Expand the libMesh dependency list (#9642)
This commit overhauls the libMesh package script in a number of ways: * We now inherit from AutotoolsPackage. * libMesh contains about a dozen third-party dependencies that can only be provided by the copy bundled with libMesh. This patch enumerates all such bundled dependencies and disables all of them by default. * libMesh supports compilation with external installations of boost, eigen, hdf5, slepc, and tbb; this patch adds all of them to package.py. * libMesh will look for a few system executables (xz, bzip, gdb) by default. This is now disabled. * libMesh will now used a copy of perl installed by spack instead of trying to find the system copy. * Compilation with non-system MPI installations requires an additional flag (--with-mpi=); this has been added.
This commit is contained in:
David Wells
Peter Scheibel
parent
c43689deb0
commit
c96c38a08f
@ -6,7 +6,7 @@
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from spack import *
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class Libmesh(Package):
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class Libmesh(AutotoolsPackage):
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"""The libMesh library provides a framework for the numerical simulation of
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partial differential equations using arbitrary unstructured
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discretizations on serial and parallel platforms."""
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@ -19,29 +19,194 @@ class Libmesh(Package):
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version('1.2.1', sha256='11c22c7d96874a17de6b8c74caa45d6745d40bf3610e88b2bd28fd3381f5ba70')
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version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
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# support for libraries that are only available through the bundled copies:
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# TODO libMesh 1.2.1 gained the ability to specify a path to capnproto
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variant('capnproto', default=False, description='Compile with the bundled capnproto serialization library')
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variant('exodusii', default=False, description='Compile with the bundled ExodusII output library')
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variant('fparser', default=False, description='Compile with the bundled fparser function parser library')
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variant('gmv', default=False, description='Compile with the bundled gmv format IO library')
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variant('laspack', default=False, description='Compile with the bundled laspack interative solver library')
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variant('libhilbert', default=False, description='Compile with the bundled libHilbert partitioning library')
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variant('metaphysicl', default=False, description='Compile with the bundled metaphysicl AD library')
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variant('metis', default=False, description='Compile with the bundled METIS graph partitioning library')
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variant('nanoflann', default=False, description='Compile with the bundled nanoflann graph library')
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variant('nemesis', default=False, description='Compile with the bundled nemesis IO library')
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variant('netcdf', default=False, description='Compile with the bundled NETCDF IO library')
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# TODO the copy of parmetis bundled with libMesh assumes that we use the
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# bundled copy of metis, but previous versions of this build script use an
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# external metis installation. Be conservative and completely disable
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# parmetis support to preserve the old behavior (and to prevent compiling
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# with two different copies of metis).
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#
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# variant('parmetis', default=False,
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# description='Compile with the bundled PARMETIS graph library')
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variant('qhull', default=False, description='Compile with the bundled qhull mesh generation library')
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variant('sfc', default=False, description='Compile with the bundled sfcurves partitioning library')
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variant('tetgen', default=False, description='Compile with the bundled tetgen mesh generation library')
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variant('triangle', default=False, description='Compile with the bundled Triangle mesh generation library')
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# support for libraries that may be externally installed:
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variant('boost', default=False, description='Compile with components dependent on boost')
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variant('eigen', default=False, description='support for dense linear algebra with Eigen')
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variant('hdf5', default=False, description='Compile with support for HDF5 files')
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variant('slepc', default=False, description='Compile with support for the SLEPc eigensolver')
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# other features:
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variant('debug', default=False, description='Compile with support for debugging')
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variant('mpi', default=True, description='Enables MPI parallelism')
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variant('slepc', default=False, description='SLEPc eigensolver')
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# While it is possible to configure libMesh to use openMP with neither
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# pthreads nor TBB, no openMP code can actually be reached without enabling
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# pthreads as well. Hence, since enabling openMP while disabling pthreads
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# is not useful, we include openMP in the same variant to make it clear
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# which scheduler is ultimately used.
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variant('threads', default='none',
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description='Enable threading support (with a particular '
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'scheduler, in the case of openmp and tbb)',
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values=('none', 'pthreads', 'tbb', 'openmp'), multi=False)
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# Parallel version of libMesh needs MPI & parallel solvers
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conflicts('+metaphysicl', when='@:1.2.999',
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msg='The interface to metaphysicl is not available in libMesh '
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'versions older than 1.3.0. Please explicitly disable this '
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'variant.')
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depends_on('boost', when='+boost')
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# The Scotch dependency of Eigen is not used by libMesh. Since Scotch can
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# only be used with certain versions of flex it conflicts with several
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# versions of GCC, so explicitly disable it.
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depends_on('eigen~scotch', when='+eigen')
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depends_on('hdf5+mpi', when='+hdf5+mpi')
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depends_on('mpi', when='+mpi')
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depends_on('mpi', when='+slepc')
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# compilation dependencies depend on perl
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depends_on('perl')
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depends_on('petsc+mpi', when='+mpi')
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# SLEPc version needs SLEPc and requires MPI
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depends_on('petsc+metis', when='+metis')
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depends_on('slepc', when='+slepc')
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conflicts('~mpi', when='+slepc')
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depends_on('tbb', when='threads=tbb')
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def install(self, spec, prefix):
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config_args = ["--prefix=%s" % prefix]
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def configure_args(self):
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options = []
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if '+mpi' in spec:
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config_args.append('CC=%s' % spec['mpi'].mpicc)
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config_args.append('CXX=%s' % spec['mpi'].mpicxx)
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config_args.append('PETSC_DIR=%s' % spec['petsc'].prefix)
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# GLIBCXX debugging is not, by default, supported by other libraries,
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# so unconditionally disable it for libmesh
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options.append('--enable-glibcxx-debugging=no')
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if '+slepc' in spec:
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config_args.append('SLEPC_DIR=%s' % spec['slepc'].prefix)
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# All bundled dependencies are explicitly disabled, so we do not need
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# to perform this check:
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options.append('--disable-strict-lgpl')
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configure(*config_args)
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# The Hinnant unique pointer implementation is incompatible with boost
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# (and not necessary with C++11 support), so unconditionally disable
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# it:
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options.append('--disable-hinnant-unique-ptr')
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# libMesh does not allow for us to specify an installation location for
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# zlib, an undocumented dependency of gzstreams: hence we must
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# unconditionally disable gzstreams.
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options.append('--enable-gzstreams=no')
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# Similarly, since we cannot specify a location for bzip2 or xz, so
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# disable them to avoid picking up system installations:
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options.append('--disable-bzip2')
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options.append('--disable-xz')
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# TODO enable GDB backtracing. Disable for now to avoid picking up the
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# system gdb installation:
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options.append('--without-gdb-command')
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make()
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make('install')
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# TODO add X11 as a dependency to get tecplot working
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options.append('--enable-tecio=no')
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options.append('--enable-tecplot=no')
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# handle the bundled libraries that are not themselves dependencies of
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# other bundled libaries:
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for bundled_library in ['capnproto', 'exodusii', 'fparser', 'gmv',
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'laspack', 'libHilbert', 'metaphysicl',
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'nanoflann', 'nemesis', 'parmetis', 'qhull',
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'sfc', 'tetgen', 'triangle']:
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if '+' + bundled_library.lower() in self.spec:
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options.append('--enable-' + bundled_library + "=yes")
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else:
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options.append('--enable-' + bundled_library + "=no")
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# and the ones which are dependencies of other bundled libraries:
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if '+exodusii' in self.spec or '+netcdf' in self.spec:
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options.append('--enable-netcdf=yes')
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else:
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options.append('--enable-netcdf=no')
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# handle external library dependencies:
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if '+boost' in self.spec:
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options.append('--with-boost=%s' % self.spec['boost'].prefix)
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else:
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options.append('--enable-boost=no')
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if '+eigen' in self.spec:
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options.append('--with-eigen=%s' % self.spec['eigen'].prefix)
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else:
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options.append('--enable-eigen=no')
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if '+hdf5' in self.spec:
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options.append('--with-hdf5=%s' % self.spec['hdf5'].prefix)
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else:
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options.append('--enable-hdf5=no')
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# This is necessary with libMesh 1.2.1 to prevent a configure
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# error:
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if '+netcdf' not in self.spec:
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options.append('--disable-netcdf-4')
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if '+metis' in self.spec:
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options.append('--with-metis=PETSc')
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if '+petsc' in self.spec:
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options.append('--enable-petsc=yes')
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options.append('PETSC_DIR=%s' % self.spec['petsc'].prefix)
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else:
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options.append('--enable-petsc=no')
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if '+slepc' in self.spec:
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options.append('SLEPC_DIR=%s' % self.spec['slepc'].prefix)
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else:
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options.append('--enable-slepc=no')
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# and, finally, other things:
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if '+debug' in self.spec:
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options.append('--with-methods=dbg')
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else:
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options.append('--with-methods=opt')
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if '+mpi' in self.spec:
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options.append('CC=%s' % self.spec['mpi'].mpicc)
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options.append('CXX=%s' % self.spec['mpi'].mpicxx)
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options.append('--with-mpi=%s' % self.spec['mpi'].prefix)
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else:
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options.append('--disable-mpi')
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# libMesh will try to link with the system MPI library unless we
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# provide explicit overrides
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options.append('CC=%s' % self.compiler.cc)
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options.append('CXX=%s' % self.compiler.cxx)
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if 'threads=openmp' in self.spec:
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# OpenMP cannot be used if pthreads is not available: see
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# parallel/threads_pthread.h and parallel/threads.h
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options.append('--enable-openmp=yes')
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options.append('--with-thread-model=pthread')
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options.append('--enable-pthreads=yes')
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else:
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options.append('--enable-openmp=no')
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if 'threads=pthreads' in self.spec:
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options.append('--with-thread-model=pthread')
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options.append('--enable-pthreads=yes')
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else:
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if 'threads=openmp' not in self.spec:
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options.append('--enable-pthreads=no')
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if 'threads=tbb' in self.spec:
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options.append('--with-thread-model=tbb')
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options.append('--enable-tbb=yes')
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options.append('--with-tbb=%s' % self.spec['tbb'].prefix)
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else:
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options.append('--enable-tbb=no')
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return options
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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spack_env.append_flags('PERL', self.spec['perl'].command.path)
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