diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index dd86b17a53ab8b98e257f8827df2290f5dad1f10..6b152f786311decc2206e2dd657260b18cb88873 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -41,10 +41,17 @@ class ArpackNg(Package):
depends_on('blas')
depends_on('lapack')
+ depends_on('automake')
+ depends_on('autoconf')
+ depends_on('libtool@2.4.2:')
+
depends_on('mpi', when='+mpi')
def install(self, spec, prefix):
# Apparently autotools are not bootstrapped
+ # TODO: switch to use the CMake build in the next version
+ # rather than bootstrapping.
+ which('libtoolize')()
bootstrap = Executable('./bootstrap')
options = ['--prefix=%s' % prefix]
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..7aaf33380e6b5e1fe09645b164c20c8cde9d5d33
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -0,0 +1,239 @@
+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."""
+ homepage = "https://www.dealii.org"
+ url = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"
+
+ version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
+ version('dev', git='https://github.com/dealii/dealii.git')
+
+ 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('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)')
+ variant('oce', default=True, description='Compile with OCE')
+ variant('p4est', default=True, description='Compile with P4est (only with MPI)')
+ variant('petsc', default=True, description='Compile with Petsc (only with MPI)')
+ variant('slepc', default=True, description='Compile with Slepc (only with Petsc and MPI)')
+ variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)')
+
+ # required dependencies, light version
+ depends_on ("blas")
+ depends_on ("boost", when='~mpi')
+ depends_on ("boost+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")
+
+ # optional dependencies
+ depends_on ("mpi", when="+mpi")
+ depends_on ("arpack-ng+mpi", when='+arpack+mpi')
+ depends_on ("doxygen", when='+doc')
+ depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
+ depends_on ("metis", 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") #FIXME
+ #depends_on ("astyle") #FIXME
+
+ def install(self, spec, prefix):
+ options = []
+ options.extend(std_cmake_args)
+
+ # CMAKE_BUILD_TYPE should be DebugRelease | Debug | Release
+ for word in options[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ options.remove(word)
+
+ dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
+ options.extend([
+ '-DCMAKE_BUILD_TYPE=DebugRelease',
+ '-DDEAL_II_COMPONENT_EXAMPLES=ON',
+ '-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
+ '-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,
+ '-DP4EST_DIR=%s' % spec['p4est'].prefix,
+ '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
+ '-DTBB_DIR=%s' % spec['tbb'].prefix,
+ '-DZLIB_DIR=%s' % spec['zlib'].prefix
+ ])
+
+ # MPI
+ 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'),
+ ])
+ else:
+ options.extend([
+ '-DDEAL_II_WITH_MPI:BOOL=OFF',
+ ])
+
+ # Optional dependencies for which librariy names are the same as CMake variables
+ for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
+ 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())
+ ])
+ else:
+ options.extend([
+ '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper())
+ ])
+
+ # doxygen
+ options.extend([
+ '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'),
+ ])
+
+
+ # arpack
+ if '+arpack' in spec:
+ options.extend([
+ '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
+ '-DDEAL_II_WITH_ARPACK=ON',
+ '-DDEAL_II_ARPACK_WITH_PARPACK=ON'
+ ])
+ else:
+ options.extend([
+ '-DDEAL_II_WITH_ARPACK=OFF'
+ ])
+
+ # since Netcdf is spread among two, need to do it by hand:
+ 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),
+ ])
+ else:
+ options.extend([
+ '-DDEAL_II_WITH_NETCDF=OFF'
+ ])
+
+ # Open Cascade
+ if '+oce' in spec:
+ options.extend([
+ '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
+ '-DDEAL_II_WITH_OPENCASCADE=ON'
+ ])
+ else:
+ options.extend([
+ '-DDEAL_II_WITH_OPENCASCADE=OFF'
+ ])
+
+ cmake('.', *options)
+
+ make()
+ make("test")
+ make("install")
+
+ # run some MPI examples with different solvers from PETSc and Trilinos
+ env['DEAL_II_DIR'] = prefix
+ print('=====================================')
+ print('============ EXAMPLES ===============')
+ print('=====================================')
+ # take bare-bones step-3
+ print('=====================================')
+ print('============ Step-3 =================')
+ print('=====================================')
+ with working_dir('examples/step-3'):
+ cmake('.')
+ make('release')
+ make('run',parallel=False)
+
+ # take step-40 which can use both PETSc and Trilinos
+ # FIXME: switch step-40 to MPI run
+ with working_dir('examples/step-40'):
+ print('=====================================')
+ 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')
+ cmake('.')
+ if '^petsc' in spec:
+ make('release')
+ 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')
+ if '^trilinos+hypre' in spec:
+ make('release')
+ 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 \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
+ filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
+ if '^trilinos+superlu-dist' in spec:
+ make('release')
+ make('run',paralle=False)
+
+ print('=====================================')
+ print('====== Step-40 Trilinos MUMPS =======')
+ print('=====================================')
+ # switch to Mumps
+ filter_file(r'(Amesos_Superludist)', ('Amesos_Mumps'), 'step-40.cc')
+ if '^trilinos+mumps' in spec:
+ make('release')
+ make('run',parallel=False)
+
+ print('=====================================')
+ print('============ Step-36 ================')
+ print('=====================================')
+ with working_dir('examples/step-36'):
+ if 'slepc' in spec:
+ cmake('.')
+ make('release')
+ make('run',parallel=False)
+
+ print('=====================================')
+ print('============ Step-54 ================')
+ print('=====================================')
+ with working_dir('examples/step-54'):
+ if 'oce' in spec:
+ cmake('.')
+ make('release')
+ if sys.platform != 'darwin': #FIXME
+ make('run',parallel=False)