entire Trilinos file for review.

var/spack/repos/builtin/packages/trilinos/package.py

@@ -0,0 +1,347 @@
+##############################################################################
+# 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 *
+import os
+import sys
+
+# Trilinos is complicated to build, as an inspiration a couple of links to
+# other repositories which build it:
+# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
+# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
+# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb and some
+# relevant documentation/examples:
+# https://github.com/trilinos/Trilinos/issues/175
+
+
+class Trilinos(Package):
+    """The Trilinos Project is an effort to develop algorithms and enabling
+    technologies within an object-oriented software framework for the solution
+    of large-scale, complex multi-physics engineering and scientific problems.
+    A unique design feature of Trilinos is its focus on packages.
+    """
+    homepage = "https://trilinos.org/"
+    base_url = "https://github.com/trilinos/Trilinos/archive"
+
+    version('12.8.1', '01c0026f1e2050842857db941060ecd5')
+    version('12.6.4', 'c2ea7b5aa0d10bcabdb9b9a6e3bac3ea')
+    version('12.6.3', '8de5cc00981a0ca0defea6199b2fe4c1')
+    version('12.6.2', 'dc7f9924872778798149ecadd81605a5')
+    version('12.6.1', '8aecea78546e7558f63ecc9a3b2949da')
+    version('12.4.2', '4c25a757d86bde3531090bd900a2cea8')
+    version('12.2.1', '85d011f7f99a776a9c6c2625e8cb721c')
+    version('12.0.1', 'bcb3fdefd14d05dd6aa65ba4c5b9aa0e')
+    version('11.14.3', 'dea62e57ebe51a886bee0b10a2176969')
+    version('11.14.2', 'e7c3cdbbfe3279a8a68838b873ad6d51')
+    version('11.14.1', 'b7760b142eef66c79ed13de7c9560f81')
+
+    def url_for_version(self, version):
+        return '%s/trilinos-release-%s.tar.gz' % \
+            (Trilinos.base_url, version.dashed)
+
+    variant('metis',        default=True,
+            description='Compile with METIS and ParMETIS')
+    variant('mumps',        default=True,
+            description='Compile with support for MUMPS solvers')
+    variant('superlu-dist', default=True,
+            description='Compile with SuperluDist solvers')
+    variant('hypre',        default=True,
+            description='Compile with Hypre preconditioner')
+    variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('suite-sparse', default=True,
+            description='Compile with SuiteSparse solvers')
+    # not everyone has py-numpy activated, keep it disabled by default to avoid
+    # configure errors
+    variant('python',       default=False, description='Build python wrappers')
+    variant('shared',       default=True,
+            description='Enables the build of shared libraries')
+    variant('debug',        default=False,
+            description='Builds a debug version of the libraries')
+    variant('boost',        default=True, description='Compile with Boost')
+
+    depends_on('cmake', type='build')
+
+    # Everything should be compiled with -fpic
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost', when='+boost')
+    depends_on('matio')
+    depends_on('glm')
+    depends_on('metis@5:', when='+metis')
+    depends_on('suite-sparse', when='+suite-sparse')
+
+    # MPI related dependencies
+    depends_on('mpi')
+    depends_on('netcdf+mpi')
+    depends_on('parmetis', when='+metis')
+    # Trilinos' Tribits config system is limited which makes it very tricky to
+    # link Amesos with static MUMPS, see
+    # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+    # One could work it out by getting linking flags from mpif90 --showme:link
+    # (or alike) and adding results to -DTrilinos_EXTRA_LINK_FLAGS together
+    # with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and it may
+    # 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@: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')
+    depends_on('py-numpy', when='+python')
+    depends_on('swig', when='+python')
+
+    patch('umfpack_from_suitesparse.patch')
+
+    # check that the combination of variants makes sense
+    def variants_check(self):
+        if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
+            # For Trilinos v11 we need to force SuperLUDist=OFF, since only the
+            # deprecated SuperLUDist v3.3 together with an Amesos patch is
+            # working.
+            raise RuntimeError('The superlu-dist variant can only be used' +
+                               ' with Trilinos @12.0.1:')
+
+    def install(self, spec, prefix):
+        self.variants_check()
+
+        cxx_flags = []
+        options = []
+        options.extend(std_cmake_args)
+
+        mpi_bin = spec['mpi'].prefix.bin
+        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
+        blas = spec['blas'].blas_libs
+        lapack = spec['lapack'].lapack_libs
+        options.extend([
+            '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+            '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
+            '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
+            '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
+            '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
+            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DTPL_ENABLE_MPI:BOOL=ON',
+            '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
+            '-DTPL_ENABLE_BLAS=ON',
+            '-DBLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
+            '-DBLAS_LIBRARY_DIRS=%s' % ';'.join(blas.directories),
+            '-DTPL_ENABLE_LAPACK=ON',
+            '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
+            '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories),
+            '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
+            '-DTrilinos_ENABLE_CXX11:BOOL=ON',
+            '-DTPL_ENABLE_Netcdf:BOOL=ON',
+            '-DTPL_ENABLE_HYPRE:BOOL=%s' % (
+                'ON' if '+hypre' in spec else 'OFF')
+        ])
+
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
+        if '+boost' in spec:
+            options.extend([
+                '-DTPL_ENABLE_Boost:BOOL=ON',
+                '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
+                '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
+
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
+        # Fortran lib
+        libgfortran = os.path.dirname(os.popen(
+            '%s --print-file-name libgfortran.a' %
+            join_path(mpi_bin, 'mpif90')).read())
+        options.extend([
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
+                libgfortran),
+            '-DTrilinos_ENABLE_Fortran=ON'
+        ])
+
+        # for build-debug only:
+        # options.extend([
+        #    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        # ])
+
+        # suite-sparse related
+        if '+suite-sparse' in spec:
+            options.extend([
+                # FIXME: Trilinos seems to be looking for static libs only,
+                # patch CMake TPL file?
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+                # '-DTPL_ENABLE_Cholmod:BOOL=ON',
+                # '-DCholmod_LIBRARY_DIRS:PATH=%s' % (
+                #    spec['suite-sparse'].prefix.lib,
+                # '-DCholmod_INCLUDE_DIRS:PATH=%s' % (
+                #    spec['suite-sparse'].prefix.include,
+                '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+                '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % (
+                    spec['suite-sparse'].prefix.lib),
+                '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % (
+                    spec['suite-sparse'].prefix.include),
+                '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;' +
+                'suitesparseconfig'
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+                '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
+            ])
+
+        # metis / parmetis
+        if '+metis' in spec:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=ON',
+                '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+                '-DMETIS_LIBRARY_NAMES=metis',
+                '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+                '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+                '-DParMETIS_LIBRARY_DIRS=%s;%s' % (
+                    spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
+                '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % (
+                    spec['parmetis'].prefix.include)
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=OFF',
+                '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
+            ])
+
+        # mumps / scalapack
+        if '+mumps' in spec:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=ON',
+                '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+                # order is important!
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord',
+                '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+                # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+                '-DSCALAPACK_LIBRARY_NAMES=scalapack'
+            ])
+            # see
+            # https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
+            cxx_flags.extend([
+                '-DMUMPS_5_0'
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
+                '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
+            ])
+
+        # superlu-dist:
+        if '+superlu-dist' in spec:
+            # Amesos, conflicting types of double and complex SLU_D
+            # see
+            # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+            # and
+            # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+            options.extend([
+                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+                '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+            ])
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+                '-DSuperLUDist_LIBRARY_DIRS=%s' %
+                spec['superlu-dist'].prefix.lib,
+                '-DSuperLUDist_INCLUDE_DIRS=%s' %
+                spec['superlu-dist'].prefix.include
+            ])
+            if spec.satisfies('^superlu-dist@4.0:'):
+                options.extend([
+                    '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
+            ])
+
+        # python
+        if '+python' in spec:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+            ])
+        else:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+            ])
+
+        # collect CXX flags:
+        options.extend([
+            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
+        ])
+
+        # disable due to compiler / config errors:
+        options.extend([
+            '-DTrilinos_ENABLE_SEACAS=OFF',
+            '-DTrilinos_ENABLE_Pike=OFF',
+            '-DTrilinos_ENABLE_STK=OFF'
+        ])
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_ENABLE_FEI=OFF'
+            ])
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
+
+            # When trilinos is built with Python, libpytrilinos is included
+            # through cmake configure files. Namely, Trilinos_LIBRARIES in
+            # TrilinosConfig.cmake contains pytrilinos. This leads to a
+            # run-time error: Symbol not found: _PyBool_Type and prevents
+            # Trilinos to be used in any C++ code, which links executable
+            # against the libraries listed in Trilinos_LIBRARIES.  See
+            # https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
+            # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
+            if '+python' in self.spec:
+                filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',
+                            (r'\1\3'),
+                            '%s/cmake/Trilinos/TrilinosConfig.cmake' %
+                            prefix.lib)
+
+            # The shared libraries are not installed correctly on Darwin;
+            # correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)

var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch

@@ -0,0 +1,12 @@
+diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake
+index 963eb71..998cd02 100644
+--- a/cmake/TPLs/FindTPLUMFPACK.cmake
++++ b/cmake/TPLs/FindTPLUMFPACK.cmake
+@@ -55,6 +55,6 @@
+
+
+ TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK
+-  REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++  REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h
+   REQUIRED_LIBS_NAMES umfpack amd
+   )