From a18a6420748da96aafdd00b8ce1a9d80995a10a4 Mon Sep 17 00:00:00 2001 From: Lukasz Date: Sun, 22 Jul 2018 21:26:30 +0100 Subject: 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 --- var/spack/repos/builtin/packages/adol-c/package.py | 1 + var/spack/repos/builtin/packages/med/package.py | 71 ++++++++++++++ .../repos/builtin/packages/mofem-cephas/package.py | 100 +++++++++++++++++++ .../packages/mofem-fracture-module/package.py | 107 +++++++++++++++++++++ .../mofem-minimal-surface-equation/package.py | 95 ++++++++++++++++++ .../packages/mofem-users-modules/package.py | 82 ++++++++++++++++ 6 files changed, 456 insertions(+) create mode 100644 var/spack/repos/builtin/packages/med/package.py create mode 100644 var/spack/repos/builtin/packages/mofem-cephas/package.py create mode 100644 var/spack/repos/builtin/packages/mofem-fracture-module/package.py create mode 100644 var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py create mode 100644 var/spack/repos/builtin/packages/mofem-users-modules/package.py (limited to 'var') 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 -- cgit v1.2.3-60-g2f50