add MoFEM packages (#8700)

* add mofem-cephas package

* add mofem fracture module

* add user modules build and fracture modyle

* add minimal surface module

* add slepc variant

* bump mofem core lib version

* bump mofem core lib version

* bump version

* fix bug

* set upper bound to petsc version  and other chanes

* fix indentation

* add minimal med file installation

* chcekc with flake8 and installation with spack packages

* add variants to med package

* upper bound to adol-c and remove obsolete internal package install

* fix basic module install

* module install from external source in extended prefix

* remove obsolte code and reverse to variant doxygen

* fix git adress

* improve packaging for mofem users modules

* fix flake8

* move dependencies after variants

* move  root_cmakelists_dir right before cmake_args

* remove unused variants

* use append for single element

* replace root_cmakelists_dir

* use install_tree instead copy tree

* simplify code

* remove phase and mkdirp

* add run tests

* instal ext modules to ext_users_modules directory

* move version below url

* simplify directory name

* use underscore in variant name

* remove unused variable

* fix link to blas libs

* add missing boost dependence

* fix problem with copying module source code

* change variant name form doxygen to docs

* add expanded description

* make installation consistent with spack

* fix flake8

* make extensions installed

* code comments and minor corrections

* make slepc variant false by default

6 files changed, 456 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
index 2947556f80..b6f00b7eeb 100644
--- a/var/spack/repos/builtin/packages/adol-c/package.py
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -37,6 +37,7 @@ class AdolC(AutotoolsPackage):
     version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7')
     version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865')
     version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
+    version('2.5.2', '96f81b80e93cca57398066ea4afe28f0')
 
     variant('advanced_branching', default=False,
             description='Enable advanced branching to reduce retaping')
diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py
new file mode 100644
index 0000000000..353ed091aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/med/package.py
@@ -0,0 +1,71 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+
+
+class Med(CMakePackage):
+    """The MED file format is a specialization of the HDF5 standard."""
+
+    homepage = "http://docs.salome-platform.org/latest/dev/MEDCoupling/med-file.html"
+    url = "http://files.salome-platform.org/Salome/other/med-3.2.0.tar.gz"
+
+    maintainers = ['likask']
+
+    version('3.2.0', 'eb61df92f0624feb6328f517cd756a23')
+
+    variant('api23', default=True, description='Enable API2.3')
+
+    depends_on('mpi')
+    depends_on('hdf5@:1.8.19+mpi')
+
+    # FIXME This is minimal installation.
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+api23' in spec:
+            options.extend([
+                '-DCMAKE_CXX_FLAGS:STRING=-DMED_API_23=1',
+                '-DCMAKE_C_FLAGS:STRING=-DMED_API_23=1',
+                '-DMED_API_23=1'])
+
+        options.extend([
+            '-DMEDFILE_USE_MPI=YES'
+            '-DMEDFILE_BUILD_TESTS={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DMEDFILE_BUILD_PYTHON=OFF',
+            '-DMEDFILE_INSTALL_DOC=OFF',
+            '-DMEDFILE_BUILD_SHARED_LIBS=OFF',
+            '-DMEDFILE_BUILD_STATIC_LIBS=ON',
+            '-DCMAKE_Fortran_COMPILER='])
+
+        options.extend([
+            '-DHDF5_ROOT_DIR=%s' % spec['hdf5'].prefix,
+            '-DMPI_ROOT_DIR=%s' % spec['mpi'].prefix])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py
new file mode 100644
index 0000000000..f98f0a6379
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py
@@ -0,0 +1,100 @@
+##############################################################################
+# 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+
+
+class MofemCephas(CMakePackage):
+    """mofem-cephas core library"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem-cephas.git"
+
+    maintainers = ['likask']
+
+    version('0.8.7', git='https://bitbucket.org/likask/mofem-cephas.git',
+        tag='v0.8.7', submodules=True)
+    version('develop',
+        git='https://bitbucket.org/likask/mofem-cephas.git',
+        branch='develop', submodules=True)
+
+    # This option can be only used for development of core lib
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking to source')
+    variant('adol-c', default=True, description='Compile with Adol-C')
+    variant('tetgen', default=True, description='Compile with Tetgen')
+    variant('med', default=True, description='Compile with Med')
+    variant('slepc', default=False, description='Compile with Slepc')
+
+    depends_on("mpi")
+    depends_on("boost")
+    depends_on("parmetis")
+    # Fixed version of hdf5, to remove some problems with dependent
+    # packages, f.e. MED format
+    depends_on("hdf5@:1.8.19+hl+mpi")
+    depends_on("petsc@:3.9.2+mumps+mpi")
+    depends_on('slepc', when='+slepc')
+    depends_on("moab")
+    # Upper bound set to ADOL-C until issues with memory leaks
+    # for versions 2.6: fully resolved
+    depends_on("adol-c@2.5.2~examples", when="+adol-c")
+    depends_on("tetgen", when="+tetgen")
+    depends_on("med", when='+med')
+
+    extendable = True
+
+    root_cmakelists_dir = 'mofem'
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DPETSC_DIR=%s' % spec['petsc'].prefix,
+            '-DPETSC_ARCH=',
+            '-DMOAB_DIR=%s' % spec['moab'].prefix,
+            '-DBOOST_DIR=%s' % spec['boost'].prefix])
+
+        # build tests
+        options.append('-DMOFEM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        # variant packages
+        if '+adol-c' in spec:
+            options.append('-DADOL-C_DIR=%s' % spec['adol-c'].prefix)
+
+        if '+tetgen' in spec:
+            options.append('-DTETGEN_DIR=%s' % spec['tetgen'].prefix)
+
+        if '+med' in spec:
+            options.append('-DMED_DIR=%s' % spec['med'].prefix)
+
+        if '+slepc' in spec:
+            options.append('-DSLEPC_DIR=%s' % spec['slepc'].prefix)
+
+        # copy users modules, i.e. stand alone vs linked users modules
+        options.append(
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO'))
+        return options
diff --git a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
new file mode 100644
index 0000000000..0369aba7d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
@@ -0,0 +1,107 @@
+##############################################################################
+# 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+
+
+class MofemFractureModule(CMakePackage):
+    """mofem fracture module"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem_um_fracture_mechanics"
+
+    maintainers = ['likask']
+
+    version('0.9.42',
+        git='https://bitbucket.org/likask/mofem_um_fracture_mechanics',
+        tag='v0.9.42')
+    version('develop',
+        git='https://bitbucket.org/likask/mofem_um_fracture_mechanics',
+        branch='develop')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem-cephas package set cmake
+    # environment to install extension from extension repository. It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # Set module version
+        if self.spec.version == Version('develop'):
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % 0,
+                '-DFM_VERSION_MINOR=%s' % 0,
+                '-DFM_VERSION_BUILD=%s' % 0])
+        else:
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % self.spec.version[0],
+                '-DFM_VERSION_MINOR=%s' % self.spec.version[1],
+                '-DFM_VERSION_BUILD=%s' % self.spec.version[2]])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.fracture_mechanics)
diff --git a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
new file mode 100644
index 0000000000..761fbc178a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
@@ -0,0 +1,95 @@
+##############################################################################
+# 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+
+
+class MofemMinimalSurfaceEquation(CMakePackage):
+    """mofem minimal surface equation"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation"
+
+    maintainers = ['likask']
+
+    version('0.3.9',
+        git='https://bitbucket.org/likask/mofem_um_minimal_surface_equation',
+        tag='v0.3.9')
+    version('develop',
+        git='https://bitbucket.org/likask/mofem_um_minimal_surface_equation',
+        branch='develop')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem - cephas package set cmake
+    # environment to install extension from extension repository.It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.minimal_surface_equation)
diff --git a/var/spack/repos/builtin/packages/mofem-users-modules/package.py b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
new file mode 100644
index 0000000000..acab4417d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
@@ -0,0 +1,82 @@
+##############################################################################
+# 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/spack/spack
+# Please also see the NOTICE and LICENSE files 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 *
+
+
+class MofemUsersModules(CMakePackage):
+    """MofemUsersModules creates installation environment for user-provided
+    modules and extends of mofem-cephas package. The CMakeList.txt file for
+    user modules is located in mofem-cephas/user_modules prefix.
+    MofemUsersModules itself does not contain any code (is a dummy with a
+    single dummy version). It provide sources location of users modules, i.e.
+    mofem-fracture-module. Those are kept as a stand-alone package (instead
+    of resources) as they have different versions and developers. One can
+    install the extension, f.e. spack installs extension spack install
+    mofem-fracture-module. Next, create a symlink to run the code, f.e. spack
+    view symlink um_view mofem-cephas, and activate the extension, i.e. spack
+    activate um_view mofem-minimal-surface-equation. Basic mofem
+    functionality is available when with spack install mofem-users-modules,
+    it provides simple examples for calculating elasticity problems,
+    magnetostatics, saturated and unsaturated flow and a couple more. For
+    more information how to work with Spack and MoFEM see
+    http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem-joseph/downloads/users_modules_dummy"
+    version('1.0', '5a8b22c9cdcad7bbad92b1590d55edb1', expand=False)
+
+    maintainers = ['likask']
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options