diff options
55 files changed, 1778 insertions, 123 deletions
@@ -59,7 +59,8 @@ can join it here: At the moment, contributing to Spack is relatively simple. Just send us a [pull request](https://help.github.com/articles/using-pull-requests/). -When you send your request, make ``develop`` the destination branch. +When you send your request, make ``develop`` the destination branch on the +[Spack repository](https://github.com/LLNL/spack). Spack is using a rough approximation of the [Git Flow](http://nvie.com/posts/a-successful-git-branching-model/) diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 46ca03bec4..70d46a7f77 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -27,7 +27,8 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree' 'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file', 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink', 'set_executable', 'copy_mode', 'unset_executable_mode', - 'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name'] + 'remove_dead_links', 'remove_linked_tree', 'find_library_path', + 'fix_darwin_install_name'] import os import glob @@ -395,6 +396,7 @@ def remove_linked_tree(path): else: shutil.rmtree(path, True) + def fix_darwin_install_name(path): """ Fix install name of dynamic libraries on Darwin to have full path. @@ -420,3 +422,17 @@ def fix_darwin_install_name(path): if dep == os.path.basename(loc): subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0] break + + +def find_library_path(libname, *paths): + """Searches for a file called <libname> in each path. + + Return: + directory where the library was found, if found. None otherwise. + + """ + for path in paths: + library = join_path(path, libname) + if os.path.exists(library): + return path + return None diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 119a255a34..640db0c1d1 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -59,6 +59,11 @@ SPACK_SHORT_SPEC = 'SPACK_SHORT_SPEC' SPACK_DEBUG_LOG_DIR = 'SPACK_DEBUG_LOG_DIR' +# Platform-specific library suffix. +dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so' + + + class MakeExecutable(Executable): """Special callable executable object for make so the user can specify parallel or not on a per-invocation basis. Using @@ -246,6 +251,9 @@ def set_module_variables_for_package(pkg, module): # a Prefix object. m.prefix = pkg.prefix + # Platform-specific library suffix. + m.dso_suffix = dso_suffix + def get_rpaths(pkg): """Get a list of all the rpaths for a package.""" diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py index cf478d3763..20a3fc5fc2 100644 --- a/lib/spack/spack/cmd/pkg.py +++ b/lib/spack/spack/cmd/pkg.py @@ -77,7 +77,8 @@ def get_git(): def list_packages(rev): git = get_git() - relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep + pkgpath = os.path.join(spack.packages_path, 'packages') + relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep output = git('ls-tree', '--full-tree', '--name-only', rev, relpath, output=str) return sorted(line[len(relpath):] for line in output.split('\n') if line) diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py index 5786780efb..975bb54ef7 100644 --- a/lib/spack/spack/cmd/stage.py +++ b/lib/spack/spack/cmd/stage.py @@ -35,6 +35,9 @@ def setup_parser(subparser): subparser.add_argument( '-n', '--no-checksum', action='store_true', dest='no_checksum', help="Do not check downloaded packages against checksum") + subparser.add_argument( + '-p', '--path', dest='path', + help="Path to stage package, does not add to spack tree") subparser.add_argument( 'specs', nargs=argparse.REMAINDER, help="specs of packages to stage") @@ -50,4 +53,6 @@ def stage(parser, args): specs = spack.cmd.parse_specs(args.specs, concretize=True) for spec in specs: package = spack.repo.get(spec) + if args.path: + package.path = args.path package.do_stage() diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 9af3221837..4065553131 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -335,6 +335,9 @@ class Package(object): if '.' in self.name: self.name = self.name[self.name.rindex('.') + 1:] + # Allow custom staging paths for packages + self.path=None + # Sanity check attributes required by Spack directives. spack.directives.ensure_dicts(type(self)) @@ -445,7 +448,8 @@ class Package(object): resource_stage_folder = self._resource_stage(resource) resource_mirror = join_path(self.name, os.path.basename(fetcher.url)) stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource, - name=resource_stage_folder, mirror_path=resource_mirror) + name=resource_stage_folder, mirror_path=resource_mirror, + path=self.path) return stage def _make_root_stage(self, fetcher): @@ -455,7 +459,7 @@ class Package(object): s = self.spec stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash()) # Build the composite stage - stage = Stage(fetcher, mirror_path=mp, name=stage_name) + stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path) return stage def _make_stage(self): @@ -709,7 +713,6 @@ class Package(object): if spack.do_checksum and self.version in self.versions: self.stage.check() - def do_stage(self, mirror_only=False): """Unpacks the fetched tarball, then changes into the expanded tarball directory.""" @@ -926,6 +929,9 @@ class Package(object): install(env_path, env_install_path) dump_packages(self.spec, packages_dir) + # Run post install hooks before build stage is removed. + spack.hooks.post_install(self) + # Stop timer. self._total_time = time.time() - start_time build_time = self._total_time - self._fetch_time @@ -954,9 +960,6 @@ class Package(object): # the database, so that we don't need to re-read from file. spack.installed_db.add(self.spec, self.prefix) - # Once everything else is done, run post install hooks - spack.hooks.post_install(self) - def sanity_check_prefix(self): """This function checks whether install succeeded.""" diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index f88f82fc2d..d711752c20 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -89,7 +89,7 @@ class Stage(object): """ def __init__(self, url_or_fetch_strategy, - name=None, mirror_path=None, keep=False): + name=None, mirror_path=None, keep=False, path=None): """Create a stage object. Parameters: url_or_fetch_strategy @@ -135,7 +135,10 @@ class Stage(object): # Try to construct here a temporary name for the stage directory # If this is a named stage, then construct a named path. - self.path = join_path(spack.stage_path, self.name) + if path is not None: + self.path = path + else: + self.path = join_path(spack.stage_path, self.name) # Flag to decide whether to delete the stage folder on exit or not self.keep = keep diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py new file mode 100644 index 0000000000..8f19c84d22 --- /dev/null +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file 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 General Public License (as published by +# the Free Software Foundation) version 2.1 dated 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 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 AprUtil(Package): + """Apache Portable Runtime Utility""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz' + + version('1.5.4', '866825c04da827c6e5f53daff5569f42') + + depends_on('apr') + + def install(self, spec, prefix): + + # configure, build, install: + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py new file mode 100644 index 0000000000..8a440766ec --- /dev/null +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file 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 General Public License (as published by +# the Free Software Foundation) version 2.1 dated 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 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 Apr(Package): + """Apache portable runtime.""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz' + + version('1.5.2', '98492e965963f852ab29f9e61b2ad700') + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index dd86b17a53..6b152f7863 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/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py new file mode 100644 index 0000000000..7260fd74a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -0,0 +1,17 @@ +from spack import * +import os + +class Astyle(Package): + """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.""" + homepage = "http://astyle.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz" + + version('2.04', '30b1193a758b0909d06e7ee8dd9627f6') + + def install(self, spec, prefix): + + with working_dir('src'): + make('-f', + join_path(self.stage.source_path,'build','clang','Makefile'), + parallel=False) + install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 1f93d39769..91a4e3b415 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -30,6 +30,7 @@ class Cmake(Package): homepage = 'https://www.cmake.org' url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' + version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') version('3.4.0', 'cd3034e0a44256a0917e254167217fc8') diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py new file mode 100644 index 0000000000..ea083d8651 --- /dev/null +++ b/var/spack/repos/builtin/packages/cuda/package.py @@ -0,0 +1,47 @@ +from spack import * +from glob import glob +import os + +class Cuda(Package): + """CUDA is a parallel computing platform and programming model invented by + NVIDIA. It enables dramatic increases in computing performance by harnessing + the power of the graphics processing unit (GPU). + + Note: NVIDIA does not provide a download URL for CUDA so you will need to + download it yourself. Go to https://developer.nvidia.com/cuda-downloads + and select your Operating System, Architecture, Distribution, and Version. + For the Installer Type, select runfile and click Download. Spack will search + your current directory for this file. Alternatively, add this file to a + mirror so that Spack can find it. For instructions on how to set up a mirror, + see http://software.llnl.gov/spack/mirrors.html + + Note: This package does not currently install the drivers necessary to run + CUDA. These will need to be installed manually. See: + http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.""" + + homepage = "http://www.nvidia.com/object/cuda_home_new.html" + + version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False, + url="file://%s/cuda_7.5.18_linux.run" % os.getcwd()) + version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False, + url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd()) + + + def install(self, spec, prefix): + runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0] + chmod = which('chmod') + chmod('+x', runfile) + runfile = which(runfile) + + # Note: NVIDIA does not officially support many newer versions of compilers. + # For example, on CentOS 6, you must use GCC 4.4.7 or older. See: + # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements + # for details. + + runfile( + '--silent', # disable interactive prompts + '--verbose', # create verbose log file + '--toolkit', # install CUDA Toolkit + '--toolkitpath=%s' % prefix + ) + diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 294b0de54e..422f5a19eb 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -13,6 +13,7 @@ class Dbus(Package): homepage = "http://dbus.freedesktop.org/" url = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz" + version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b') version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36') version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43') version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8') 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 0000000000..0b76db3827 --- /dev/null +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -0,0 +1,238 @@ +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') + make('run',parallel=False) diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index 3d4a4e47a7..3a1deba9e1 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -4,6 +4,7 @@ #------------------------------------------------------------------------------ from spack import * +import sys class Doxygen(Package): """Doxygen is the de facto standard tool for generating documentation @@ -17,6 +18,10 @@ class Doxygen(Package): version('1.8.10', '79767ccd986f12a0f949015efb5f058f') depends_on("cmake@2.8.12:") + # flex does not build on OSX, but it's provided there anyway + depends_on("flex", sys.platform != 'darwin') + depends_on("bison", sys.platform != 'darwin') + def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index 59f362ab46..0dad57a9f6 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -24,7 +24,7 @@ class Espresso(Package): depends_on('fftw~mpi', when='~mpi') depends_on('fftw+mpi', when='+mpi') depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation - + def check_variants(self, spec): error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active' if '+scalapack' in spec and '~mpi' in spec: @@ -32,14 +32,11 @@ class Espresso(Package): if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): raise RuntimeError(error.format(variant='elpa')) - def setup_environment(self, spack_env, run_env): - # Espresso copies every executable in prefix without creating sub-folders - run_env.prepend_path('PATH', self.prefix) - def install(self, spec, prefix): + from glob import glob self.check_variants(spec) - options = ['-prefix=%s' % prefix] + options = ['-prefix=%s' % prefix.bin] if '+mpi' in spec: options.append('--enable-parallel') @@ -65,5 +62,11 @@ class Espresso(Package): configure(*options) make('all') - make('install') + + if spec.architecture.startswith('darwin'): + mkdirp(prefix.bin) + for filename in glob("bin/*.x"): + install(filename, prefix.bin) + else: + make('install') diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py new file mode 100644 index 0000000000..4f1f1ec2dd --- /dev/null +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -0,0 +1,69 @@ +from spack import * + +class Gdal(Package): + """ + GDAL is a translator library for raster and vector geospatial + data formats that is released under an X/MIT style Open Source + license by the Open Source Geospatial Foundation. As a library, + it presents a single raster abstract data model and vector + abstract data model to the calling application for all supported + formats. It also comes with a variety of useful command line + utilities for data translation and processing + """ + + homepage = "http://www.gdal.org/" + url = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz" + list_url = "http://download.osgeo.org/gdal/" + list_depth = 2 + + version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5') + + extends('python') + + variant('hdf5', default=False, description='Enable HDF5 support') + variant('hdf', default=False, description='Enable HDF4 support') + variant('openjpeg', default=False, description='Enable JPEG2000 support') + variant('geos', default=False, description='Enable GEOS support') + variant('kea', default=False, description='Enable KEA support') + variant('netcdf', default=False, description='Enable netcdf support') + + depends_on('swig') + depends_on("hdf5", when='+hdf5') + depends_on("hdf", when='+hdf') + depends_on("openjpeg", when='+openjpeg') + depends_on("geos", when='+geos') + depends_on("kealib", when='+kea') + depends_on("netcdf", when='+netcdf') + depends_on("libtiff") + depends_on("libpng") + depends_on("zlib") + depends_on("proj") + depends_on("py-numpy") + + parallel = False + + def install(self, spec, prefix): + args = [] + args.append("--prefix=%s" % prefix) + args.append("--with-liblzma=yes") + args.append("--with-zlib=%s" % spec['zlib'].prefix) + args.append("--with-python=%s" % spec['python'].prefix.bin + "/python") + args.append("--without-libtool") + + if '+geos' in spec: + args.append('--with-geos=yes') + if '+hdf' in spec: + args.append('--with-hdf4=%s' % spec['hdf'].prefix) + if '+hdf5' in spec: + args.append('--with-hdf5=%s' % spec['hdf5'].prefix) + if '+openjpeg' in spec: + args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix) + if '+kea' in spec: + args.append('--with-kea=yes') + if '+netcdf' in spec: + args.append('--with-netcdf=%s' % spec['netcdf'].prefix) + + configure(*args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 4a2657e32f..030703f286 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -1,4 +1,5 @@ from spack import * +import os class Geos(Package): """GEOS (Geometry Engine - Open Source) is a C++ port of the Java @@ -10,6 +11,10 @@ class Geos(Package): homepage = "http://trac.osgeo.org/geos/" url = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2" + # Verison 3.5.0 supports Autotools and CMake + version('3.5.0', '136842690be7f504fba46b3c539438dd') + + # Versions through 3.4.2 have CMake, but only Autotools is supported version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae') version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e') version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488') @@ -21,11 +26,22 @@ class Geos(Package): version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1') version('3.3.3', '8454e653d7ecca475153cc88fd1daa26') - extends('python') - depends_on('swig') +# # Python3 is not supported. +# variant('python', default=False, description='Enable Python support') + +# extends('python', when='+python') +# depends_on('python', when='+python') +# depends_on('swig', when='+python') def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--enable-python") + args = ["--prefix=%s" % prefix] +# if '+python' in spec: +# os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin', +# 'python' if spec['python'].version[:1][0] <= 2 else 'python3') +# os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig') +# +# args.append("--enable-python") + + configure(*args) make() make("install") diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py new file mode 100644 index 0000000000..663b758747 --- /dev/null +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -0,0 +1,24 @@ +from spack import * + +class Googletest(Package): + """Google test framework for C++. Also called gtest.""" + homepage = "https://github.com/google/googletest" + url = "https://github.com/google/googletest/tarball/release-1.7.0" + + version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4') + + depends_on("cmake") + + def install(self, spec, prefix): + which('cmake')('.', *std_cmake_args) + + make() + + # Google Test doesn't have a make install + # We have to do our own install here. + install_tree('include', prefix.include) + + mkdirp(prefix.lib) + install('./libgtest.a', '%s' % prefix.lib) + install('./libgtest_main.a', '%s' % prefix.lib) + diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py index 7af7da1881..ecf92620d4 100644 --- a/var/spack/repos/builtin/packages/graphviz/package.py +++ b/var/spack/repos/builtin/packages/graphviz/package.py @@ -7,6 +7,12 @@ class Graphviz(Package): version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae') + # By default disable optional Perl language support to prevent build issues + # related to missing Perl packages. If spack begins support for Perl in the + # future, this package can be updated to depend_on('perl') and the + # ncecessary devel packages. + variant('perl', default=False, description='Enable if you need the optional Perl language bindings.') + parallel = False depends_on("swig") @@ -14,8 +20,10 @@ class Graphviz(Package): depends_on("ghostscript") def install(self, spec, prefix): - configure("--prefix=%s" %prefix) + options = ['--prefix=%s' % prefix] + if not '+perl' in spec: + options.append('--disable-perl') + configure(*options) make() make("install") - diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py new file mode 100644 index 0000000000..d310b7687a --- /dev/null +++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py @@ -0,0 +1,73 @@ +from spack import * +import os + +class HoomdBlue(Package): + """HOOMD-blue is a general-purpose particle simulation toolkit. It scales + from a single CPU core to thousands of GPUs. + + You define particle initial conditions and interactions in a high-level + python script. Then tell HOOMD-blue how you want to execute the job and it + takes care of the rest. Python job scripts give you unlimited flexibility + to create custom initialization routines, control simulation parameters, + and perform in situ analysis.""" + + homepage = "https://codeblue.umich.edu/hoomd-blue/index.html" + url = "https://bitbucket.org/glotzer/hoomd-blue/get/v1.3.3.tar.bz2" + + version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273') + + variant('mpi', default=True, description='Compile with MPI enabled') + variant('cuda', default=True, description='Compile with CUDA Toolkit') + variant('doc', default=True, description='Generate documentation') + + extends('python') + depends_on('py-numpy') + depends_on('boost+python') + depends_on('cmake') + depends_on('mpi', when='+mpi') + depends_on('cuda', when='+cuda') + depends_on('doxygen', when='+doc') + + def install(self, spec, prefix): + + cmake_args = [ + '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin, + '-DBOOST_ROOT=%s' % spec['boost' ].prefix + ] + + # MPI support + if '+mpi' in spec: + os.environ['MPI_HOME'] = spec['mpi'].prefix + cmake_args.append('-DENABLE_MPI=ON') + else: + cmake_args.append('-DENABLE_MPI=OFF') + + # CUDA support + if '+cuda' in spec: + cmake_args.append('-DENABLE_CUDA=ON') + else: + cmake_args.append('-DENABLE_CUDA=OFF') + + # CUDA-aware MPI library support + #if '+cuda' in spec and '+mpi' in spec: + # cmake_args.append('-DENABLE_MPI_CUDA=ON') + #else: + # cmake_args.append('-DENABLE_MPI_CUDA=OFF') + + # There may be a bug in the MPI-CUDA code. See: + # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ + # This prevented "make test" from passing for me. + cmake_args.append('-DENABLE_MPI_CUDA=OFF') + + # Documentation + if '+doc' in spec: + cmake_args.append('-DENABLE_DOXYGEN=ON') + else: + cmake_args.append('-DENABLE_DOXYGEN=OFF') + + cmake_args.extend(std_cmake_args) + cmake('.', *cmake_args) + + make() + make("test") + make("install") diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py new file mode 100644 index 0000000000..475d21e1d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -0,0 +1,35 @@ +from spack import * + +class Kealib(Package): + """An HDF5 Based Raster File Format + + KEALib provides an implementation of the GDAL data model. + The format supports raster attribute tables, image pyramids, + meta-data and in-built statistics while also handling very + large files and compression throughout. + + Based on the HDF5 standard, it also provides a base from which + other formats can be derived and is a good choice for long + term data archiving. An independent software library (libkea) + provides complete access to the KEA image format and a GDAL + driver allowing KEA images to be used from any GDAL supported software. + + Development work on this project has been funded by Landcare Research. + """ + homepage = "http://kealib.org/" + url = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz" + + version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d') + + depends_on("hdf5") + + def install(self, spec, prefix): + with working_dir('trunk', create=False): + cmake_args = [] + cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix) + cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include) + cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib) + cmake('.', *cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index 00736b7811..d5d779f796 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -2,7 +2,7 @@ from spack import * class Libdrm(Package): """A userspace library for accessing the DRM, direct - rendering manager, on Linux, BSD and other operating + rendering manager, on Linux, BSD and other operating systems that support the ioctl interface.""" homepage = "http://dri.freedesktop.org/libdrm/" # no real website... @@ -11,6 +11,8 @@ class Libdrm(Package): version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') version('2.4.33', '86e4e3debe7087d5404461e0032231c8') + depends_on('libpciaccess') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index e02b08663e..73c8c62341 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -9,6 +9,8 @@ class Libpng(Package): version('1.6.15', '829a256f3de9307731d4f52dc071916d') version('1.6.14', '2101b3de1d5f348925990f9aa8405660') + depends_on('zlib') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index b20dc8dd60..2d7955e08d 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -78,6 +78,9 @@ class Mpich(Package): if not self.compiler.fc: config_args.append("--disable-fc") + if not self.compiler.fc and not self.compiler.f77: + config_args.append("--disable-fortran") + configure(*config_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index c4b7ce3b04..05436332ac 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -31,8 +31,16 @@ class NetlibLapack(Package): depends_on('cmake') depends_on('blas', when='+external-blas') - def install(self, spec, prefix): - cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), + + def patch(self): + # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name. + filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', + '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True) + + + def install_one(self, spec, prefix, shared): + cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'), + '-DCBLAS=ON', # always build CBLAS '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] if '+external-blas' in spec: @@ -45,7 +53,33 @@ class NetlibLapack(Package): cmake_args.extend(std_cmake_args) - with working_dir('spack-build', create=True): + build_dir = 'spack-build' + ('-shared' if shared else '-static') + with working_dir(build_dir, create=True): cmake('..', *cmake_args) make() make("install") + + + def install(self, spec, prefix): + # Always build static libraries. + self.install_one(spec, prefix, False) + + # Build shared libraries if requested. + if '+shared' in spec: + self.install_one(spec, prefix, True) + + + def setup_dependent_package(self, module, dspec): + # This is WIP for a prototype interface for virtual packages. + # We can update this as more builds start depending on BLAS/LAPACK. + libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib) + + self.spec.blas_static_lib = join_path(libdir, 'libblas.a') + self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a') + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, 'libblas.%s' % dso_suffix) + self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix) + + + diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py index 9e6bf4e358..0722dd49a6 100644 --- a/var/spack/repos/builtin/packages/ninja/package.py +++ b/var/spack/repos/builtin/packages/ninja/package.py @@ -16,7 +16,7 @@ class Ninja(Package): cp = which('cp') - bindir = os.path.join(prefix, 'bin') + bindir = os.path.join(prefix, 'bin/') mkdir(bindir) - cp('-a', '-t', bindir, 'ninja') - cp('-ra', 'misc', prefix) + cp('-a', 'ninja', bindir) + cp('-a', 'misc', prefix) diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py new file mode 100644 index 0000000000..e72c60fadb --- /dev/null +++ b/var/spack/repos/builtin/packages/numdiff/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file 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 General Public License (as published by +# the Free Software Foundation) version 2.1 dated 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 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 * +import sys + +class Numdiff(Package): + """Numdiff is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric + differences or/and different numeric formats.""" + + homepage = 'https://www.nongnu.org/numdiff' + url = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz' + + version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e') + + depends_on('gettext', sys.platform=='darwin') + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/oce/null.patch b/var/spack/repos/builtin/packages/oce/null.patch new file mode 100644 index 0000000000..42a3f0e44f --- /dev/null +++ b/var/spack/repos/builtin/packages/oce/null.patch @@ -0,0 +1,482 @@ +From 61cb965b9ffeca419005bc15e635e67589c421dd Mon Sep 17 00:00:00 2001 +From: Martin Siggel <martin.siggel@dlr.de> +Date: Thu, 28 Jan 2016 19:05:00 +0100 +Subject: [PATCH] Workaround clang optimizations for null references + +OCCT/OCE includes some evil code that uses NULL references, +which are normally not possible. Clang removes code in +branches like if(&myNullRef==NULL) as it assumes this can +never be true. This fix was inspired from the mantis issue +http://tracker.dev.opencascade.org/view.php?id=26042. This +code will be fixed in OCCT 7, but we might require the fix +for earlier releases as well. + +Fixes issue #576 +--- + inc/PLib.hxx | 2 +- + src/BSplCLib/BSplCLib.cxx | 16 ++++++------- + src/BSplCLib/BSplCLib_2.cxx | 6 ++--- + src/BSplCLib/BSplCLib_CurveComputation.gxx | 26 ++++++++++----------- + src/BSplSLib/BSplSLib.cxx | 36 +++++++++++++++--------------- + src/BSplSLib/BSplSLib_BzSyntaxes.cxx | 2 +- + src/PLib/PLib.cxx | 10 ++++----- + 7 files changed, 49 insertions(+), 49 deletions(-) + +diff --git a/inc/PLib.hxx b/inc/PLib.hxx +index 7513234..52b1f84 100644 +--- a/inc/PLib.hxx ++++ b/inc/PLib.hxx +@@ -343,6 +343,6 @@ friend class PLib_DoubleJacobiPolynomial; + + + +- ++#define IS_NULL_REF(ref) ((reinterpret_cast<size_t>(&ref) & 0xFFFFFF) == 0) + + #endif // _PLib_HeaderFile +diff --git a/src/BSplCLib/BSplCLib.cxx b/src/BSplCLib/BSplCLib.cxx +index 683e4ab..2a2d9ea 100644 +--- a/src/BSplCLib/BSplCLib.cxx ++++ b/src/BSplCLib/BSplCLib.cxx +@@ -298,7 +298,7 @@ void BSplCLib::LocateParameter + Standard_Real& NewU) + { + Standard_Integer first,last; +- if (&Mults) { ++ if (!IS_NULL_REF(Mults)) { + if (Periodic) { + first = Knots.Lower(); + last = Knots.Upper(); +@@ -1434,7 +1434,7 @@ void BSplCLib::BuildKnots(const Standard_Integer Degree, + const Standard_Real * pkn = &Knots(KLower); + pkn -= KLower; + Standard_Real *knot = &LK; +- if (&Mults == NULL) { ++ if (IS_NULL_REF(Mults)) { + switch (Degree) { + case 1 : { + Standard_Integer j = Index ; +@@ -1672,7 +1672,7 @@ Standard_Boolean BSplCLib::PrepareInsertKnots + const Standard_Real Tolerance, + const Standard_Boolean Add) + { +- Standard_Boolean addflat = &AddMults == NULL; ++ Standard_Boolean addflat = IS_NULL_REF(AddMults); + + Standard_Integer first,last; + if (Periodic) { +@@ -1856,7 +1856,7 @@ void BSplCLib::InsertKnots + const Standard_Real Tolerance, + const Standard_Boolean Add) + { +- Standard_Boolean addflat = &AddMults == NULL; ++ Standard_Boolean addflat = IS_NULL_REF(AddMults); + + Standard_Integer i,k,mult,firstmult; + Standard_Integer index,kn,curnk,curk; +@@ -3902,7 +3902,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + num_poles = FlatKnots.Length() - Deg1; + switch (ArrayDimension) { + case 2 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -3970,7 +3970,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + break; + } + case 3 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -4047,7 +4047,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + break; + } + case 4 : { +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +@@ -4134,7 +4134,7 @@ void BSplCLib::Resolution( Standard_Real& Poles, + } + default : { + Standard_Integer kk; +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + const Standard_Real * WG = &Weights(Weights.Lower()); + min_weights = WG[0]; + +diff --git a/src/BSplCLib/BSplCLib_2.cxx b/src/BSplCLib/BSplCLib_2.cxx +index 35c4639..653b7cd 100644 +--- a/src/BSplCLib/BSplCLib_2.cxx ++++ b/src/BSplCLib/BSplCLib_2.cxx +@@ -70,7 +70,7 @@ void BSplCLib::BuildEval(const Standard_Integer Degree, + Standard_Integer i; + Standard_Integer ip = PLower + Index - 1; + Standard_Real w, *pole = &LP; +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + + for (i = 0; i <= Degree; i++) { + ip++; +@@ -115,13 +115,13 @@ static void PrepareEval + + // make the knots + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); + + // check truly rational +- rational = (&Weights != NULL); ++ rational = (!IS_NULL_REF(Weights)); + if (rational) { + Standard_Integer WLower = Weights.Lower() + index; + rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree); +diff --git a/src/BSplCLib/BSplCLib_CurveComputation.gxx b/src/BSplCLib/BSplCLib_CurveComputation.gxx +index e71b4e0..9d42643 100644 +--- a/src/BSplCLib/BSplCLib_CurveComputation.gxx ++++ b/src/BSplCLib/BSplCLib_CurveComputation.gxx +@@ -92,7 +92,7 @@ Standard_Boolean BSplCLib::RemoveKnot + TColStd_Array1OfInteger& NewMults, + const Standard_Real Tolerance) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -133,7 +133,7 @@ void BSplCLib::InsertKnots + const Standard_Real Epsilon, + const Standard_Boolean Add) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -222,7 +222,7 @@ void BSplCLib::IncreaseDegree + TColStd_Array1OfReal& NewKnots, + TColStd_Array1OfInteger& NewMults) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -256,7 +256,7 @@ void BSplCLib::Unperiodize + Array1OfPoints& NewPoles, + TColStd_Array1OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -292,7 +292,7 @@ void BSplCLib::Trimming(const Standard_Integer Degree, + Array1OfPoints& NewPoles, + TColStd_Array1OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim; + dim = Dimension_gen; + if (rational) dim++; +@@ -339,7 +339,7 @@ void BSplCLib::BuildEval(const Standard_Integer Degree, + Standard_Integer PUpper = Poles.Upper(); + Standard_Integer i; + Standard_Integer ip = PLower + Index - 1; +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + for (i = 0; i <= Degree; i++) { + ip++; + if (ip > PUpper) ip = PLower; +@@ -384,13 +384,13 @@ static void PrepareEval + + // make the knots + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); + + // check truly rational +- rational = (&Weights != NULL); ++ rational = (!IS_NULL_REF(Weights)); + if (rational) { + Standard_Integer WLower = Weights.Lower() + index; + rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree); +@@ -741,7 +741,7 @@ void BSplCLib::CacheD0(const Standard_Real Parameter, + Degree * Dimension_gen, + PArray[0], + myPoint[0]) ; +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + PLib::NoDerivativeEvalPolynomial(NewParameter, +@@ -798,7 +798,7 @@ void BSplCLib::CacheD1(const Standard_Real Parameter, + + ModifyCoords (LocalPDerivatives + Dimension_gen, /= SpanLenght); + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + PLib::EvalPolynomial(NewParameter, +@@ -878,7 +878,7 @@ void BSplCLib::CacheD2(const Standard_Real Parameter, + Index += Dimension_gen; + } + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + +@@ -971,7 +971,7 @@ void BSplCLib::CacheD3(const Standard_Real Parameter, + Index += Dimension_gen; + } + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + Standard_Real * + WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ; + +@@ -1081,7 +1081,7 @@ void BSplCLib::BuildCache + LocalValue *= SpanDomain / (Standard_Real) ii ; + } + +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + for (ii = 1 ; ii <= Degree + 1 ; ii++) + CacheWeights(ii) = 0.0e0 ; + CacheWeights(1) = 1.0e0 ; +diff --git a/src/BSplSLib/BSplSLib.cxx b/src/BSplSLib/BSplSLib.cxx +index 5ad633c..07040d5 100644 +--- a/src/BSplSLib/BSplSLib.cxx ++++ b/src/BSplSLib/BSplSLib.cxx +@@ -309,12 +309,12 @@ static Standard_Boolean PrepareEval (const Standard_Real U, + BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots1); + BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots2); + +- if (&UMults == NULL) ++ if (IS_NULL_REF(UMults)) + uindex -= UKLower + UDegree; + else + uindex = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults); + +- if (&VMults == NULL) ++ if (IS_NULL_REF(VMults)) + vindex -= VKLower + VDegree; + else + vindex = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults); +@@ -460,12 +460,12 @@ static Standard_Boolean PrepareEval (const Standard_Real U, + BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots2); + BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots1); + +- if (&UMults == NULL) ++ if (IS_NULL_REF(UMults)) + uindex -= UKLower + UDegree; + else + uindex = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults); + +- if (&VMults == NULL) ++ if (IS_NULL_REF(VMults)) + vindex -= VKLower + VDegree; + else + vindex = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults); +@@ -1299,7 +1299,7 @@ void BSplSLib::Iso(const Standard_Real Param, + { + Standard_Integer index = 0; + Standard_Real u = Param; +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = rational ? 4 : 3; + + // compute local knots +@@ -1307,7 +1307,7 @@ void BSplSLib::Iso(const Standard_Real Param, + NCollection_LocalArray<Standard_Real> locknots1 (2*Degree); + BSplCLib::LocateParameter(Degree,Knots,Mults,u,Periodic,index,u); + BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*locknots1); +- if (&Mults == NULL) ++ if (IS_NULL_REF(Mults)) + index -= Knots.Lower() + Degree; + else + index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults); +@@ -1381,7 +1381,7 @@ void BSplSLib::Iso(const Standard_Real Param, + } + + // if the input is not rational but weights are wanted +- if (!rational && (&CWeights != NULL)) { ++ if (!rational && (!IS_NULL_REF(CWeights))) { + + for (i = CWeights.Lower(); i <= CWeights.Upper(); i++) + CWeights(i) = 1.; +@@ -1741,7 +1741,7 @@ void BSplSLib::InsertKnots(const Standard_Boolean UDirection, + const Standard_Real Epsilon, + const Standard_Boolean Add ) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1787,7 +1787,7 @@ Standard_Boolean BSplSLib::RemoveKnot + TColStd_Array1OfInteger& NewMults, + const Standard_Real Tolerance) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1834,7 +1834,7 @@ void BSplSLib::IncreaseDegree + TColStd_Array1OfReal& NewKnots, + TColStd_Array1OfInteger& NewMults) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1876,7 +1876,7 @@ void BSplSLib::Unperiodize + TColgp_Array2OfPnt& NewPoles, + TColStd_Array2OfReal& NewWeights) + { +- Standard_Boolean rational = &Weights != NULL; ++ Standard_Boolean rational = !IS_NULL_REF(Weights); + Standard_Integer dim = 3; + if (rational) dim++; + +@@ -1929,7 +1929,7 @@ void BSplSLib::BuildCache + Standard_Boolean rational,rational_u,rational_v,flag_u_or_v; + Standard_Integer kk,d1,d1p1,d2,d2p1,ii,jj,iii,jjj,Index; + Standard_Real u1,min_degree_domain,max_degree_domain,f,factor[2],u2; +- if (&Weights != NULL) ++ if (!IS_NULL_REF(Weights)) + rational_u = rational_v = Standard_True; + else + rational_u = rational_v = Standard_False; +@@ -2025,7 +2025,7 @@ void BSplSLib::BuildCache + } + factor[0] *= max_degree_domain / (Standard_Real) (iii) ; + } +- if (&Weights != NULL) { ++ if (!IS_NULL_REF(Weights)) { + // + // means that PrepareEval did found out that the surface was + // locally polynomial but since the surface is constructed +@@ -2110,7 +2110,7 @@ void BSplSLib::CacheD0(const Standard_Real UParameter, + (min_degree << 1) + min_degree, + locpoles[0], + myPoint[0]) ; +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +@@ -2190,7 +2190,7 @@ void BSplSLib::CacheD1(const Standard_Real UParameter, + // the coefficients + // + // +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + + local_poles_array [0][0][0] = 0.0e0 ; + local_poles_array [0][0][1] = 0.0e0 ; +@@ -2275,7 +2275,7 @@ void BSplSLib::CacheD1(const Standard_Real UParameter, + locpoles[dimension], + local_poles_array[1][0][0]) ; + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +@@ -2435,7 +2435,7 @@ void BSplSLib::CacheD2(const Standard_Real UParameter, + // the coefficients + // + // +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + + local_poles_and_weights_array[0][0][0] = 0.0e0 ; + local_poles_and_weights_array[0][0][1] = 0.0e0 ; +@@ -2564,7 +2564,7 @@ void BSplSLib::CacheD2(const Standard_Real UParameter, + locpoles[dimension + dimension], + local_poles_array[2][0][0]) ; + +- if (&WeightsArray != NULL) { ++ if (!IS_NULL_REF(WeightsArray)) { + dimension = min_degree + 1 ; + Standard_Real * + WArray = (Standard_Real *) +diff --git a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx +index 0faf6b6..f2c0f74 100644 +--- a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx ++++ b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx +@@ -68,7 +68,7 @@ void BSplSLib::PolesCoefficients (const TColgp_Array2OfPnt& Poles, + biduflatknots,bidvflatknots, + Poles,Weights, + CPoles,CWeights); +- if (&Weights == NULL) { ++ if (IS_NULL_REF(Weights)) { + + for (ii = 1; ii <= uclas; ii++) { + +diff --git a/src/PLib/PLib.cxx b/src/PLib/PLib.cxx +index 23fa302..7ee231f 100644 +--- a/src/PLib/PLib.cxx ++++ b/src/PLib/PLib.cxx +@@ -2427,7 +2427,7 @@ void PLib::CoefficientsPoles (const Standard_Integer dim, + TColStd_Array1OfReal& Poles, + TColStd_Array1OfReal& Weights) + { +- Standard_Boolean rat = &WCoefs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoefs); + Standard_Integer loc = Coefs.Lower(); + Standard_Integer lop = Poles.Lower(); + Standard_Integer lowc=0; +@@ -2550,7 +2550,7 @@ void PLib::Trimming(const Standard_Real U1, + Standard_Integer indc, indw=0; + Standard_Integer upc = Coefs.Upper() - dim + 1, upw=0; + Standard_Integer len = Coefs.Length()/dim; +- Standard_Boolean rat = &WCoefs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoefs); + + if (rat) { + if(len != WCoefs.Length()) +@@ -2607,7 +2607,7 @@ void PLib::CoefficientsPoles (const TColgp_Array2OfPnt& Coefs, + TColgp_Array2OfPnt& Poles, + TColStd_Array2OfReal& Weights) + { +- Standard_Boolean rat = (&WCoefs != NULL); ++ Standard_Boolean rat = (!IS_NULL_REF(WCoefs)); + Standard_Integer LowerRow = Poles.LowerRow(); + Standard_Integer UpperRow = Poles.UpperRow(); + Standard_Integer LowerCol = Poles.LowerCol(); +@@ -2701,7 +2701,7 @@ void PLib::UTrimming(const Standard_Real U1, + TColgp_Array2OfPnt& Coeffs, + TColStd_Array2OfReal& WCoeffs) + { +- Standard_Boolean rat = &WCoeffs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoeffs); + Standard_Integer lr = Coeffs.LowerRow(); + Standard_Integer ur = Coeffs.UpperRow(); + Standard_Integer lc = Coeffs.LowerCol(); +@@ -2735,7 +2735,7 @@ void PLib::VTrimming(const Standard_Real V1, + TColgp_Array2OfPnt& Coeffs, + TColStd_Array2OfReal& WCoeffs) + { +- Standard_Boolean rat = &WCoeffs != NULL; ++ Standard_Boolean rat = !IS_NULL_REF(WCoeffs); + Standard_Integer lr = Coeffs.LowerRow(); + Standard_Integer ur = Coeffs.UpperRow(); + Standard_Integer lc = Coeffs.LowerCol();
\ No newline at end of file diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 4d5081ac9d..3fe6638e66 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -13,9 +13,20 @@ class Oce(Package): version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') - version('0.15' , '7ec541a1c350ca8a684f74980e48801c') + + variant('tbb', default=True, description='Build with Intel Threading Building Blocks') depends_on('cmake@2.8:') + depends_on('tbb', when='+tbb') + + # There is a bug in OCE which appears with Clang (version?) or GCC 6.0 + # and has to do with compiler optimization, see + # https://github.com/tpaviot/oce/issues/576 + # http://tracker.dev.opencascade.org/view.php?id=26042 + # https://github.com/tpaviot/oce/issues/605 + # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch + patch('null.patch',when='@0.16:0.17.1') + def install(self, spec, prefix): options = [] @@ -23,12 +34,12 @@ class Oce(Package): options.extend([ '-DOCE_INSTALL_PREFIX=%s' % prefix, '-DOCE_BUILD_SHARED_LIB:BOOL=ON', - '-DOCE_BUILD_TYPE:STRING=Release', + '-DCMAKE_BUILD_TYPE:STRING=Release', '-DOCE_DATAEXCHANGE:BOOL=ON', '-DOCE_DISABLE_X11:BOOL=ON', '-DOCE_DRAW:BOOL=OFF', '-DOCE_MODEL:BOOL=ON', - '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb + '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'), '-DOCE_OCAF:BOOL=ON', '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', '-DOCE_VISUALISATION:BOOL=OFF', @@ -46,6 +57,11 @@ class Oce(Package): make("install/strip") + # OCE tests build is brocken at least on Darwin. + # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib + # see https://github.com/tpaviot/oce/issues/612 + # make("test") + # The shared libraries are not installed correctly on Darwin; correct this if (sys.platform == 'darwin'): fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 1d10f217c4..4ec829a85b 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,5 +1,6 @@ from spack import * import sys +import os class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -10,29 +11,60 @@ class Openblas(Package): version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + variant('shared', default=True, description="Build shared libraries as well as static libs.") + # virtual dependency provides('blas') provides('lapack') + def install(self, spec, prefix): - extra=[] + make_defs = ['CC=%s' % spack_cc, + 'FC=%s' % spack_fc] + + make_targets = ['libs', 'netlib'] + + # Build shared if variant is set. + if '+shared' in spec: + make_targets += ['shared'] + else: + make_defs += ['NO_SHARED=1'] + + # fix missing _dggsvd_ and _sggsvd_ if spec.satisfies('@0.2.16'): - extra.extend([ - 'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_ - ]) + make_defs += ['BUILD_LAPACK_DEPRECATED=1'] + + make_args = make_defs + make_targets + make(*make_args) - make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra) - make("tests") - make('install', "PREFIX='%s'" % prefix) + make("tests", *make_defs) + + # no quotes around prefix (spack doesn't use a shell) + make('install', "PREFIX=%s" % prefix, *make_defs) - lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' # Blas virtual package should provide blas.a and libblas.a with working_dir(prefix.lib): symlink('libopenblas.a', 'blas.a') symlink('libopenblas.a', 'libblas.a') - symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix) + if '+shared' in spec: + symlink('libopenblas.%s' % dso_suffix, 'libblas.%s' % dso_suffix) # Lapack virtual package should provide liblapack.a with working_dir(prefix.lib): symlink('libopenblas.a', 'liblapack.a') - symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix) + if '+shared' in spec: + symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix) + + + def setup_dependent_package(self, module, dspec): + # This is WIP for a prototype interface for virtual packages. + # We can update this as more builds start depending on BLAS/LAPACK. + libdir = find_library_path('libopenblas.a', self.prefix.lib64, self.prefix.lib) + + self.spec.blas_static_lib = join_path(libdir, 'libopenblas.a') + self.spec.lapack_static_lib = self.spec.blas_static_lib + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py new file mode 100644 index 0000000000..afec197d11 --- /dev/null +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -0,0 +1,26 @@ +from spack import * + +class Openjpeg(Package): + """ + OpenJPEG is an open-source JPEG 2000 codec written in C language. + It has been developed in order to promote the use of JPEG 2000, a + still-image compression standard from the Joint Photographic + Experts Group (JPEG). + Since April 2015, it is officially recognized by ISO/IEC and + ITU-T as a JPEG 2000 Reference Software. + """ + homepage = "https://github.com/uclouvain/openjpeg" + url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz" + + version('2.1' , '3e1c451c087f8462955426da38aa3b3d') + version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') + version('2.0' , 'cdf266530fee8af87454f15feb619609') + version('1.5.2', '545f98923430369a6b046ef3632ef95c') + version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index e9b7c8a732..5c1fc6cc92 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -71,19 +71,10 @@ class Petsc(Package): errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) else: - if self.compiler.name == "clang": - compiler_opts = [ - '--with-mpi=1', - '--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation - '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), - '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), - ] - else: - compiler_opts = [ - '--with-mpi=1', - '--with-mpi-dir=%s' % self.spec['mpi'].prefix, - ] + compiler_opts = [ + '--with-mpi=1', + '--with-mpi-dir=%s' % self.spec['mpi'].prefix, + ] return compiler_opts def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py new file mode 100644 index 0000000000..0aa4208b4d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyBottleneck(Package): + """Bottleneck is a collection of fast NumPy array functions written in Cython.""" + homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0" + url = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz" + + version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') + + extends('python', ignore=r'bin/f2py$') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 68eb735ad9..072355026e 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -3,10 +3,14 @@ from spack import * class PyCython(Package): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" - url = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz" + url = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz" - version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') + version('0.23.5', '66b62989a67c55af016c916da36e7514') + version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e') + + # These versions contain illegal Python3 code... version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6') + version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') extends('python') diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index 0a17f2f2d2..b67e91ace6 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -7,6 +7,7 @@ class PyDateutil(Package): version('2.4.0', '75714163bb96bedd07685cdb2071b8bc') version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2') + version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py deleted file mode 100644 index 59005428e4..0000000000 --- a/var/spack/repos/builtin/packages/py-libxml2/package.py +++ /dev/null @@ -1,15 +0,0 @@ -from spack import * - -class PyLibxml2(Package): - """A Python wrapper around libxml2.""" - homepage = "https://xmlsoft.org/python.html" - url = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz" - - version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3') - - extends('python') - depends_on('libxml2') - depends_on('libxslt') - - def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 2167735fb8..45e77dd631 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -12,7 +12,7 @@ class PyMatplotlib(Package): variant('gui', default=False, description='Enable GUI') variant('ipython', default=False, description='Enable ipython support') - extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') + extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$') depends_on('py-pyside', when='+gui') depends_on('py-ipython', when='+ipython') diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index 4fee99098e..c2c2b52e03 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -10,6 +10,7 @@ class PyNose(Package): version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') + version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') extends('python', ignore=r'bin/nosetests.*$') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 89f8a525b1..081a79dec6 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -7,8 +7,9 @@ class PyNumexpr(Package): url = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz" version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd') + version('2.5', '84f66cced45ba3e30dcf77a937763aaa') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index a08e612df6..40988fb44a 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -9,6 +9,7 @@ class PyNumpy(Package): homepage = "http://www.numpy.org/" url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" + version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b') version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad') version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') version('1.9.1', '78842b73560ec378142665e712ae4ad9') diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 5b9997faa9..2320b1f92f 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -8,18 +8,15 @@ class PyPandas(Package): version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') + version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-dateutil') depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-scipy') depends_on('py-setuptools') depends_on('py-pytz') - depends_on('libdrm') - depends_on('libpciaccess') - depends_on('llvm') - depends_on('mesa') + depends_on('py-numexpr') + depends_on('py-bottleneck') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index da6311a784..060cf0cde4 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -7,6 +7,7 @@ class PyPytz(Package): version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7') version('2015.4', '417a47b1c432d90333e42084a605d3d8') + version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29') extends('python') diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index c2161c90c4..4d47c641ee 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -11,9 +11,15 @@ class PyScipy(Package): extends('python') depends_on('py-nose') - depends_on('py-numpy') - depends_on('blas') - depends_on('lapack') + depends_on('py-numpy+blas+lapack') def install(self, spec, prefix): + if 'atlas' in spec: + # libatlas.so actually isn't always installed, but this + # seems to make the build autodetect things correctly. + env['ATLAS'] = join_path(spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix) + else: + env['BLAS'] = spec['blas'].blas_shared_lib + env['LAPACK'] = spec['lapack'].lapack_shared_lib + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 26c048bfd4..c6d9be1add 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -9,6 +9,7 @@ class PySetuptools(Package): version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') version('19.2', '78353b1f80375ca5e088f4b4627ffe03') + version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') extends('python') diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 05c5bd00a9..df277100f7 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -6,6 +6,7 @@ class PySix(Package): url = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz" version('1.9.0', '476881ef4012262dfc8adc645ee786c4') + version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py new file mode 100644 index 0000000000..984b4196b1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -0,0 +1,19 @@ +from spack import * + +class PyTuiview(Package): + """ + TuiView is a lightweight raster GIS with powerful raster attribute + table manipulation abilities. + """ + homepage = "https://bitbucket.org/chchrsc/tuiview" + url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" + + version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') + + extends("python") + depends_on("py-pyqt") + depends_on("py-numpy") + depends_on("gdal") + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index 037a6fc59f..09303d37b4 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -8,6 +8,7 @@ class PyVirtualenv(Package): version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49') version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db') + version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index d08e8e81e1..ab09469042 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -1,41 +1,31 @@ -import os from spack import * import os class Qt(Package): """Qt is a comprehensive cross-platform C++ application framework.""" - homepage = "http://qt.io" - list_url = 'http://download.qt-project.org/official_releases/qt/' - list_depth = 2 - - version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5', - url='http://download.qt-project.org/official_releases/qt/5.4/5.4.2/single/qt-everywhere-opensource-src-5.4.2.tar.gz') - - version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6', - url='http://download.qt-project.org/official_releases/qt/5.4/5.4.0/single/qt-everywhere-opensource-src-5.4.0.tar.gz') - - version('5.3.2', 'febb001129927a70174467ecb508a682', - url='http://download.qt.io/archive/qt/5.3/5.3.2/single/qt-everywhere-opensource-src-5.3.2.tar.gz') - - version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8', - url='http://download.qt.io/archive/qt/5.2/5.2.1/single/qt-everywhere-opensource-src-5.2.1.tar.gz') - - version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb', - url="http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz") + homepage = 'http://qt.io' + url = 'http://download.qt.io/archive/qt/5.5/5.5.1/single/qt-everywhere-opensource-src-5.5.1.tar.gz' - version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009', - url="http://download.qt.io/archive/qt/3/qt-x11-free-3.3.8b.tar.gz") + version('5.5.1', '59f0216819152b77536cf660b015d784') + version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5') + version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6') + version('5.3.2', 'febb001129927a70174467ecb508a682') + version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8') + version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb') + version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009') - variant('mesa', default=False, description='depend on mesa') # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project - variant('krellpatch', default=False, description="build with openspeedshop based patch.") + variant('krellpatch', default=False, description="Build with openspeedshop based patch.") + variant('mesa', default=False, description="Depend on mesa.") + variant('gtk', default=False, description="Build with gtkplus.") + patch('qt3krell.patch', when='@3.3.8b+krellpatch') # Use system openssl for security. #depends_on("openssl") depends_on("glib") - depends_on("gtkplus") + depends_on("gtkplus", when='+gtk') depends_on("libxml2") depends_on("zlib") depends_on("dbus", when='@4:') @@ -56,6 +46,34 @@ class Qt(Package): depends_on("libxcb") + def url_for_version(self, version): + url = "http://download.qt.io/archive/qt/" + + if version >= Version('5'): + url += "%s/%s/single/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version, version) + elif version >= Version('4.8'): + url += "%s/%s/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version, version) + elif version >= Version('4.6'): + url += "%s/qt-everywhere-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version) + elif version >= Version('4.0'): + url += "%s/qt-x11-opensource-src-%s.tar.gz" % \ + (version.up_to(2), version) + elif version >= Version('3'): + url += "%s/qt-x11-free-%s.tar.gz" % \ + (version.up_to(1), version) + elif version >= Version('2.1'): + url += "%s/qt-x11-%s.tar.gz" % \ + (version.up_to(1), version) + else: + url += "%s/qt-%s.tar.gz" % \ + (version.up_to(1), version) + + return url + + def setup_environment(self, spack_env, env): env.set('QTDIR', self.prefix) @@ -88,7 +106,7 @@ class Qt(Package): '-v', '-opensource', '-opengl', - "-release", + '-release', '-shared', '-confirm-license', '-openssl-linked', @@ -97,7 +115,7 @@ class Qt(Package): '-no-openvg', '-no-pch', # NIS is deprecated in more recent glibc - "-no-nis"] + '-no-nis'] # Don't disable all the database drivers, but should # really get them into spack at some point. diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py new file mode 100644 index 0000000000..5db1c3eb92 --- /dev/null +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -0,0 +1,77 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file 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 General Public License (as published by +# the Free Software Foundation) version 2.1 dated 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 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 * +#import os + +class Subversion(Package): + """Apache Subversion - an open source version control system.""" + homepage = 'https://subversion.apache.org/' + url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' + + version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') + version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') + + depends_on('apr') + depends_on('apr-util') + depends_on('zlib') + depends_on('sqlite') + + # Optional: We need swig if we want the Perl, Python or Ruby + # bindings. + #depends_on('swig') + #depends_on('python') + #depends_on('perl') + #depends_on('ruby') + + def install(self, spec, prefix): + + # configure, build, install: + # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + options.append('--with-apr-util=%s' % spec['apr-util'].prefix) + options.append('--with-zlib=%s' % spec['zlib'].prefix) + options.append('--with-sqlite=%s' % spec['sqlite'].prefix) + #options.append('--with-swig=%s' % spec['swig'].prefix) + + configure(*options) + make() + make('install') + + # python bindings + #make('swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + #make('install-swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + + # perl bindings + #make('swig-pl') + #make('install-swig-pl') + + # ruby bindings + #make('swig-rb') + #make('isntall-swig-rb') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index b57f9967c3..c2196dcec4 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -23,4 +23,14 @@ class SuiteSparse(Package): # FIXME : this actually uses the current workaround # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') + make('install', 'INSTALL=%s' % prefix, + + # inject Spack compiler wrappers + 'AUTOCC=no', + 'CC=cc', + 'CXX=c++', + 'F77=f77', + + # BLAS arguments require path to libraries + 'BLAS=-lblas', + 'LAPACK=-llapack') diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index edc40476e3..6223848c68 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,15 +1,22 @@ from spack import * +import os, sys, glob - +# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it: +# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111 +# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package +# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh +# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb +# and some relevant documentation/examples: +# https://github.com/trilinos/Trilinos/issues/175 class Trilinos(Package): - """ - The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented + """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. """ homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') version('12.0.1', 'bd99741d047471e127b8296b2ec08017') @@ -17,8 +24,16 @@ class Trilinos(Package): version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('metis', default=True, description='Compile with METIS and ParMETIS') + variant('mumps', default=True, description='Compile with support for MUMPS solvers') + variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') + variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('hdf5', default=True, description='Compile with HDF5') + variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors + variant('python', default=False, description='Build python wrappers') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds a debug version of the libraries') # Everything should be compiled with -fpic depends_on('blas') @@ -27,28 +42,205 @@ class Trilinos(Package): depends_on('matio') depends_on('glm') depends_on('swig') + depends_on('metis',when='+metis') + depends_on('suite-sparse',when='+suite-sparse') # MPI related dependencies depends_on('mpi') depends_on('netcdf+mpi') + depends_on('parmetis',when='+metis') + # Trilinos' Tribits config system is limited which makes it + # very tricky to link Amesos with static MUMPS, see + # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html + # One could work it out by getting linking flags from mpif90 --showme:link (or alike) + # and adding results to -DTrilinos_EXTRA_LINK_FLAGS + # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and + # it may work at the end. But let's avoid all this by simply using shared libs + depends_on('mumps@5.0:+mpi+shared',when='+mumps') + depends_on('scalapack',when='+mumps') + depends_on('superlu-dist',when='+superlu-dist') + depends_on('hypre~internal-superlu',when='+hypre') + depends_on('hdf5+mpi',when='+hdf5') + + depends_on('python',when='+python') - depends_on('python') # Needs py-numpy activated + patch('umfpack_from_suitesparse.patch') + + # check that the combination of variants makes sense + def variants_check(self): + if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'): + # For Trilinos v11 we need to force SuperLUDist=OFF, + # since only the deprecated SuperLUDist v3.3 together with an Amesos patch + # is working. + raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:') def install(self, spec, prefix): + self.variants_check() + + cxx_flags = [] options = [] options.extend(std_cmake_args) + mpi_bin = spec['mpi'].prefix.bin options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', + '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', + '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', - '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'), '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), - '-DTPL_ENABLE_MPI:STRING=ON', - '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, - '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix + '-DTPL_ENABLE_MPI:BOOL=ON', + '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, + '-DTPL_ENABLE_BLAS=ON', + '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names + '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, + '-DTPL_ENABLE_LAPACK=ON', + '-DLAPACK_LIBRARY_NAMES=lapack', + '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, + '-DTPL_ENABLE_Boost:BOOL=ON', + '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, + '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, + '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', + '-DTrilinos_ENABLE_CXX11:BOOL=ON', + '-DTPL_ENABLE_Netcdf:BOOL=ON', + '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'), + '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'), ]) + # Fortran lib + libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) + options.extend([ + '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, + '-DTrilinos_ENABLE_Fortran=ON' + ]) + + # for build-debug only: + #options.extend([ + # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + #]) + + # suite-sparse related + if '+suite-sparse' in spec: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? + #'-DTPL_ENABLE_Cholmod:BOOL=ON', + #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DTPL_ENABLE_UMFPACK:BOOL=ON', + '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' + ]) + else: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', + '-DTPL_ENABLE_UMFPACK:BOOL=OFF', + ]) + + # metis / parmetis + if '+metis' in spec: + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=ON', + '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, + '-DMETIS_LIBRARY_NAMES=metis', + '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include, + '-DTPL_ENABLE_ParMETIS:BOOL=ON', + '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib), + '-DParMETIS_LIBRARY_NAMES=parmetis;metis', + '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include + ]) + else: + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=OFF', + '-DTPL_ENABLE_ParMETIS:BOOL=OFF', + ]) + + # mumps / scalapack + if '+mumps' in spec: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=ON', + '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, + '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important! + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', + '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + ]) + # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS + cxx_flags.extend([ + '-DMUMPS_5_0' + ]) + else: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=OFF', + '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', + ]) + + # superlu-dist: + if '+superlu-dist' in spec: + # Amesos, conflicting types of double and complex SLU_D + # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html + # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html + options.extend([ + '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', + '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' + ]) + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=ON', + '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, + '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include + ]) + if spec.satisfies('^superlu-dist@4.0:'): + options.extend([ + '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' + ]) + else: + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=OFF', + ]) + + + # python + if '+python' in spec: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON' + ]) + else: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' + ]) + + # collect CXX flags: + options.extend([ + '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)), + ]) + + # disable due to compiler / config errors: + options.extend([ + '-DTrilinos_ENABLE_SEACAS=OFF', + '-DTrilinos_ENABLE_Pike=OFF', + '-DTrilinos_ENABLE_STK=OFF' + ]) + if sys.platform == 'darwin': + options.extend([ + '-DTrilinos_ENABLE_FEI=OFF' + ]) + + with working_dir('spack-build', create=True): cmake('..', *options) make() make('install') + + # When trilinos is built with Python, libpytrilinos is included through + # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake + # contains pytrilinos. This leads to a run-time error: + # Symbol not found: _PyBool_Type + # and prevents Trilinos to be used in any C++ code, which links executable + # against the libraries listed in Trilinos_LIBRARIES. + # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509 + # A workaround it to remove PyTrilinos from the COMPONENTS_LIST : + if '+python' in self.spec: + filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch new file mode 100644 index 0000000000..9defc55527 --- /dev/null +++ b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch @@ -0,0 +1,12 @@ +diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake +index 963eb71..998cd02 100644 +--- a/cmake/TPLs/FindTPLUMFPACK.cmake ++++ b/cmake/TPLs/FindTPLUMFPACK.cmake +@@ -55,6 +55,6 @@ + + + TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK +- REQUIRED_HEADERS umfpack.h amd.h UFconfig.h ++ REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h + REQUIRED_LIBS_NAMES umfpack amd + ) diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 4a27a8fedb..24382af406 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -7,11 +7,23 @@ class Vtk(Package): homepage = "http://www.vtk.org" url = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz" + version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz") + + version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz") + version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') depends_on("qt") + # VTK7 defaults to OpenGL2 rendering backend + variant('opengl2', default=True, description='Build with OpenGL instead of OpenGL2 as rendering backend') + def install(self, spec, prefix): + def feature_to_bool(feature, on='ON', off='OFF'): + if feature in spec: + return on + return off + with working_dir('spack-build', create=True): cmake_args = [ "..", @@ -35,6 +47,12 @@ class Vtk(Package): if spec['qt'].satisfies('@5'): cmake_args.append("-DVTK_QT_VERSION:STRING=5") + if spec.satisfies("@6.1.0"): + cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY") + cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY") + + cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL')) + cmake(*cmake_args) make() make("install") |