petsc: added variants and dips (#24725)

Add HPDDM, MMG, ParMMG and Tetgen to PETSc.

Add mmg version 5.5.2 (compatible with PETSc).
Add parmmg, depending on mmg.
Add pic variant to tetgen for PETSc.

9 files changed, 225 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index ee3e3c218c..971e9ca31f 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -128,6 +128,9 @@ class ArpackNg(Package):
 
         if '+shared' in spec:
             options.append('-DBUILD_SHARED_LIBS=ON')
+        else:
+            options.append('-DBUILD_SHARED_LIBS=OFF')
+            options.append('-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true')
 
         cmake('.', *options)
         make()
diff --git a/var/spack/repos/builtin/packages/freefem/acmpi.patch b/var/spack/repos/builtin/packages/freefem/acmpi.patch
new file mode 100644
index 0000000000..f6dfdc1d2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freefem/acmpi.patch
@@ -0,0 +1,11 @@
+--- a/etc/config/m4/acmpi.m4	2021-04-19 21:45:30.000000000 +0200
++++ b/etc/config/m4/acmpi.m4	2021-07-06 09:53:06.100076241 +0200
+@@ -296,7 +296,7 @@
+            test -n "$MPICC" && ff_mpicshow=`$MPICC -show` 2>/dev/null
+            test -n "$MPIFC" && ff_mpifcshow=`$MPIFC -show` 2>/dev/null
+ 	    if test "$with_mpilibs" = no -o -z "$with_mpilibs" ; then
+-		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^[-/][^WLlOgpf]|^-Wp,'|tr '\n' ' '`]
++		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n' | sed '1 d'| grep -E '^[-/][^WLlOgpf]|^-Wp,'|tr '\n' ' '`]
+ 		ff_MPI_LIB_DIRS=""
+ 		[ff_MPI_LIB=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]
+ 		[ff_MPI_LIBC=`echo $ff_mpicshow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]
diff --git a/var/spack/repos/builtin/packages/freefem/acmpi4.8.patch b/var/spack/repos/builtin/packages/freefem/acmpi4.8.patch
new file mode 100644
index 0000000000..59cbec98c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freefem/acmpi4.8.patch
@@ -0,0 +1,11 @@
+--- a/etc/config/m4/acmpi.m4	2021-04-19 21:45:30.000000000 +0200
++++ b/etc/config/m4/acmpi.m4	2021-07-06 09:53:06.100076241 +0200
+@@ -296,7 +296,7 @@
+            test -n "$MPICC" && ff_mpicshow=`$MPICC -show` 2>/dev/null
+            test -n "$MPIFC" && ff_mpifcshow=`$MPIFC -show` 2>/dev/null
+ 	    if test "$with_mpilibs" = no -o -z "$with_mpilibs" ; then
+-		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^[-/][^WLlOgp]|^-Wp,'|tr '\n' ' '`]
++		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n' | sed '1 d'| grep -E '^[-/][^WLlOgpf]|^-Wp,'|tr '\n' ' '`]
+ 		ff_MPI_LIB_DIRS=""
+ 		[ff_MPI_LIB=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]
+ 		[ff_MPI_LIBC=`echo $ff_mpicshow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]
diff --git a/var/spack/repos/builtin/packages/freefem/package.py b/var/spack/repos/builtin/packages/freefem/package.py
new file mode 100644
index 0000000000..69d2e017fd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freefem/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Freefem(AutotoolsPackage):
+    """FreeFEM is a popular 2D and 3D partial differential equations (PDE) solver.
+    It allows you to easily implement your own physics modules using the provided
+    FreeFEM language. FreeFEM offers a large list of finite elements, like the
+    Lagrange, Taylor-Hood, etc., usable in the continuous and discontinuous
+    Galerkin method framework.
+    """
+
+    homepage = "https://freefem.org"
+    url      = "https://github.com/FreeFem/FreeFem-sources/archive/refs/tags/v4.9.tar.gz"
+
+    maintainers = ['corentin-dev']
+
+    version('4.9',   sha256='299ba2b73dfff578b7890f693c1e835680bf55eba87263cabd60d81909e1e0e4')
+    version('4.8',   sha256='499b1ca24d45088226a238412ea1492d9cc3eb6088866904145511469780180d')
+    version('4.7-1', sha256='60d84424d20b5f6abaee638dc423480fc76f9c389bba1a2f23fd984e39a3fb96')
+    version('4.7',   sha256='c1797b642e9c3d543eaad4949d26ce1e986f531ee9be14fff606ea525ada9206')
+    version('4.6',   sha256='6c09af8e189fc02214b0e664b679b49832c134e29cf1ede3cab29cf754f6078f')
+    version('4.5',   sha256='5b2d4125c312da8fbedd49a72e742f18f35e0ae100c82fb493067dfad5d51432')
+
+    variant('mpi', default=False,
+            description='Activate MPI support')
+    variant('petsc', default=False,
+            description='Compile with PETSc/SLEPc')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('slepc', when='+petsc')
+
+    # Patches to help configure find correctly MPI flags
+    # when using full path for compilers.
+    patch('acmpi.patch', when='@4.9', sha256='8157d89fc19227a555b54a4f2eb1c44da8aef3192077a6df2e88093b850f4c50')
+    patch('acmpi4.8.patch', when='@:4.8', sha256='be84f7b1b8182ff0151c258056a09bda70d72a611b0a4da1fa1954df2e0fe84e')
+
+    def autoreconf(self, spec, prefix):
+        autoreconf = which('autoreconf')
+        autoreconf('-i')
+
+    def configure_args(self):
+        spec = self.spec
+        options = ['--disable-mkl',
+                   'CFLAGS=%s' % ' '.join(spec.compiler_flags['cflags']),
+                   'FFLAGS=%s' % ' '.join(spec.compiler_flags['fflags']),
+                   'CXXFLAGS=%s' % ' '.join(spec.compiler_flags['cxxflags'])]
+
+        if '+petsc' in spec:
+            options.append('--with-petsc=%s'
+                           % spec['petsc'].prefix.lib.petsc.conf.petscvariables)
+            options.append('--with-slepc-ldflags=%s'
+                           % spec['slepc'].libs.ld_flags)
+            options.append('--with-slepc-include=%s'
+                           % spec['slepc'].headers.include_flags)
+        else:
+            options.append('--without-petsc')
+            options.append('--without-slepc')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/hpddm/package.py b/var/spack/repos/builtin/packages/hpddm/package.py
new file mode 100644
index 0000000000..f2b6794777
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpddm/package.py
@@ -0,0 +1,75 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hpddm(Package):
+    """High-performance unified framework for domain decomposition methods."""
+
+    homepage = "https://github.com/hpddm/hpddm"
+    url      = "https://github.com/hpddm/hpddm"
+    git      = "https://github.com/hpddm/hpddm.git"
+
+    maintainers = ['corentin-dev']
+
+    version('main', branch='main')
+    version('2.1.2', commit='e58205623814f59bf2aec2e2bab8eafcfbd22466')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mumps')
+    depends_on('hypre')
+    depends_on('scalapack')
+    depends_on('arpack-ng')
+    depends_on('python')
+
+    def configure(self):
+        makefile_inc = []
+        # cflags = [
+        makefile_inc.append('SOLVER ?= MUMPS')
+        makefile_inc.append('SUBSOLVER ?= MUMPS')
+        makefile_inc.append('EIGENSOLVER ?= ARPACK')
+        makefile_inc.append('MPICXX ?= mpic++')
+        makefile_inc.append('MPICC ?= mpicc')
+        makefile_inc.append('MPIF90 ?= mpif90')
+        makefile_inc.append('MPIRUN ?= mpirun -np')
+
+        makefile_inc.append('override CXXFLAGS += -std=c++11 -O3 -fPIC')
+        makefile_inc.append('override CFLAGS += -std=c99 -O3')
+        makefile_inc.append('INCS =')
+        makefile_inc.append('LIBS =')
+
+        makefile_inc.append("HPDDMFLAGS ?= -DHPDM_NUMBERING=\'C\'")
+
+        makefile_inc.append('MUMPS_INCS = ')
+        makefile_inc.append('PYTHON_INCS = ')
+        makefile_inc.append('BLAS_LIBS = -lopenblas')
+        makefile_inc.append('ARPACK_LIBS = -larpack')
+        makefile_inc.append('SCALAPACK_LIBS = -lscalapack')
+        makefile_inc.append(' '.join([
+            'MUMPS_LIBS', '=',
+            '-lcmumps',
+            '-ldmumps',
+            '-lsmumps',
+            '-lzmumps',
+            '-lmumps_common',
+            '-lpord',
+            '-fopenmp']))
+        makefile_inc.append('HYPRE_LIBS = -lHYPRE')
+        makefile_inc.append('PYTHON_LIBS = -lpython3')
+
+        with working_dir('.'):
+            with open('Makefile.inc', 'w') as fh:
+                fh.write('\n'.join(makefile_inc))
+
+    def patch(self):
+        self.configure()
+
+    def install(self, spec, prefix):
+        make()
+        install_tree('include', prefix.include)
+        # make('install')
diff --git a/var/spack/repos/builtin/packages/mmg/package.py b/var/spack/repos/builtin/packages/mmg/package.py
index a420975bb3..caebb025df 100644
--- a/var/spack/repos/builtin/packages/mmg/package.py
+++ b/var/spack/repos/builtin/packages/mmg/package.py
@@ -26,6 +26,7 @@ class Mmg(CMakePackage):
     homepage = "http://www.mmgtools.org/"
     url      = "https://github.com/MmgTools/mmg/archive/v5.3.13.tar.gz"
 
+    version('5.5.2',  sha256='58e3b866101e6f0686758e16bcf9fb5fb06c85184533fc5054ef1c8adfd4be73')
     version('5.4.0',  sha256='2b5cc505018859856766be901797ff5d4789f89377038a0211176a5571039750')
     version('5.3.13', sha256='d9a5925b69b0433f942ab2c8e55659d9ccea758743354b43d54fdf88a6c3c191')
 
diff --git a/var/spack/repos/builtin/packages/parmmg/package.py b/var/spack/repos/builtin/packages/parmmg/package.py
new file mode 100644
index 0000000000..aa151d9cff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmmg/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Parmmg(CMakePackage):
+    """ParMMG is a parallel remesher based on MMG"""
+
+    homepage = "https://www.mmgtools.org"
+    url      = "https://github.com/MmgTools/ParMmg/archive/refs/tags/v1.3.0.tar.gz"
+
+    maintainers = ['corentin-dev']
+
+    version('1.3.0', sha256='d43b73a73b62545b5a31bbe25562f69c9e63ad8a6d416bd459781203e37427cf')
+    version('1.2.0', sha256='99729cc292dcb59c87e3f25d4cabf5a64841e83b624d383e1fd3fb7f960df672')
+    version('1.1.0', sha256='a5904f1f56b7809ab9ec2f6118b03a082ec2b5564355a73c74fc55426cc69600')
+    version('1.0.0', sha256='614feb815ff6cdfc9bced30e8105994f0bf3a812243619d3349203ec1851cf6d')
+
+    depends_on('mmg')
+    depends_on('metis')
+    depends_on('vtk')
+    depends_on('mpi')
+
+    variant('pic', default=True,
+            description='Build with position independent code')
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant('CMAKE_POSITION_INDEPENDENT_CODE', 'pic'),
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 4028392723..b0c6810d41 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -91,6 +91,14 @@ class Petsc(Package, CudaPackage, ROCmPackage):
             description='Activates support for HDF5 (only parallel)')
     variant('hypre',   default=True,
             description='Activates support for Hypre (only parallel)')
+    variant('hpddm',   default=False,
+            description='Activates support for HPDDM (only parallel)')
+    variant('mmg',   default=False,
+            description='Activates support for MMG')
+    variant('parmmg',   default=False,
+            description='Activates support for ParMMG (only parallel)')
+    variant('tetgen',   default=False,
+            description='Activates support for Tetgen')
     # Mumps is disabled by default, because it depends on Scalapack
     # which is not portable to all HPC systems
     variant('mumps',   default=False,
@@ -161,6 +169,8 @@ class Petsc(Package, CudaPackage, ROCmPackage):
     conflicts('+fftw', when='~mpi', msg=mpi_msg)
     conflicts('+hdf5', when='~mpi', msg=mpi_msg)
     conflicts('+hypre', when='~mpi', msg=mpi_msg)
+    conflicts('+hpddm', when='~mpi', msg=mpi_msg)
+    conflicts('+parmmg', when='~mpi', msg=mpi_msg)
     conflicts('+moab', when='~mpi', msg=mpi_msg)
     conflicts('+mumps', when='~mpi', msg=mpi_msg)
     conflicts('+p4est', when='~mpi', msg=mpi_msg)
@@ -229,6 +239,9 @@ class Petsc(Package, CudaPackage, ROCmPackage):
     depends_on('parmetis+int64', when='+metis+mpi+int64')
     depends_on('parmetis~int64', when='+metis+mpi~int64')
     depends_on('valgrind', when='+valgrind')
+    depends_on('mmg', when='+mmg')
+    depends_on('parmmg', when='+parmmg')
+    depends_on('tetgen+pic', when='+tetgen')
     # Hypre does not support complex numbers.
     # Also PETSc prefer to build it without internal superlu, likely due to
     # conflict in headers see
@@ -417,6 +430,9 @@ class Petsc(Package, CudaPackage, ROCmPackage):
                 (jpeg_sp, 'libjpeg', True, True),
                 (scalapack_sp, 'scalapack', False, True),
                 'strumpack',
+                'mmg',
+                'parmmg',
+                ('tetgen', 'tetgen', False, False),
         ):
             # Cannot check `library in spec` because of transitive deps
             # Cannot check variants because parmetis keys on +metis
@@ -472,6 +488,11 @@ class Petsc(Package, CudaPackage, ROCmPackage):
                 '--with-mkl_pardiso-dir=%s' % spec['mkl'].prefix
             )
 
+        # For the moment, HPDDM does not work as a dependency
+        # using download instead
+        if '+hpddm' in spec:
+            options.append('--download-hpddm')
+
         python('configure', '--prefix=%s' % prefix, *options)
 
         # PETSc has its own way of doing parallel make.
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
index 1efff4ea65..503c6bd297 100644
--- a/var/spack/repos/builtin/packages/tetgen/package.py
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -21,6 +21,7 @@ class Tetgen(Package):
     version('1.5.0', sha256='4d114861d5ef2063afd06ef38885ec46822e90e7b4ea38c864f76493451f9cf3', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz')
     version('1.4.3', sha256='952711bb06b7f64fd855eb24c33f08e3faf40bdd54764de10bbe5ed5b0dce034', url='http://www.tetgen.org/files/tetgen1.4.3.tar.gz')
 
+    variant('pic', default=True, description='Builds the library in pic mode.')
     variant('debug', default=False, description='Builds the library in debug mode.')
     variant('except', default=False, description='Replaces asserts with exceptions for better C++ compatibility.')
 
@@ -28,9 +29,12 @@ class Tetgen(Package):
 
     def patch(self):
         cflags = '-g -O0' if '+debug' in self.spec else '-g0 -O3'
+        cflags = cflags + ' -fPIC' if '+pic' in self.spec else cflags
+        predcflags = '-fPIC' if '+pic' in self.spec else ''
 
         mff = FileFilter('makefile')
         mff.filter(r'^(C(XX)?FLAGS\s*=)(.*)$', r'\1 {0}'.format(cflags))
+        mff.filter(r'^(PREDC(XX)?FLAGS\s*=.*)$', r'\1 {0}'.format(predcflags))
 
         if '+except' in self.spec:
             hff = FileFilter('tetgen.h')