diff options
Diffstat (limited to 'var/spack')
100 files changed, 2710 insertions, 329 deletions
diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py new file mode 100644 index 0000000000..7d63925693 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py @@ -0,0 +1,34 @@ +############################################################################## +# 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://scalability-llnl.github.io/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 Externalprereq(Package): + homepage = "http://somewhere.com" + url = "http://somewhere.com/prereq-1.0.tar.gz" + + version('1.4', 'f1234567890abcdef1234567890abcde') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py new file mode 100644 index 0000000000..c546922f87 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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://scalability-llnl.github.io/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 Externaltest(Package): + homepage = "http://somewhere.com" + url = "http://somewhere.com/test-1.0.tar.gz" + + version('1.0', '1234567890abcdef1234567890abcdef') + + depends_on('stuff') + depends_on('externaltool') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py new file mode 100644 index 0000000000..af902bd70e --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py @@ -0,0 +1,36 @@ +############################################################################## +# 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://scalability-llnl.github.io/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 Externaltool(Package): + homepage = "http://somewhere.com" + url = "http://somewhere.com/tool-1.0.tar.gz" + + version('1.0', '1234567890abcdef1234567890abcdef') + + depends_on('externalprereq') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py new file mode 100644 index 0000000000..722c1e1c53 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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://scalability-llnl.github.io/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 Externalvirtual(Package): + homepage = "http://somewhere.com" + url = "http://somewhere.com/stuff-1.0.tar.gz" + + version('1.0', '1234567890abcdef1234567890abcdef') + version('2.0', '234567890abcdef1234567890abcdef1') + + provides('stuff') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py new file mode 100644 index 0000000000..f69f16d2cc --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/hypre/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2015, 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 Hypre(Package): + """Hypre is included here as an example of a package that depends on + both LAPACK and BLAS.""" + homepage = "http://www.openblas.net" + url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + + version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + + depends_on('lapack') + depends_on('blas') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py index 55bf97f2cf..836d9c4a9f 100644 --- a/var/spack/repos/builtin.mock/packages/mpich/package.py +++ b/var/spack/repos/builtin.mock/packages/mpich/package.py @@ -38,6 +38,7 @@ class Mpich(Package): version('3.0.2', 'foobarbaz') version('3.0.1', 'foobarbaz') version('3.0', 'foobarbaz') + version('1.0', 'foobarbas') provides('mpi@:3', when='@3:') provides('mpi@:1', when='@:1') diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py new file mode 100644 index 0000000000..509bfb71e5 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2015, 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 OpenblasWithLapack(Package): + """Dummy version of OpenBLAS that also provides LAPACK, for testing.""" + homepage = "http://www.openblas.net" + url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + + version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + + provides('lapack') + provides('blas') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py new file mode 100644 index 0000000000..614071cf53 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -0,0 +1,61 @@ +from spack import * + + +class ArpackNg(Package): + """ + ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. + + Important Features: + + * Reverse Communication Interface. + * Single and Double Precision Real Arithmetic Versions for Symmetric, + Non-symmetric, Standard or Generalized Problems. + * Single and Double Precision Complex Arithmetic Versions for Standard or + Generalized Problems. + * Routines for Banded Matrices - Standard or Generalized Problems. + * Routines for The Singular Value Decomposition. + * Example driver routines that may be used as templates to implement numerous + Shift-Invert strategies for all problem types, data types and precision. + + This project is a joint project between Debian, Octave and Scilab in order to + provide a common and maintained version of arpack. + + Indeed, no single release has been published by Rice university for the last + few years and since many software (Octave, Scilab, R, Matlab...) forked it and + implemented their own modifications, arpack-ng aims to tackle this by providing + a common repository and maintained versions. + + arpack-ng is replacing arpack almost everywhere. + """ + homepage = 'https://github.com/opencollab/arpack-ng' + url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz' + + version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') + + variant('shared', default=True, description='Enables the build of shared libraries') + variant('mpi', default=False, description='Activates MPI support') + + # The function pdlamch10 does not set the return variable. This is fixed upstream + # see https://github.com/opencollab/arpack-ng/issues/34 + patch('pdlamch10.patch', when='@3.3:') + + depends_on('blas') + depends_on('lapack') + depends_on('mpi', when='+mpi') + + def install(self, spec, prefix): + # Apparently autotools are not bootstrapped + bootstrap = Executable('./bootstrap') + + options = ['--prefix=%s' % prefix] + + if '+mpi' in spec: + options.append('--enable-mpi') + + if '~shared' in spec: + options.append('--enable-shared=no') + + bootstrap() + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch new file mode 100644 index 0000000000..922828909f --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch @@ -0,0 +1,15 @@ +diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f +index 6571da9..2882c2e 100644 +--- a/PARPACK/SRC/MPI/pdlamch10.f ++++ b/PARPACK/SRC/MPI/pdlamch10.f +@@ -86,8 +86,8 @@ + TEMP = TEMP1 + END IF + * +- PDLAMCH = TEMP ++ PDLAMCH10 = TEMP + * +-* End of PDLAMCH ++* End of PDLAMCH10 + * + END diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index 5189faf054..6412e810a6 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -6,6 +6,7 @@ class Autoconf(Package): url = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz" version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') + version('2.62', '6c1f3b3734999035d77da5024aab4fbd') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index 9115822730..2172a42030 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -5,7 +5,9 @@ class Automake(Package): homepage = "http://www.gnu.org/software/automake/" url = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz" + version('1.15', '716946a105ca228ab545fc37a70df3a3') version('1.14.1', 'd052a3e884631b9c7892f2efce542d75') + version('1.11.6', '0286dc30295b62985ca51919202ecfcc') depends_on('autoconf') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index de04221e33..897539a439 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -4,10 +4,13 @@ class Binutils(Package): """GNU binutils, which contain the linker, assembler, objdump and others""" homepage = "http://www.gnu.org/software/binutils/" - version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2") - version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.24.tar.bz2") - version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.23.2.tar.bz2") - version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.20.1.tar.bz2") + url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" + + version('2.26', '64146a0faa3b411ba774f47d41de239f') + version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66') + version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b') + version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') + version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell variant('krellpatch', default=False, description="build with openspeedshop based patch.") diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py new file mode 100644 index 0000000000..9413b276fe --- /dev/null +++ b/var/spack/repos/builtin/packages/blitz/package.py @@ -0,0 +1,15 @@ +from spack import * + +class Blitz(Package): + """N-dimensional arrays for C++""" + homepage = "http://github.com/blitzpp/blitz" + url = "https://github.com/blitzpp/blitz/tarball/1.0.0" + + version('1.0.0', '9f040b9827fe22228a892603671a77af') + + # No dependencies + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/boost/boost_11856.patch b/var/spack/repos/builtin/packages/boost/boost_11856.patch new file mode 100644 index 0000000000..3b4052ca18 --- /dev/null +++ b/var/spack/repos/builtin/packages/boost/boost_11856.patch @@ -0,0 +1,34 @@ +--- a/libs/container/src/pool_resource.cpp 2015-11-06 12:49:55.000000000 -0800 ++++ b/libs/container/src/pool_resource.cpp 2015-12-22 07:54:36.202131121 -0800 +@@ -32,11 +32,11 @@ + class pool_data_t + : public block_slist_base<> + { +- typedef block_slist_base<> block_slist_base; ++ typedef block_slist_base<> block_slist_base_t; + + public: + explicit pool_data_t(std::size_t initial_blocks_per_chunk) +- : block_slist_base(), next_blocks_per_chunk(initial_blocks_per_chunk) ++ : block_slist_base_t(), next_blocks_per_chunk(initial_blocks_per_chunk) + { slist_algo::init_header(&free_slist); } + + void *allocate_block() BOOST_NOEXCEPT +@@ -59,7 +59,7 @@ + void release(memory_resource &upstream) + { + slist_algo::init_header(&free_slist); +- this->block_slist_base::release(upstream); ++ this->block_slist_base_t::release(upstream); + next_blocks_per_chunk = pool_options_minimum_max_blocks_per_chunk; + } + +@@ -72,7 +72,7 @@ + + //Minimum block size is at least max_align, so all pools allocate sizes that are multiple of max_align, + //meaning that all blocks are max_align-aligned. +- char *p = static_cast<char *>(block_slist_base::allocate(blocks_per_chunk*pool_block, mr)); ++ char *p = static_cast<char *>(block_slist_base_t::allocate(blocks_per_chunk*pool_block, mr)); + + //Create header types. This is no-throw + for(std::size_t i = 0, max = blocks_per_chunk; i != max; ++i){ diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 3427b74ad6..fb1f5daee7 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -1,4 +1,5 @@ from spack import * +import spack class Boost(Package): """Boost provides free peer-reviewed portable C++ source @@ -44,15 +45,50 @@ class Boost(Package): version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5') version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0') + default_install_libs = set(['atomic', + 'chrono', + 'date_time', + 'filesystem', + 'graph', + 'iostreams', + 'locale', + 'log', + 'math', + 'program_options', + 'random', + 'regex', + 'serialization', + 'signals', + 'system', + 'test', + 'thread', + 'wave']) + + # mpi/python are not installed by default because they pull in many + # dependencies and/or because there is a great deal of customization + # possible (and it would be difficult to choose sensible defaults) + default_noinstall_libs = set(['mpi', 'python']) + + all_libs = default_install_libs | default_noinstall_libs + + for lib in all_libs: + variant(lib, default=(lib not in default_noinstall_libs), + description="Compile with {0} library".format(lib)) + variant('debug', default=False, description='Switch to the debug version of Boost') - variant('python', default=False, description='Activate the component Boost.Python') - variant('mpi', default=False, description='Activate the component Boost.MPI') - variant('compression', default=True, description='Activate the compression Boost.iostreams') + variant('shared', default=True, description="Additionally build shared libraries") + variant('multithreaded', default=True, description="Build multi-threaded versions of libraries") + variant('singlethreaded', default=True, description="Build single-threaded versions of libraries") + variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)") + depends_on('icu', when='+icu_support') depends_on('python', when='+python') depends_on('mpi', when='+mpi') - depends_on('bzip2', when='+compression') - depends_on('zlib', when='+compression') + depends_on('bzip2', when='+iostreams') + depends_on('zlib', when='+iostreams') + + # Patch fix from https://svn.boost.org/trac/boost/ticket/11856 + patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7') def url_for_version(self, version): """Handle Boost's weird URLs, which write the version two different ways.""" @@ -77,22 +113,20 @@ class Boost(Package): # fallback to gcc if no toolset found return 'gcc' - def determine_bootstrap_options(self, spec, options): - options.append('--with-toolset=%s' % self.determine_toolset(spec)) + def determine_bootstrap_options(self, spec, withLibs, options): + boostToolsetId = self.determine_toolset(spec) + options.append('--with-toolset=%s' % boostToolsetId) + options.append("--with-libraries=%s" % ','.join(withLibs)) - without_libs = [] - if '~mpi' in spec: - without_libs.append('mpi') - if '~python' in spec: - without_libs.append('python') - else: + if '+python' in spec: options.append('--with-python=%s' % join_path(spec['python'].prefix.bin, 'python')) - if without_libs: - options.append('--without-libraries=%s' % ','.join(without_libs)) - with open('user-config.jam', 'w') as f: + compiler_wrapper = join_path(spack.build_env_path, 'c++') + f.write("using {0} : : {1} ;\n".format(boostToolsetId, + compiler_wrapper)) + if '+mpi' in spec: f.write('using mpi : %s ;\n' % join_path(spec['mpi'].prefix.bin, 'mpicxx')) @@ -107,12 +141,10 @@ class Boost(Package): else: options.append('variant=release') - if '~compression' in spec: - options.extend([ - '-s', 'NO_BZIP2=1', - '-s', 'NO_ZLIB=1']) + if '+icu_support' in spec: + options.extend(['-s', 'ICU_PATH=%s' % spec['icu'].prefix]) - if '+compression' in spec: + if '+iostreams' in spec: options.extend([ '-s', 'BZIP2_INCLUDE=%s' % spec['bzip2'].prefix.include, '-s', 'BZIP2_LIBPATH=%s' % spec['bzip2'].prefix.lib, @@ -120,20 +152,46 @@ class Boost(Package): '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib, ]) + linkTypes = ['static'] + if '+shared' in spec: + linkTypes.append('shared') + + threadingOpts = [] + if '+multithreaded' in spec: + threadingOpts.append('multi') + if '+singlethreaded' in spec: + threadingOpts.append('single') + if not threadingOpts: + raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled") + options.extend([ 'toolset=%s' % self.determine_toolset(spec), - 'link=static,shared', - 'threading=single,multi', + 'link=%s' % ','.join(linkTypes), '--layout=tagged']) + + return threadingOpts def install(self, spec, prefix): + withLibs = list() + for lib in Boost.all_libs: + if "+{0}".format(lib) in spec: + withLibs.append(lib) + if not withLibs: + # if no libraries are specified for compilation, then you dont have + # to configure/build anything, just copy over to the prefix directory. + src = join_path(self.stage.source_path, 'boost') + mkdirp(join_path(prefix, 'include')) + dst = join_path(prefix, 'include', 'boost') + install_tree(src, dst) + return + # to make Boost find the user-config.jam env['BOOST_BUILD_PATH'] = './' bootstrap = Executable('./bootstrap.sh') bootstrap_options = ['--prefix=%s' % prefix] - self.determine_bootstrap_options(spec, bootstrap_options) + self.determine_bootstrap_options(spec, withLibs, bootstrap_options) bootstrap(*bootstrap_options) @@ -143,6 +201,10 @@ class Boost(Package): b2 = Executable(b2name) b2_options = ['-j', '%s' % make_jobs] - self.determine_b2_options(spec, b2_options) + threadingOpts = self.determine_b2_options(spec, b2_options) - b2('install', *b2_options) + # In theory it could be done on one call but it fails on + # Boost.MPI if the threading options are not separated. + for threadingOpt in threadingOpts: + b2('install', 'threading=%s' % threadingOpt, *b2_options) + diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py new file mode 100644 index 0000000000..d51b4a4dd5 --- /dev/null +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -0,0 +1,25 @@ +from spack import * + +class Caliper(Package): + """ + Caliper is a generic context annotation system. It gives programmers the + ability to provide arbitrary program context information to (performance) + tools at runtime. + """ + + homepage = "https://github.com/LLNL/Caliper" + url = "" + + version('master', git='ssh://git@github.com:LLNL/Caliper.git') + + variant('mpi', default=False, description='Enable MPI function wrappers.') + + depends_on('libunwind') + depends_on('papi') + depends_on('mpi', when='+mpi') + + def install(self, spec, prefix): + with working_dir('build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py index 97356433be..ef4a2736db 100644 --- a/var/spack/repos/builtin/packages/cgal/package.py +++ b/var/spack/repos/builtin/packages/cgal/package.py @@ -46,6 +46,7 @@ class Cgal(Package): depends_on('mpfr') depends_on('gmp') depends_on('zlib') + depends_on('cmake') # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL) # FIXME : Optional third party libraries missing diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index f67ae21ebd..cc93c7067c 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -28,23 +28,58 @@ class Cmake(Package): """A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" homepage = 'https://www.cmake.org' + url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' - version('2.8.10.2', '097278785da7182ec0aea8769d06860c', - url = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz') - - version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f', - url = 'http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz') - - version('3.4.0', 'cd3034e0a44256a0917e254167217fc8', - url = 'http://cmake.org/files/v3.4/cmake-3.4.0.tar.gz') + version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') + version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') + version('3.4.0', 'cd3034e0a44256a0917e254167217fc8') + version('3.3.1', '52638576f4e1e621fed6c3410d3a1b12') + version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f') + version('2.8.10.2', '097278785da7182ec0aea8769d06860c') variant('ncurses', default=True, description='Enables the build of the ncurses gui') + variant('qt', default=False, description='Enables the build of cmake-gui') + variant('doc', default=False, description='Enables the generation of html and man page documentation') depends_on('ncurses', when='+ncurses') + depends_on('qt', when='+qt') + depends_on('python@2.7.11:', when='+doc') + depends_on('py-sphinx', when='+doc') + + def url_for_version(self, version): + """Handle CMake's version-based custom URLs.""" + return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version) + + def validate(self, spec): + """ + Checks if incompatible versions of qt were specified + + :param spec: spec of the package + :raises RuntimeError: in case of inconsistencies + """ + + if '+qt' in spec and spec.satisfies('^qt@5.4.0'): + msg = 'qt-5.4.0 has broken CMake modules.' + raise RuntimeError(msg) def install(self, spec, prefix): - configure('--prefix=' + prefix, - '--parallel=' + str(make_jobs), - '--', '-DCMAKE_USE_OPENSSL=ON') + # Consistency check + self.validate(spec) + + # configure, build, install: + options = ['--prefix=%s' % prefix] + options.append('--parallel=%s' % str(make_jobs)) + + if '+qt' in spec: + options.append('--qt-gui') + + if '+doc' in spec: + options.append('--sphinx-html') + options.append('--sphinx-man') + + options.append('--') + options.append('-DCMAKE_USE_OPENSSL=ON') + + configure(*options) make() make('install') diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py new file mode 100644 index 0000000000..7377016a6b --- /dev/null +++ b/var/spack/repos/builtin/packages/cmocka/package.py @@ -0,0 +1,16 @@ +from spack import * + +class Cmocka(Package): + """Unit-testing framework in pure C""" + homepage = "https://cmocka.org/" + url = "https://cmocka.org/files/1.0/cmocka-1.0.1.tar.xz" + + version('1.0.1', 'ed861e501a21a92b2af63e466df2015e') + parallel = False + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py new file mode 100644 index 0000000000..1693c4b160 --- /dev/null +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -0,0 +1,31 @@ +import glob +from spack import * + +class Cryptopp(Package): + """Crypto++ is an open-source C++ library of cryptographic schemes. The + library supports a number of different cryptography algorithms, including + authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), + public-key encryption (RSA, DSA), and a few obsolete/historical encryption + algorithms (MD5, Panama).""" + + homepage = "http://www.cryptopp.com/" + url = "http://www.cryptopp.com/cryptopp563.zip" + + version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') + version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') + + def install(self, spec, prefix): + make() + + mkdirp(prefix.include) + for hfile in glob.glob('*.h*'): + install(hfile, prefix.include) + + mkdirp(prefix.lib) + install('libcryptopp.a', prefix.lib) + + def url_for_version(self, version): + version_tuple = tuple(v for v in iter(version)) + version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "") + + return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string) diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 9e684445c7..ab6305fc08 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -7,6 +7,7 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') version('7.45.0', '62c1a352b28558f25ba6209214beadc8') version('7.44.0', '6b952ca00e5473b16a11f05f06aa8dae') diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py new file mode 100644 index 0000000000..5ec82ef83d --- /dev/null +++ b/var/spack/repos/builtin/packages/dakota/package.py @@ -0,0 +1,55 @@ +from spack import * + + +class Dakota(Package): + """ + The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems + analysis methods. Dakota contains algorithms for: + + - optimization with gradient and non gradient-based methods; + - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; + - parameter estimation with nonlinear least squares methods; + - sensitivity/variance analysis with design of experiments and parameter study methods. + + These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, + surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. + """ + + homepage = 'https://dakota.sandia.gov/' + url = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.3-public.src.tar.gz' + _url_str = 'https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-{version}-public.src.tar.gz' + + version('6.3', '05a58d209fae604af234c894c3f73f6d') + + variant('debug', default=False, description='Builds a debug version of the libraries') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('mpi', default=True, description='Activates MPI support') + + depends_on('blas') + depends_on('lapack') + depends_on('mpi', when='+mpi') + + depends_on('python') + depends_on('boost') + + def url_for_version(self, version): + return Dakota._url_str.format(version=version) + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + + options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF')]) + + if '+mpi' in spec: + options.extend(['-DDAKOTA_HAVE_MPI:BOOL=ON', + '-DMPI_CXX_COMPILER:STRING=%s' % join_path(spec['mpi'].prefix.bin, 'mpicxx')]) + + build_directory = join_path(self.stage.path, 'spack-build') + source_directory = self.stage.source_path + + with working_dir(build_directory, create=True): + cmake(source_directory, *options) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py new file mode 100644 index 0000000000..8d6e672f86 --- /dev/null +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -0,0 +1,69 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by David Beckingsale, david@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 Eigen(Package): + """ + Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms + """ + + homepage = 'http://eigen.tuxfamily.org/' + url = 'http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2' + + version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184', url='http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2') + + variant('debug', default=False, description='Builds the library in debug mode') + + variant('metis', default=True, description='Enables metis backend') + variant('scotch', default=True, description='Enables scotch backend') + variant('fftw', default=True, description='Enables FFTW backend') + variant('suitesparse', default=True, description='Enables SuiteSparse support') + + # TODO : dependency on googlehash, superlu, adolc missing + + depends_on('metis', when='+metis') + depends_on('scotch', when='+scotch') + depends_on('fftw', when='+fftw') + depends_on('suite-sparse', when='+suitesparse') + depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0 + depends_on('gmp') + + def install(self, spec, prefix): + + options = [] + options.extend(std_cmake_args) + + build_directory = join_path(self.stage.path, 'spack-build') + source_directory = self.stage.source_path + + if '+debug' in spec: + options.append('-DCMAKE_BUILD_TYPE:STRING=Debug') + + with working_dir(build_directory, create=True): + cmake(source_directory, *options) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py new file mode 100644 index 0000000000..2ade5b0b37 --- /dev/null +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -0,0 +1,55 @@ +############################################################################## +# 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 Elpa(Package): + """ + Eigenvalue solvers for Petaflop-Applications (ELPA) + """ + + homepage = 'http://elpa.mpcdf.mpg.de/' + url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' + + version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6', url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz') + + variant('openmp', default=False, description='Activates OpenMP support') + + depends_on('mpi') + depends_on('blas') + depends_on('lapack') + depends_on('scalapack') + + def install(self, spec, prefix): + + options = ["--prefix=%s" % prefix] + + if '+openmp' in spec: + options.append("--enable-openmp") + + configure(*options) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py new file mode 100644 index 0000000000..caa264857e --- /dev/null +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Emacs(Package): + """The Emacs programmable text editor.""" + homepage = "https://www.gnu.org/software/emacs" + url = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz" + + version('24.5', 'd74b597503a68105e61b5b9f6d065b44') + + depends_on('ncurses') + # Emacs also depends on: + # GTK or other widget library + # libtiff, png, etc. + # For now, we assume the system provides all that stuff. + # For Ubuntu 14.04 LTS: + # sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py new file mode 100644 index 0000000000..a2bf58f585 --- /dev/null +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -0,0 +1,65 @@ +from spack import * + +import os + +class Espresso(Package): + """ + QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials + modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + """ + homepage = 'http://quantum-espresso.org' + url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz' + + version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3') + + variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support') + variant('openmp', default=False, description='Enables openMP support') + variant('scalapack', default=True, description='Enables scalapack support') + variant('elpa', default=True, description='Use elpa as an eigenvalue solver') + + depends_on('blas') + depends_on('lapack') + + depends_on('mpi', when='+mpi') + 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: + raise RuntimeError(error.format(variant='scalapack')) + if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): + raise RuntimeError(error.format(variant='elpa')) + + def install(self, spec, prefix): + self.check_variants(spec) + + options = ['-prefix=%s' % prefix] + + if '+mpi' in spec: + options.append('--enable-parallel') + + if '+openmp' in spec: + options.append('--enable-openmp') + + if '+scalapack' in spec: + options.append('--with-scalapack=yes') + + if '+elpa' in spec: + options.append('--with-elpa=yes') + + # Add a list of directories to search + search_list = [] + for name, dependency_spec in spec.dependencies.iteritems(): + search_list.extend([dependency_spec.prefix.lib, + dependency_spec.prefix.lib64]) + + search_list = " ".join(search_list) + options.append('LIBDIRS=%s' % search_list) + options.append('F90=%s' % os.environ['FC']) + + configure(*options) + make('all') + make('install') + diff --git a/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch new file mode 100644 index 0000000000..25355269ca --- /dev/null +++ b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch @@ -0,0 +1,12 @@ +diff --git a/cmake-exodus b/cmake-exodus +index 787fd9d..ed073a2 100755 +--- a/cmake-exodus ++++ b/cmake-exodus +@@ -1,4 +1,6 @@ +-EXTRA_ARGS=$@ ++#!/bin/bash ++ ++EXTRA_ARGS=-DSEACASProj_ENABLE_CXX11=OFF + + ### Change this to point to the compilers you want to use + CC=gcc diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py new file mode 100644 index 0000000000..af258b7e6e --- /dev/null +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -0,0 +1,49 @@ +from spack import * + +# TODO: Add support for a C++11 enabled installation that filters out the +# TODO: "C++11-Disabled" flag (but only if the spec compiler supports C++11). + +# TODO: Add support for parallel installation that uses MPI. + +# TODO: Create installation options for NetCDF that support larger page size +# TODO: suggested by Exodus (see the repository "README" file). + +class Exodusii(Package): + """Exodus II is a C++/Fortran library developed to store and retrieve data for + finite element analyses. It's used for preprocessing (problem definition), + postprocessing (results visualization), and data transfer between codes. + An Exodus II data file is a random access, machine independent, binary + file that is written and read via C, C++, or Fortran API routines.""" + + homepage = "https://github.com/gsjaardema/seacas" + url = "https://github.com/gsjaardema/seacas/archive/master.zip" + + version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529') + + # TODO: Make this a build dependency once build dependencies are supported + # (see: https://github.com/LLNL/spack/pull/378). + depends_on('cmake@2.8.7:') + depends_on('hdf5~shared~mpi') + depends_on('netcdf~mpi') + + patch('exodus-cmake.patch') + + def patch(self): + ff = FileFilter('cmake-exodus') + + ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}', + 'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, string=True) + ff.filter('NetCDF_DIR:PATH=${TPL}', + 'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, string=True) + ff.filter('HDF5_ROOT:PATH=${TPL}', + 'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, string=True) + + def install(self, spec, prefix): + mkdirp('build') + cd('build') + + cmake_exodus = Executable('../cmake-exodus') + cmake_exodus() + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py index 082da5bf0b..3f925c6546 100644 --- a/var/spack/repos/builtin/packages/expat/package.py +++ b/var/spack/repos/builtin/packages/expat/package.py @@ -7,6 +7,7 @@ class Expat(Package): version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd') + depends_on('cmake') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py index 4d2b964242..bc129aaf1a 100644 --- a/var/spack/repos/builtin/packages/fftw/package.py +++ b/var/spack/repos/builtin/packages/fftw/package.py @@ -47,6 +47,8 @@ class Fftw(Package): depends_on('mpi', when='+mpi') + # TODO : add support for architecture specific optimizations as soon as targets are supported + def install(self, spec, prefix): options = ['--prefix=%s' % prefix, '--enable-shared', diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py index 1225558705..b5a4a2d209 100644 --- a/var/spack/repos/builtin/packages/fish/package.py +++ b/var/spack/repos/builtin/packages/fish/package.py @@ -7,7 +7,8 @@ class Fish(Package): homepage = "http://fishshell.com/" url = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz" - list_url = homepage + list_url = "http://fishshell.com/files/" + list_depth = 2 version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a') diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 61b16f3fd8..f8958ee290 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -36,8 +36,6 @@ class Gcc(Package): list_url = 'http://open-source-box.org/gcc/' list_depth = 2 - DEPENDS_ON_ISL_PREDICATE = '@5.0:' - version('5.3.0', 'c9616fd448f980259c31de613e575719') version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467') version('4.9.3', '6f831b4d251872736e8e9cc09746f327') @@ -50,15 +48,14 @@ class Gcc(Package): version('4.5.4', '27e459c2566b8209ab064570e1b378f7') variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO") - + depends_on("mpfr") depends_on("gmp") - depends_on("mpc") # when @4.5: + depends_on("mpc", when='@4.5:') + depends_on("isl", when='@5.0:') depends_on("binutils~libiberty", when='~gold') depends_on("binutils~libiberty+gold", when='+gold') - # Save these until we can do optional deps. - depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE) #depends_on("ppl") #depends_on("cloog") @@ -91,7 +88,7 @@ class Gcc(Package): "--with-as=%s/bin/as" % spec['binutils'].prefix] options.extend(binutils_options) # Isl - if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE): + if 'isl' in spec: isl_options = ["--with-isl=%s" % spec['isl'].prefix] options.extend(isl_options) @@ -102,7 +99,7 @@ class Gcc(Package): configure(*options) make() make("install") - + self.write_rpath_specs() @@ -121,7 +118,7 @@ class Gcc(Package): return gcc = Executable(join_path(self.prefix.bin, 'gcc')) - lines = gcc('-dumpspecs', return_output=True).strip().split("\n") + lines = gcc('-dumpspecs', output=str).strip().split("\n") specs_file = join_path(self.spec_dir, 'specs') with closing(open(specs_file, 'w')) as out: for line in lines: diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index dd02b426b9..b346fe80c2 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -6,7 +6,7 @@ # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. # LLNL-CODE-647188 # -# For details, see https://llnl.github.io/spack +# For details, see https://software.llnl.gov/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 diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index ddc5078c4d..586b6ce3c3 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -5,14 +5,22 @@ class Git(Package): system designed to handle everything from small to very large projects with speed and efficiency.""" homepage = "http://git-scm.com" - url = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.gz" + url = "https://github.com/git/git/tarball/v2.7.1" - version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') - version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') - version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') - version('2.6.0', 'eb76a07148d94802a1745d759716a57e') - version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') - version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') + version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c') + version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6') + version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060') + + + # See here for info on vulnerable Git versions: + # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/ + # All the following are vulnerable + #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') + #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') + #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') + #version('2.6.0', 'eb76a07148d94802a1745d759716a57e') + #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') + #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') # Git compiles with curl support by default on but if your system @@ -24,6 +32,7 @@ class Git(Package): variant("expat", default=False, description="Add the internal support of expat for https push") depends_on("openssl") + depends_on("autoconf") depends_on("curl", when="+curl") depends_on("expat", when="+expat") @@ -47,6 +56,7 @@ class Git(Package): if '+expat' in spec: configure_args.append("--with-expat=%s" % spec['expat'].prefix) + which('autoreconf')('-i') configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py new file mode 100644 index 0000000000..cb376b3f03 --- /dev/null +++ b/var/spack/repos/builtin/packages/gl2ps/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Gl2ps(Package): + """GL2PS is a C library providing high quality vector output for any + OpenGL application.""" + + homepage = "http://www.geuz.org/gl2ps/" + url = "http://geuz.org/gl2ps/src/gl2ps-1.3.9.tgz" + + version('1.3.9', '377b2bcad62d528e7096e76358f41140') + + depends_on("libpng") + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py new file mode 100644 index 0000000000..5fe8399308 --- /dev/null +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -0,0 +1,56 @@ +from spack import * + + +class Gromacs(Package): + """ + GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for + simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry + department of University of Groningen, and is now maintained by contributors in universities and research centers + across the world. + + GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. + It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is + released under the GNU Lesser General Public License. + """ + + homepage = 'http://www.gromacs.org' + url = 'ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz' + + version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98') + + variant('mpi', default=True, description='Activate MPI support') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Enables debug mode') + variant('double', default=False, description='Produces a double precision version of the executables') + + depends_on('mpi', when='+mpi') + + depends_on('fftw') + + # TODO : add GPU support + + def install(self, spec, prefix): + + options = [] + + if '+mpi' in spec: + options.append('-DGMX_MPI:BOOL=ON') + + if '+double' in spec: + options.append('-DGMX_DOUBLE:BOOL=ON') + + if '~shared' in spec: + options.append('-DBUILD_SHARED_LIBS:BOOL=OFF') + + if '+debug' in spec: + options.append('-DCMAKE_BUILD_TYPE:STRING=Debug') + else: + options.append('-DCMAKE_BUILD_TYPE:STRING=Release') + + options.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + + cmake('..', *options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py new file mode 100644 index 0000000000..ac6435f2a2 --- /dev/null +++ b/var/spack/repos/builtin/packages/hdf/package.py @@ -0,0 +1,45 @@ +from spack import * + +class Hdf(Package): + """HDF4 (also known as HDF) is a library and multi-object + file format for storing and managing data between machines.""" + + homepage = "https://www.hdfgroup.org/products/hdf4/" + url = "https://www.hdfgroup.org/ftp/HDF/releases/HDF4.2.11/src/hdf-4.2.11.tar.gz" + list_url = "https://www.hdfgroup.org/ftp/HDF/releases/" + list_depth = 3 + + version('4.2.11', '063f9928f3a19cc21367b71c3b8bbf19') + + variant('szip', default=False, description="Enable szip support") + + depends_on("jpeg") + depends_on("szip", when='+szip') + depends_on("zlib") + + + def url_for_version(self, version): + return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(version) + "/src/hdf-" + str(version) + ".tar.gz" + + + def install(self, spec, prefix): + config_args = [ + 'CFLAGS=-fPIC', + '--prefix=%s' % prefix, + '--with-jpeg=%s' % spec['jpeg'].prefix, + '--with-zlib=%s' % spec['zlib'].prefix, + '--disable-netcdf', # must be disabled to build NetCDF with HDF4 support + '--enable-fortran', + '--disable-shared', # fortran and shared libraries are not compatible + '--enable-static', + '--enable-production' + ] + + # SZip support + if '+szip' in spec: + config_args.append('--with-szlib=%s' % spec['szip'].prefix) + + configure(*config_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 9a40164341..513a38ee8a 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -1,5 +1,31 @@ +############################################################################## +# 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 Hdf5(Package): """HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for @@ -7,7 +33,7 @@ class Hdf5(Package): """ homepage = "http://www.hdfgroup.org/HDF5/" - url = "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz" + url = "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz" list_url = "http://www.hdfgroup.org/ftp/HDF5/releases" list_depth = 3 @@ -15,26 +41,64 @@ class Hdf5(Package): version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') + variant('debug', default=False, description='Builds a debug version of the library') + variant('shared', default=True, description='Builds a shared version of the library') + variant('cxx', default=True, description='Enable C++ support') variant('fortran', default=True, description='Enable Fortran support') + variant('mpi', default=False, description='Enable MPI support') - variant('threadsafe', default=False, description='Enable multithreading') + variant('szip', default=False, description='Enable szip support') + variant('threadsafe', default=False, description='Enable thread-safe capabilities') depends_on("mpi", when='+mpi') + depends_on("szip", when='+szip') depends_on("zlib") - # TODO: currently hard-coded to use OpenMPI + def validate(self, spec): + """ + Checks if incompatible variants have been activated at the same time + + :param spec: spec of the package + :raises RuntimeError: in case of inconsistencies + """ + if '+fortran' in spec and not self.compiler.fc: + msg = 'cannot build a fortran variant without a fortran compiler' + raise RuntimeError(msg) + + if '+threadsafe' in spec and ('+cxx' in spec or '+fortran' in spec): + raise RuntimeError("cannot use variant +threadsafe with either +cxx or +fortran") + def install(self, spec, prefix): + self.validate(spec) + # Handle compilation after spec validation extra_args = [] + + # Always enable this option. This does not actually enable any + # features: it only *allows* the user to specify certain + # combinations of other arguments. Enabling it just skips a + # sanity check in configure, so this doesn't merit a variant. + extra_args.append("--enable-unsupported") + + if '+debug' in spec: + extra_args.append('--enable-debug=all') + else: + extra_args.append('--enable-production') + + if '+shared' in spec: + extra_args.append('--enable-shared') + else: + extra_args.append('--enable-static-exec') + if '+cxx' in spec: - extra_args.extend([ - '--enable-cxx' - ]) + extra_args.append('--enable-cxx') + if '+fortran' in spec: extra_args.extend([ '--enable-fortran', '--enable-fortran2003' ]) + if '+mpi' in spec: # The HDF5 configure script warns if cxx and mpi are enabled # together. There doesn't seem to be a real reason for this, except @@ -43,27 +107,28 @@ class Hdf5(Package): # this is not actually a problem. extra_args.extend([ "--enable-parallel", - "--enable-unsupported", "CC=%s" % spec['mpi'].prefix.bin + "/mpicc", - "CXX=%s" % spec['mpi'].prefix.bin + "/mpic++", - "FC=%s" % spec['mpi'].prefix.bin + "/mpifort", ]) - if '+threads' in spec: - if '+cxx' in spec or '+fortran' in spec: - die("Cannot use variant +threads with either +cxx or +fortran") + + if '+cxx' in spec: + extra_args.append("CXX=%s" % spec['mpi'].prefix.bin + "/mpic++") + + if '+fortran' in spec: + extra_args.append("FC=%s" % spec['mpi'].prefix.bin + "/mpifort") + + if '+szip' in spec: + extra_args.append("--with-szlib=%s" % spec['szip'].prefix) + + if '+threadsafe' in spec: extra_args.extend([ '--enable-threadsafe', '--disable-hl', - 'CPPFLAGS=-DHDatexit=""', - 'CFLAGS=-DHDatexit=""' ]) configure( "--prefix=%s" % prefix, "--with-zlib=%s" % spec['zlib'].prefix, - "--enable-shared", *extra_args) - make() make("install") diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py new file mode 100644 index 0000000000..3dae3c4170 --- /dev/null +++ b/var/spack/repos/builtin/packages/hpx5/package.py @@ -0,0 +1,52 @@ +from spack import * +import os + +class Hpx5(Package): + """The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an + open source, portable, performance-oriented runtime developed at + CREST (Indiana University). HPX-5 provides a distributed + programming model allowing programs to run unmodified on systems + from a single SMP to large clusters and supercomputers with + thousands of nodes. HPX-5 supports a wide variety of Intel and ARM + platforms. It is being used by a broad range of scientific + applications enabling scientists to write code that performs and + scales better than contemporary runtimes.""" + homepage = "http://hpx.crest.iu.edu" + url = "http://hpx.crest.iu.edu/release/hpx-2.0.0.tar.gz" + + version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6') + version('1.3.0', '2260ecc7f850e71a4d365a43017d8cee') + version('1.2.0', '4972005f85566af4afe8b71afbf1480f') + version('1.1.0', '646afb460ecb7e0eea713a634933ce4f') + version('1.0.0', '8020822adf6090bd59ed7fe465f6c6cb') + + variant('debug', default=False, description='Build a debug version of HPX-5') + variant('photon', default=False, description='Enable Photon support') + variant('mpi', default=False, description='Enable MPI support') + + depends_on("mpi", when='+mpi') + depends_on("mpi", when='+photon') + + def install(self, spec, prefix): + extra_args = [] + if '+debug' in spec: + extra_args.extend([ + '--enable-debug', + 'CFLAGS=-g -O0' + ]) + else: + extra_args.append('CFLAGS=-O3') + + if '+mpi' in spec: + extra_args.append('--enable-mpi') + + if '+photon' in spec: + extra_args.extend([ + '--enable-mpi', + '--enable-photon' + ]) + + os.chdir("./hpx/") + configure('--prefix=%s' % prefix, *extra_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index 7ebede76a3..ab7205646e 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -14,15 +14,18 @@ class Hwloc(Package): efficiently.""" homepage = "http://www.open-mpi.org/projects/hwloc/" url = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz" + list_url = "http://www.open-mpi.org/software/hwloc/" + list_depth = 3 - version('1.11.2', '486169cbe111cdea57be12638828ebbf', - url='http://www.open-mpi.org/software/hwloc/v1.11/downloads/hwloc-1.11.2.tar.bz2') - version('1.11.1', '002742efd3a8431f98d6315365a2b543', - url='http://www.open-mpi.org/software/hwloc/v1.11/downloads/hwloc-1.11.1.tar.bz2') - version('1.9', '1f9f9155682fe8946a97c08896109508') + version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23') + version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc') + version('1.9', '1f9f9155682fe8946a97c08896109508') depends_on('libpciaccess') + def url_for_version(self, version): + return "http://www.open-mpi.org/software/hwloc/v%s/downloads/hwloc-%s.tar.gz" % (version.up_to(2), version) + def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 0f7f14dd89..242ee100d7 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -1,4 +1,5 @@ from spack import * +import os class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -8,8 +9,11 @@ class Hypre(Package): homepage = "http://computation.llnl.gov/project/linear_solvers/software.php" url = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz" + version('2.10.1', 'dc048c4cabb3cd549af72591474ad674') version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') + variant('shared', default=True, description="Build shared library version (disables static library)") + depends_on("mpi") depends_on("blas") depends_on("lapack") @@ -17,16 +21,26 @@ class Hypre(Package): def install(self, spec, prefix): blas_dir = spec['blas'].prefix lapack_dir = spec['lapack'].prefix + mpi_dir = spec['mpi'].prefix + + os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc') + os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx') + os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77') + + + configure_args = [ + "--prefix=%s" % prefix, + "--with-lapack-libs=lapack", + "--with-lapack-lib-dirs=%s/lib" % lapack_dir, + "--with-blas-libs=blas", + "--with-blas-lib-dirs=%s/lib" % blas_dir] + if '+shared' in self.spec: + configure_args.append("--enable-shared") # Hypre's source is staged under ./src so we'll have to manually # cd into it. with working_dir("src"): - configure( - "--prefix=%s" % prefix, - "--with-blas-libs=blas", - "--with-blas-lib-dirs=%s/lib" % blas_dir, - "--with-lapack-libs=\"lapack blas\"", - "--with-lapack-lib-dirs=%s/lib" % lapack_dir, - "--with-MPI") + configure(*configure_args) + make() make("install") diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index f8f5fc21bd..cbcc53ac0a 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -28,7 +28,7 @@ class Jdk(Package): '-H', # specify required License Agreement cookie 'Cookie: oraclelicense=accept-securebackup-cookie'] - def do_fetch(self): + def do_fetch(self, mirror_only=False): # Add our custom curl commandline options tty.msg( "[Jdk] Adding required commandline options to curl " + @@ -39,7 +39,7 @@ class Jdk(Package): spack.curl.add_default_arg(option) # Now perform the actual fetch - super(Jdk, self).do_fetch() + super(Jdk, self).do_fetch(mirror_only) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py index bcd5212b9e..faed8bad37 100644 --- a/var/spack/repos/builtin/packages/libedit/package.py +++ b/var/spack/repos/builtin/packages/libedit/package.py @@ -7,6 +7,8 @@ class Libedit(Package): version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz") + depends_on('ncurses') + def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 29bc21b65c..9f16708af5 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,6 +38,8 @@ class Libelf(Package): provides('elf') + sanity_check_is_file = 'include/libelf.h' + def install(self, spec, prefix): configure("--prefix=" + prefix, "--enable-shared", diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py index 11b1083d67..714a155dc0 100644 --- a/var/spack/repos/builtin/packages/libevent/package.py +++ b/var/spack/repos/builtin/packages/libevent/package.py @@ -22,9 +22,16 @@ class Libevent(Package): version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc') version('2.0.12', '42986228baf95e325778ed328a93e070') + variant('openssl', default=True, description="Build with encryption enabled at the libevent level.") + depends_on('openssl', when='+openssl') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure_args = [] + if '+openssl' in spec: + configure_args.append('--enable-openssl') + else: + configure_args.append('--enable-openssl') + configure("--prefix=%s" % prefix, *configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py index 6c1d1a10a7..dd5fc2408a 100644 --- a/var/spack/repos/builtin/packages/libgpg-error/package.py +++ b/var/spack/repos/builtin/packages/libgpg-error/package.py @@ -9,6 +9,7 @@ class LibgpgError(Package): homepage = "https://www.gnupg.org/related_software/libgpg-error" url = "ftp://ftp.gnupg.org/gcrypt/libgpg-error/libgpg-error-1.18.tar.bz2" + version('1.21', 'ab0b5aba6d0a185b41d07bda804fd8b2') version('1.18', '12312802d2065774b787cbfc22cc04e9') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py new file mode 100644 index 0000000000..4b486198ec --- /dev/null +++ b/var/spack/repos/builtin/packages/libsigsegv/package.py @@ -0,0 +1,15 @@ +from spack import * + +class Libsigsegv(Package): + """GNU libsigsegv is a library for handling page faults in user mode.""" + homepage = "https://www.gnu.org/software/libsigsegv/" + url = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz" + + version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix, + '--enable-shared') + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index a2b2c6eccc..1d25d59e50 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -1,5 +1,5 @@ ############################################################################## -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Copyright (c) 2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # # This file is part of Spack. @@ -34,7 +34,7 @@ class Llvm(Package): it is the full name of the project. """ homepage = 'http://llvm.org/' - url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz' + url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz' version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package @@ -52,7 +52,7 @@ class Llvm(Package): depends_on('cmake @2.8.12.2:') # Universal dependency - depends_on('python@2.7:') + depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y # lldb dependencies depends_on('ncurses', when='+lldb') @@ -118,6 +118,51 @@ class Llvm(Package): } releases = [ { + 'version' : 'trunk', + 'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk', + 'resources' : { + 'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk', + 'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk', + 'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk', + 'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk', + 'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk', + 'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk', + 'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk', + 'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk', + 'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk', + } + }, + { + 'version' : '3.8.0', + 'md5':'07a7a74f3c6bd65de4702bf941b511a0', + 'resources' : { + 'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025', + 'openmp' : '8fd7cc35d48051613cf1e750e9f22e40', + 'polly' : '1b3b20f52d34a4024e21a4ea7112caa7', + 'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a', + 'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7', + 'clang' : 'cc99e7019bb74e6459e80863606250c5', + 'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036', + 'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e', + 'llvm-libunwind' : '162ade468607f153cca12be90b5194fa', + } + }, + { + 'version' : '3.7.1', + 'md5':'bf8b3a2c79e61212c5409041dfdbd319', + 'resources' : { + 'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01', + 'openmp' : 'b4ad08cda4e5c22e42b66062b140438e', + 'polly' : '3a2a7367002740881637f4d47bca4dc3', + 'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140', + 'libcxxabi' : '52d925afac9f97e9dcac90745255c169', + 'clang' : '0acd026b5529164197563d135a8fd83e', + 'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2', + 'lldb' : 'a106d8a0d21fc84d76953822fbaf3398', + 'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c', + } + }, + { 'version' : '3.7.0', 'md5':'b98b9495e5655a672d6cb83e1a180f8e', 'resources' : { @@ -161,15 +206,25 @@ class Llvm(Package): ] for release in releases: - version(release['version'], release['md5'], url=llvm_url % release) - - for name, md5 in release['resources'].items(): - resource(name=name, - url=resources[name]['url'] % release, - md5=md5, - destination=resources[name]['destination'], - when='@%(version)s' % release, - placement=resources[name].get('placement', None)) + if release['version'] == 'trunk' : + version(release['version'], svn=release['repo']) + + for name, repo in release['resources'].items(): + resource(name=name, + svn=repo, + destination=resources[name]['destination'], + when='@%(version)s' % release, + placement=resources[name].get('placement', None)) + else: + version(release['version'], release['md5'], url=llvm_url % release) + + for name, md5 in release['resources'].items(): + resource(name=name, + url=resources[name]['url'] % release, + md5=md5, + destination=resources[name]['destination'], + when='@%(version)s' % release, + placement=resources[name].get('placement', None)) def install(self, spec, prefix): env['CXXFLAGS'] = self.compiler.cxx11_flag diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py new file mode 100644 index 0000000000..a4b9dcb623 --- /dev/null +++ b/var/spack/repos/builtin/packages/m4/package.py @@ -0,0 +1,25 @@ +from spack import * + +class M4(Package): + """GNU M4 is an implementation of the traditional Unix macro processor.""" + homepage = "https://www.gnu.org/software/m4/m4.html" + url = "ftp://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz" + + version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76') + + patch('pgi.patch', when='@1.4.17') + + variant('sigsegv', default=True, description="Build the libsigsegv dependency") + + depends_on('libsigsegv', when='+sigsegv') + + def install(self, spec, prefix): + configure_args = [] + if 'libsigsegv' in spec: + configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix) + else: + configure_args.append('--without-libsigsegv-prefix') + + configure("--prefix=%s" % prefix, *configure_args) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/m4/pgi.patch b/var/spack/repos/builtin/packages/m4/pgi.patch new file mode 100644 index 0000000000..1ad63e2cf1 --- /dev/null +++ b/var/spack/repos/builtin/packages/m4/pgi.patch @@ -0,0 +1,10 @@ +--- a/lib/config.hin ++++ b/lib/config.hin +@@ -1510,6 +1510,7 @@ + ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \ + : (199901L <= __STDC_VERSION__ \ + && !defined __HP_cc \ ++ && !defined __PGI \ + && !(defined __SUNPRO_C && __STDC__))) \ + && !defined _GL_EXTERN_INLINE_APPLE_BUG) + # define _GL_INLINE inline diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py index 50477a0ccb..108fec678f 100644 --- a/var/spack/repos/builtin/packages/mpc/package.py +++ b/var/spack/repos/builtin/packages/mpc/package.py @@ -37,6 +37,12 @@ class Mpc(Package): depends_on("gmp") depends_on("mpfr") + def url_for_version(self, version): + if version < Version("1.0.1"): + return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version + else: + return "ftp://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py index 2758b0da2e..7e6e7d5bb6 100644 --- a/var/spack/repos/builtin/packages/mpfr/package.py +++ b/var/spack/repos/builtin/packages/mpfr/package.py @@ -28,12 +28,13 @@ class Mpfr(Package): """The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.""" homepage = "http://www.mpfr.org" - url = "http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.bz2" + url = "https://gforge.inria.fr/frs/download.php/latestfile/159/mpfr-3.1.2.tar.bz2" + version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4') version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138') version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19') - depends_on('gmp@4.1.0:') + depends_on('gmp') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 00b7dfda75..b20dc8dd60 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Mpich(Package): """MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.""" @@ -41,21 +42,33 @@ class Mpich(Package): version('3.1', '5643dd176499bfb7d25079aaff25f2ec') version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') + variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def setup_dependent_environment(self, module, spec, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - os.environ['MPICH_CC'] = 'cc' - os.environ['MPICH_CXX'] = 'c++' - os.environ['MPICH_F77'] = 'f77' - os.environ['MPICH_F90'] = 'f90' + def setup_dependent_environment(self, env, dependent_spec): + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_f90) + env.set('MPICH_FC', spack_fc) + def setup_dependent_package(self, module, dep_spec): + """For dependencies, make mpicc's use spack wrapper.""" + # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? + module.mpicc = join_path(self.prefix.bin, 'mpicc') def install(self, spec, prefix): config_args = ["--prefix=" + prefix, "--enable-shared"] + # Variants + if '+verbs' in spec: + config_args.append("--with-ibverbs") + else: + config_args.append("--without-ibverbs") + # TODO: Spack should make it so that you can't actually find # these compilers if they're "disabled" for the current # compiler configuration. diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc new file mode 100644 index 0000000000..2e6a041878 --- /dev/null +++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc @@ -0,0 +1,38 @@ +LPORDDIR = $(topdir)/PORD/lib/ +IPORD = -I$(topdir)/PORD/include/ +LPORD = -L$(LPORDDIR) -lpord + +ORDERINGSC = $(ORDERINGSF) +LORDERINGS = $(LMETIS) $(LPORD) $(LSCOTCH) +IORDERINGSF = $(ISCOTCH) +IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH) + +PLAT = +LIBEXT = .a +OUTC = -o +OUTF = -o +RM = /bin/rm -f +AR = ar vr +RANLIB = ranlib + +INCSEQ = -I$(topdir)/libseq +LIBSEQ = -L$(topdir)/libseq -lmpiseq + +INCPAR = +LIBPAR = $(SCALAP) + +LIBOTHERS = -lpthread + +#Sequential: +ifeq ($(MUMPS_TYPE),seq) +INCS = $(INCSEQ) +LIBS = $(LIBSEQ) +LIBSEQNEEDED = libseqneeded +endif + +#Parallel: +ifeq ($(MUMPS_TYPE),par) +INCS = $(INCPAR) +LIBS = $(LIBPAR) +LIBSEQNEEDED = +endif diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py new file mode 100644 index 0000000000..5c120c37df --- /dev/null +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -0,0 +1,143 @@ +from spack import * +import os + + +class Mumps(Package): + """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" + + homepage = "http://mumps.enseeiht.fr" + url = "http://mumps.enseeiht.fr/MUMPS_5.0.1.tar.gz" + + version('5.0.1', 'b477573fdcc87babe861f62316833db0') + + variant('mpi', default=True, description='Activate the compilation of MUMPS with the MPI support') + variant('scotch', default=False, description='Activate Scotch as a possible ordering library') + variant('ptscotch', default=False, description='Activate PT-Scotch as a possible ordering library') + variant('metis', default=False, description='Activate Metis as a possible ordering library') + variant('parmetis', default=False, description='Activate Parmetis as a possible ordering library') + variant('double', default=True, description='Activate the compilation of dmumps') + variant('float', default=True, description='Activate the compilation of smumps') + variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') + variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') + + + depends_on('scotch + esmumps', when='~ptscotch+scotch') + depends_on('scotch + esmumps + mpi', when='+ptscotch') + depends_on('metis', when='+metis') + depends_on('parmetis', when="+parmetis") + depends_on('blas') + depends_on('lapack') + depends_on('scalapack', when='+mpi') + depends_on('mpi', when='+mpi') + + # this function is not a patch function because in case scalapack + # is needed it uses self.spec['scalapack'].fc_link set by the + # setup_dependent_environment in scalapck. This happen after patch + # end before install + # def patch(self): + def write_makefile_inc(self): + if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: + raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') + + makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] + + orderings = ['-Dpord'] + + if '+ptscotch' in self.spec or '+scotch' in self.spec: + join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') + makefile_conf.extend( + ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, + "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, + join_lib, + join_lib.join(['esmumps', 'scotch', 'scotcherr']))]) + orderings.append('-Dscotch') + if '+ptscotch' in self.spec: + orderings.append('-Dptscotch') + + if '+parmetis' in self.spec and '+metis' in self.spec: + libname = 'parmetis' if '+parmetis' in self.spec else 'metis' + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) + + orderings.append('-Dparmetis') + elif '+metis' in self.spec: + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) + + orderings.append('-Dmetis') + + makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) + + # TODO: test this part, it needs a full blas, scalapack and + # partitionning environment with 64bit integers + if '+idx64' in self.spec: + makefile_conf.extend( + # the fortran compilation flags most probably are + # working only for intel and gnu compilers this is + # perhaps something the compiler should provide + ['OPTF = -O -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8', + 'OPTL = -O ', + 'OPTC = -O -DINTSIZE64']) + else: + makefile_conf.extend( + ['OPTF = -O -DALLOW_NON_INIT', + 'OPTL = -O ', + 'OPTC = -O ']) + + + if '+mpi' in self.spec: + makefile_conf.extend( + ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), + "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + "SCALAP = %s" % self.spec['scalapack'].fc_link, + "MUMPS_TYPE = par"]) + else: + makefile_conf.extend( + ["CC = cc", + "FC = fc", + "FL = fc", + "MUMPS_TYPE = seq"]) + + # TODO: change the value to the correct one according to the + # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER + makefile_conf.append("CDEFS = -DAdd_") + + + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), + 'Makefile.inc') + with open(makefile_inc_template, "r") as fh: + makefile_conf.extend(fh.read().split('\n')) + + with working_dir('.'): + with open("Makefile.inc", "w") as fh: + makefile_inc = '\n'.join(makefile_conf) + fh.write(makefile_inc) + + + + def install(self, spec, prefix): + make_libs = [] + + # the coice to compile ?examples is to have kind of a sanity + # check on the libraries generated. + if '+float' in spec: + make_libs.append('sexamples') + if '+complex' in spec: + make_libs.append('cexamples') + + if '+double' in spec: + make_libs.append('dexamples') + if '+complex' in spec: + make_libs.append('zexamples') + + self.write_makefile_inc() + + make(*make_libs) + + install_tree('lib', prefix.lib) + install_tree('include', prefix.include) + if '~mpi' in spec: + install('libseq/libmpiseq.a', prefix.lib) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 23a11b3171..e4e95f92af 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -4,15 +4,13 @@ import os class Mvapich2(Package): """MVAPICH2 is an MPI implementation for Infiniband networks.""" homepage = "http://mvapich.cse.ohio-state.edu/" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2b.tar.gz" - version('2.2a', 'b8ceb4fc5f5a97add9b3ff1b9cbe39d2', - url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2a.tar.gz') + version('2.2b', '5651e8b7a72d7c77ca68da48f3a5d108') + version('2.2a', 'b8ceb4fc5f5a97add9b3ff1b9cbe39d2') + version('2.0', '9fbb68a4111a8b6338e476dc657388b4') + version('1.9', '5dc58ed08fd3142c260b70fe297e127c') - version('2.0', '9fbb68a4111a8b6338e476dc657388b4', - url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz') - - version('1.9', '5dc58ed08fd3142c260b70fe297e127c', - url="http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz") patch('ad_lustre_rwcontig_open_source.patch', when='@1.9') provides('mpi@:2.2', when='@1.9') # MVAPICH2-1.9 supports MPI 2.2 @@ -41,16 +39,25 @@ class Mvapich2(Package): NEMESISIBTCP = 'nemesisibtcp' NEMESISIB = 'nemesisib' NEMESIS = 'nemesis' + MRAIL = 'mrail' SUPPORTED_NETWORKS = (PSM, SOCK, NEMESIS, NEMESISIB, NEMESISIBTCP) variant(PSM, default=False, description='Configures a build for QLogic PSM-CH3') variant(SOCK, default=False, description='Configures a build for TCP/IP-CH3') variant(NEMESISIBTCP, default=False, description='Configures a build for both OFA-IB-Nemesis and TCP/IP-Nemesis') variant(NEMESISIB, default=False, description='Configures a build for OFA-IB-Nemesis') variant(NEMESIS, default=False, description='Configures a build for TCP/IP-Nemesis') + variant(MRAIL, default=False, description='Configures a build for OFA-IB-CH3') ########## # FIXME : CUDA support is missing + def url_for_version(self, version): + base_url = "http://mvapich.cse.ohio-state.edu/download" + if version < Version('2.0'): + return "%s/mvapich2/mv2/mvapich2-%s.tar.gz" % (base_url, version) + else: + return "%s/mvapich/mv2/mvapich2-%s.tar.gz" % (base_url, version) + @staticmethod def enabled(x): """ @@ -116,8 +123,8 @@ class Mvapich2(Package): count += 1 if count > 1: raise RuntimeError('network variants are mutually exclusive (only one can be selected at a time)') - - # From here on I can suppose that ony one variant has been selected + network_options = [] + # From here on I can suppose that only one variant has been selected if self.enabled(Mvapich2.PSM) in spec: network_options = ["--with-device=ch3:psm"] elif self.enabled(Mvapich2.SOCK) in spec: @@ -128,7 +135,7 @@ class Mvapich2(Package): network_options = ["--with-device=ch3:nemesis:ib"] elif self.enabled(Mvapich2.NEMESIS) in spec: network_options = ["--with-device=ch3:nemesis"] - else: + elif self.enabled(Mvapich2.MRAIL) in spec: network_options = ["--with-device=ch3:mrail", "--with-rdma=gen2"] configure_args.extend(network_options) @@ -141,7 +148,14 @@ class Mvapich2(Package): "--enable-romio", "--disable-silent-rules", ] - if not self.compiler.f77 and not self.compiler.fc: + + if self.compiler.f77 and self.compiler.fc: + configure_args.append("--enable-fortran=all") + elif self.compiler.f77: + configure_args.append("--enable-fortran=f77") + elif self.compiler.fc: + configure_args.append("--enable-fortran=fc") + else: configure_args.append("--enable-fortran=none") # Set the type of the build (debug, release) diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py new file mode 100644 index 0000000000..10e445c81e --- /dev/null +++ b/var/spack/repos/builtin/packages/ndiff/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Ndiff(Package): + """The ndiff tool is a binary utility that compares putatively similar files + while ignoring small numeric differernces. This utility is most often used + to compare files containing a lot of floating-point numeric data that + may be slightly different due to numeric error.""" + + homepage = "http://ftp.math.utah.edu/pub/ndiff/" + url = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz" + + version('2.00', '885548b4dc26e72c5455bebb5ba6c16d') + version('1.00', 'f41ffe5d12f36cd36b6311acf46eccdc') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + mkdirp(prefix.bin) + mkdirp('%s/lib' % prefix.share) + + make('install-exe', 'install-shrlib') diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py new file mode 100644 index 0000000000..b83e964b00 --- /dev/null +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -0,0 +1,15 @@ +from spack import * + +class NetcdfCxx4(Package): + """C++ interface for NetCDF4""" + homepage = "http://www.unidata.ucar.edu/software/netcdf" + url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz" + + version('4.2', 'd019853802092cf686254aaba165fc81') + + depends_on('netcdf') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py new file mode 100644 index 0000000000..e4e33445e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -0,0 +1,16 @@ +from spack import * + +class NetcdfFortran(Package): + """Fortran interface for NetCDF4""" + + homepage = "http://www.unidata.ucar.edu/software/netcdf" + url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz" + + version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e') + + depends_on('netcdf') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch b/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch deleted file mode 100644 index 46dda5fc9d..0000000000 --- a/var/spack/repos/builtin/packages/netcdf/netcdf-4.3.3-mpi.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff -Nur netcdf-4.3.3/CMakeLists.txt netcdf-4.3.3.mpi/CMakeLists.txt ---- netcdf-4.3.3/CMakeLists.txt 2015-02-12 16:44:35.000000000 -0500 -+++ netcdf-4.3.3.mpi/CMakeLists.txt 2015-10-14 16:44:41.176300658 -0400 -@@ -753,6 +753,7 @@ - SET(USE_PARALLEL OFF CACHE BOOL "") - MESSAGE(STATUS "Cannot find HDF5 library built with parallel support. Disabling parallel build.") - ELSE() -+ FIND_PACKAGE(MPI REQUIRED) - SET(USE_PARALLEL ON CACHE BOOL "") - SET(STATUS_PARALLEL "ON") - ENDIF() -diff -Nur netcdf-4.3.3/liblib/CMakeLists.txt netcdf-4.3.3.mpi/liblib/CMakeLists.txt ---- netcdf-4.3.3/liblib/CMakeLists.txt 2015-02-12 16:44:35.000000000 -0500 -+++ netcdf-4.3.3.mpi/liblib/CMakeLists.txt 2015-10-14 16:44:57.757793634 -0400 -@@ -71,6 +71,10 @@ - SET(TLL_LIBS ${TLL_LIBS} ${CURL_LIBRARY}) - ENDIF() - -+IF(USE_PARALLEL) -+ SET(TLL_LIBS ${TLL_LIBS} ${MPI_C_LIBRARIES}) -+ENDIF() -+ - IF(USE_HDF4) - SET(TLL_LIBS ${TLL_LIBS} ${HDF4_LIBRARIES}) - ENDIF() diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 239644d894..227362399a 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -1,28 +1,76 @@ from spack import * + class Netcdf(Package): """NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data.""" + data formats that support the creation, access, and sharing of array-oriented + scientific data.""" - homepage = "http://www.unidata.ucar.edu/software/netcdf/" + homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz" + version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e') version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') - patch('netcdf-4.3.3-mpi.patch') + variant('mpi', default=True, description='Enables MPI parallelism') + variant('hdf4', default=False, description="Enable HDF4 support") # Dependencies: - depends_on("cmake @2.8.12:") - # >HDF5 - depends_on("hdf5") + depends_on("curl") # required for DAP support + depends_on("hdf", when='+hdf4') + depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support + depends_on("hdf5~mpi", when='~mpi') # required for NetCDF-4 support + depends_on("zlib") # required for NetCDF-4 support def install(self, spec, prefix): - with working_dir('spack-build', create=True): - cmake('..', - "-DCMAKE_INSTALL_PREFIX:PATH=%s" % prefix, - "-DENABLE_DAP:BOOL=OFF", # Disable DAP. - "-DBUILD_SHARED_LIBS:BOOL=OFF") # Don't build shared libraries (use static libs). - - make() - make("install") + # Environment variables + CPPFLAGS = [] + LDFLAGS = [] + LIBS = [] + + config_args = [ + "--prefix=%s" % prefix, + "--enable-fsync", + "--enable-v2", + "--enable-utilities", + "--enable-shared", + "--enable-static", + "--enable-largefile", + # necessary for HDF5 support + "--enable-netcdf-4", + "--enable-dynamic-loading", + # necessary for DAP support + "--enable-dap" + ] + + if '+mpi' in spec: + config_args.append('--enable-parallel4') + + CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix) + LDFLAGS.append( "-L%s/lib" % spec['hdf5'].prefix) + + # HDF4 support + # As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option + # You must use the environment variables CPPFLAGS and LDFLAGS + if '+hdf4' in spec: + config_args.append("--enable-hdf4") + CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix) + LDFLAGS.append( "-L%s/lib" % spec['hdf'].prefix) + LIBS.append( "-l%s" % "jpeg") + + if 'szip' in spec: + CPPFLAGS.append("-I%s/include" % spec['szip'].prefix) + LDFLAGS.append( "-L%s/lib" % spec['szip'].prefix) + LIBS.append( "-l%s" % "sz") + + # Fortran support + # In version 4.2+, NetCDF-C and NetCDF-Fortran have split. + # Use the netcdf-fortran package to install Fortran support. + + config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS)) + config_args.append('LDFLAGS=%s' % ' '.join(LDFLAGS)) + config_args.append('LIBS=%s' % ' '.join(LIBS)) + + 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 fb6b99e27c..78c5a053fe 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -12,6 +12,7 @@ class NetlibLapack(Package): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55') @@ -19,13 +20,13 @@ class NetlibLapack(Package): version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') variant('shared', default=False, description="Build shared library version") + variant('fpic', default=False, description="Build with -fpic compiler option") # virtual dependency provides('lapack') # blas is a virtual dependency. depends_on('blas') - depends_on('cmake') # Doesn't always build correctly in parallel @@ -36,24 +37,23 @@ class NetlibLapack(Package): blas = self.spec['netlib-blas'] return [join_path(blas.prefix.lib, 'blas.a')] - @when('^atlas') def get_blas_libs(self): blas = self.spec['atlas'] return [join_path(blas.prefix.lib, l) for l in ('libf77blas.a', 'libatlas.a')] - def install(self, spec, prefix): blas_libs = ";".join(self.get_blas_libs()) cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs] if '+shared' in spec: cmake_args.append('-DBUILD_SHARED_LIBS=ON') + if '+fpic' in spec: + cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON') cmake_args += std_cmake_args cmake(*cmake_args) make() make("install") - diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py new file mode 100644 index 0000000000..c3e6822cdf --- /dev/null +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -0,0 +1,51 @@ +from spack import * +import sys + +class NetlibScalapack(Package): + """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" + + homepage = "http://www.netlib.org/scalapack/" + url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" + + version('2.0.2', '2f75e600a2ba155ed9ce974a1c4b536f') + version('2.0.1', '17b8cde589ea0423afe1ec43e7499161') + version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe') + # versions before 2.0.0 are not using cmake and requires blacs as + # a separated package + + variant('shared', default=True, description='Build the shared library version') + variant('fpic', default=False, description="Build with -fpic compiler option") + + provides('scalapack') + + depends_on('mpi') + depends_on('lapack') + + def install(self, spec, prefix): + options = [ + "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'), + "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'), + "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK) + ] + + if '+fpic' in spec: + options.extend([ + "-DCMAKE_C_FLAGS=-fPIC", + "-DCMAKE_Fortran_FLAGS=-fPIC" + ]) + + options.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + cmake('..', *options) + make() + make("install") + + def setup_dependent_package(self, module, dependent_spec): + spec = self.spec + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + + spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib + spec.cc_link = spec.fc_link + spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)] diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py new file mode 100644 index 0000000000..6e99c23652 --- /dev/null +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -0,0 +1,183 @@ +from spack import * + +class Octave(Package): + """GNU Octave is a high-level language, primarily intended for numerical + computations. It provides a convenient command line interface for solving + linear and nonlinear problems numerically, and for performing other + numerical experiments using a language that is mostly compatible with + Matlab. It may also be used as a batch-oriented language.""" + + homepage = "https://www.gnu.org/software/octave/" + url = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz" + + version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799') + + # Variants + variant('readline', default=True) + variant('arpack', default=False) + variant('curl', default=False) + variant('fftw', default=False) + variant('fltk', default=False) + variant('fontconfig', default=False) + variant('freetype', default=False) + variant('glpk', default=False) + variant('gl2ps', default=False) + variant('gnuplot', default=False) + variant('magick', default=False) + variant('hdf5', default=False) + variant('jdk', default=False) + variant('llvm', default=False) + variant('opengl', default=False) + variant('qhull', default=False) + variant('qrupdate', default=False) + variant('qscintilla', default=False) + variant('qt', default=False) + variant('suiteparse', default=False) + variant('zlib', default=False) + + # Required dependencies + depends_on('blas') + depends_on('lapack') + depends_on('pcre') + + # Strongly recommended dependencies + depends_on('readline', when='+readline') + + # Optional dependencies + depends_on('arpack', when='+arpack') + depends_on('curl', when='+curl') + depends_on('fftw', when='+fftw') + depends_on('fltk', when='+fltk') + depends_on('fontconfig', when='+fontconfig') + depends_on('freetype', when='+freetype') + depends_on('glpk', when='+glpk') + depends_on('gl2ps', when='+gl2ps') + depends_on('gnuplot', when='+gnuplot') + depends_on('ImageMagick', when='+magick') + depends_on('hdf5', when='+hdf5') + depends_on('jdk', when='+jdk') + depends_on('llvm', when='+llvm') + #depends_on('opengl', when='+opengl') # TODO: add package + depends_on('qhull', when='+qhull') + depends_on('qrupdate', when='+qrupdate') + #depends_on('qscintilla', when='+qscintilla) # TODO: add package + depends_on('qt', when='+qt') + depends_on('suite-sparse',when='+suitesparse') + depends_on('zlib', when='+zlib') + + + def install(self, spec, prefix): + config_args = [ + "--prefix=%s" % prefix + ] + + # Required dependencies + config_args.extend([ + "--with-blas=%s" % spec['blas'].prefix.lib, + "--with-lapack=%s" % spec['lapack'].prefix.lib + ]) + + # Strongly recommended dependencies + if '+readline' in spec: + config_args.append('--enable-readline') + else: + config_args.append('--disable-readline') + + # Optional dependencies + if '+arpack' in spec: + config_args.extend([ + "--with-arpack-includedir=%s" % spec['arpack'].prefix.include, + "--with-arpack-libdir=%s" % spec['arpack'].prefix.lib + ]) + else: + config_args.append("--without-arpack") + + if '+curl' in spec: + config_args.extend([ + "--with-curl-includedir=%s" % spec['curl'].prefix.include, + "--with-curl-libdir=%s" % spec['curl'].prefix.lib + ]) + else: + config_args.append("--without-curl") + + if '+fftw' in spec: + config_args.extend([ + "--with-fftw3-includedir=%s" % spec['fftw'].prefix.include, + "--with-fftw3-libdir=%s" % spec['fftw'].prefix.lib, + "--with-fftw3f-includedir=%s" % spec['fftw'].prefix.include, + "--with-fftw3f-libdir=%s" % spec['fftw'].prefix.lib + ]) + else: + config_args.extend([ + "--without-fftw3", + "--without-fftw3f" + ]) + + if '+fltk' in spec: + config_args.extend([ + "--with-fltk-prefix=%s" % spec['fltk'].prefix, + "--with-fltk-exec-prefix=%s" % spec['fltk'].prefix + ]) + else: + config_args.append("--without-fltk") + + if '+glpk' in spec: + config_args.extend([ + "--with-glpk-includedir=%s" % spec['glpk'].prefix.include, + "--with-glpk-libdir=%s" % spec['glpk'].prefix.lib + ]) + else: + config_args.append("--without-glpk") + + if '+magick' in spec: + config_args.append("--with-magick=%s" % spec['ImageMagick'].prefix.lib) + + if '+hdf5' in spec: + config_args.extend([ + "--with-hdf5-includedir=%s" % spec['hdf5'].prefix.include, + "--with-hdf5-libdir=%s" % spec['hdf5'].prefix.lib + ]) + else: + config_args.append("--without-hdf5") + + if '+jdk' in spec: + config_args.extend([ + "--with-java-homedir=%s" % spec['jdk'].prefix, + "--with-java-includedir=%s" % spec['jdk'].prefix.include, + "--with-java-libdir=%s" % spec['jdk'].prefix.lib + ]) + + if '~opengl' in spec: + config_args.extend([ + "--without-opengl", + "--without-framework-opengl" + ]) + + if '+qhull' in spec: + config_args.extend([ + "--with-qhull-includedir=%s" % spec['qhull'].prefix.include, + "--with-qhull-libdir=%s" % spec['qhull'].prefix.lib + ]) + else: + config_args.append("--without-qhull") + + if '+qrupdate' in spec: + config_args.extend([ + "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include, + "--with-qrupdate-libdir=%s" % spec['qrupdate'].prefix.lib + ]) + else: + config_args.append("--without-qrupdate") + + if '+zlib' in spec: + config_args.extend([ + "--with-z-includedir=%s" % spec['zlib'].prefix.include, + "--with-z-libdir=%s" % spec['zlib'].prefix.lib + ]) + else: + config_args.append("--without-z") + + configure(*config_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 9c8fa1c694..781a1e2ec8 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,10 +1,12 @@ from spack import * +import sys class Openblas(Package): """OpenBLAS: An optimized BLAS library""" homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') # virtual dependency @@ -15,11 +17,14 @@ class Openblas(Package): make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') make('install', "PREFIX='%s'" % prefix) + 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) # 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) diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py new file mode 100644 index 0000000000..99b555323f --- /dev/null +++ b/var/spack/repos/builtin/packages/opencv/package.py @@ -0,0 +1,50 @@ +from spack import * + + +class Opencv(Package): + """ + OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C, + Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for + computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library + can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware + acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than + 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from + interactive art, to mines inspection, stitching maps on the web or through advanced robotics. + """ + homepage = 'http://opencv.org/' + url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz' + + version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3') + + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds a debug version of the libraries') + + variant('eigen', default=True, description='Activates support for eigen') + variant('ipp', default=True, description='Activates support for IPP') + + depends_on('zlib') + depends_on('libpng') + depends_on('libjpeg-turbo') + depends_on('libtiff') + + depends_on('python') + depends_on('py-numpy') + + depends_on('eigen', when='+eigen') + + # FIXME : GUI extensions missing + # FIXME : CUDA extensions still missing + + def install(self, spec, prefix): + cmake_options = [] + cmake_options.extend(std_cmake_args) + + cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), + '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF', + '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')]) + + with working_dir('spack_build', create=True): + cmake('..', *cmake_options) + make('VERBOSE=1') + make("install") diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 463719f9db..9a127f1812 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -17,45 +17,48 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') version('1.10.0', '280cf952de68369cebaca886c5ce0304') - version('1.8.8', '0dab8e602372da1425e9242ae37faf8c') - version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475') + version('1.8.8', '0dab8e602372da1425e9242ae37faf8c') + version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475') patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5") patch('llnl-platforms.patch', when="@1.6.5") - patch('configure.patch', when="@1.10.0:") + patch('configure.patch', when="@1.10.0:1.10.1") - variant('psm', default=False, description='Build support for the PSM library.') + variant('psm', default=False, description='Build support for the PSM library.') variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + # TODO : variant support for other schedulers is missing + variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support') + provides('mpi@:2.2', when='@1.6.5') provides('mpi@:3.0', when='@1.7.5:') - depends_on('hwloc') - def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def setup_dependent_environment(self, module, spec, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - os.environ['OMPI_CC'] = 'cc' - os.environ['OMPI_CXX'] = 'c++' - os.environ['OMPI_FC'] = 'f90' - os.environ['OMPI_F77'] = 'f77' + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('OMPI_CC', spack_cc) + spack_env.set('OMPI_CXX', spack_cxx) + spack_env.set('OMPI_FC', spack_fc) + spack_env.set('OMPI_F77', spack_f77) def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, "--with-hwloc=%s" % spec['hwloc'].prefix, - "--with-tm", # necessary for Torque support "--enable-shared", "--enable-static"] # Variants + if '+tm' in spec: + config_args.append("--with-tm") # necessary for Torque support + if '+psm' in spec: config_args.append("--with-psm") @@ -85,7 +88,6 @@ class Openmpi(Package): self.filter_compilers() - def filter_compilers(self): """Run after install to make the MPI compilers use the compilers that Spack built the package with. @@ -94,7 +96,7 @@ class Openmpi(Package): to Spack's generic cc, c++ and f90. We want them to be bound to whatever compiler they were built with. """ - kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : False } + kwargs = {'ignore_absent': True, 'backup': False, 'string': False} dir = os.path.join(self.prefix, 'share/openmpi/') cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt', @@ -132,5 +134,3 @@ class Openmpi(Package): if not os.path.islink(path): filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc, path, **kwargs) - - diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index bbb169ec6b..70afaf4038 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,3 +1,6 @@ +import urllib +import llnl.util.tty as tty + from spack import * class Openssl(Package): @@ -10,12 +13,51 @@ class Openssl(Package): url = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz" version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') + version('1.0.1r', '1abd905e079542ccae948af37e393d28') version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') + version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') + version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') depends_on("zlib") parallel = False + def url_for_version(self, version): + # This URL is computed pinging the place where the latest version is stored. To avoid slowdown + # due to repeated pinging, we store the URL in a private class attribute to do the job only once per version + openssl_urls = getattr(Openssl, '_openssl_url', {}) + openssl_url = openssl_urls.get(version, None) + # Same idea, but just to avoid issuing the same message multiple times + warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) + if openssl_url is None: + latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz' + older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' + # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then + # return the url for older format + version_number = '.'.join([str(x) for x in version[:-1]]) + older_url = older.format(version_number=version_number, version_full=version) + latest_url = latest.format(version=version) + response = urllib.urlopen(latest.format(version=version)) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: + openssl_url = latest_url + # Store the computed URL + openssl_urls[version] = openssl_url + # Store the updated dictionary of URLS + Openssl._openssl_url = openssl_urls + # Store the updated dictionary of warnings + Openssl._warnings_given = warnings_given_to_user + + return openssl_url + def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set # in the environment, then this will override what is set in the diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py index df43625bf5..79dad3a3d2 100644 --- a/var/spack/repos/builtin/packages/pango/package.py +++ b/var/spack/repos/builtin/packages/pango/package.py @@ -16,4 +16,4 @@ class Pango(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() - make("install") + make("install", parallel=False) diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 910e0aa9f9..53d69e28d9 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -13,6 +13,7 @@ class Papi(Package): homepage = "http://icl.cs.utk.edu/papi/index.html" url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412') version('5.4.1', '9134a99219c79767a11463a76b0b01a2') version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py new file mode 100644 index 0000000000..62a8f7ca0b --- /dev/null +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -0,0 +1,20 @@ +from spack import * + +class ParallelNetcdf(Package): + """Parallel netCDF (PnetCDF) is a library providing high-performance + parallel I/O while still maintaining file-format compatibility with + Unidata's NetCDF.""" + + homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf" + url = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz" + + version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34') + + depends_on("m4") + depends_on("mpi") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix, + "--with-mpi=%s" % spec['mpi'].prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index aaab352e66..c16054816c 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -2,9 +2,11 @@ from spack import * class Paraview(Package): homepage = 'http://www.paraview.org' - url = 'http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz' + url = 'http://www.paraview.org/files/v5.0/ParaView-v' + _url_str = 'http://www.paraview.org/files/v%s/ParaView-v%s-source.tar.gz' - version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378', url='http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz') + version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378') + version('5.0.0', '4598f0b421460c8bbc635c9a1c3bdbee') variant('python', default=False, description='Enable Python support') @@ -14,8 +16,9 @@ class Paraview(Package): variant('osmesa', default=False, description='Enable OSMesa support') variant('qt', default=False, description='Enable Qt support') + variant('opengl2', default=False, description='Enable OpenGL2 backend') - depends_on('python', when='+python') + depends_on('python@2:2.7', when='+python') depends_on('py-numpy', when='+python') depends_on('py-matplotlib', when='+python') depends_on('tcl', when='+tcl') @@ -24,8 +27,8 @@ class Paraview(Package): depends_on('bzip2') depends_on('freetype') - depends_on('hdf5') depends_on('hdf5+mpi', when='+mpi') + depends_on('hdf5~mpi', when='~mpi') depends_on('jpeg') depends_on('libpng') depends_on('libtiff') @@ -35,6 +38,11 @@ class Paraview(Package): #depends_on('sqlite') # external version not supported depends_on('zlib') + def url_for_version(self, version): + """Handle ParaView version-based custom URLs.""" + return self._url_str % (version.up_to(2), version) + + def install(self, spec, prefix): with working_dir('spack-build', create=True): def feature_to_bool(feature, on='ON', off='OFF'): diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch new file mode 100644 index 0000000000..514781b8b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ca945dd..1bf94e9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH}) + include_directories(${METIS_PATH}/include) + + # List of directories that cmake will look for CMakeLists.txt +-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) ++#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) + add_subdirectory(include) + add_subdirectory(libparmetis) + add_subdirectory(programs) diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c897dec7e4..c691cf4191 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -25,9 +25,6 @@ from spack import * -# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce -# FIXME : the installation rules to just a few lines - class Parmetis(Package): """ @@ -43,13 +40,17 @@ class Parmetis(Package): variant('debug', default=False, description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - variant('idx64', default=False, description='Use int64_t as default index type') - variant('double', default=False, description='Use double precision floating point types') - depends_on('cmake @2.8:') # build dependency depends_on('mpi') - # FIXME : this should conflict with metis as it builds its own version internally + patch('enable_external_metis.patch') + depends_on('metis') + + # bug fixes from PETSc developers + # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ + patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch') + # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ + patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') depends_on('gdb', when='+gdb') @@ -63,8 +64,8 @@ class Parmetis(Package): # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case # FIXME : they use a non-standard name - options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), - '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source), + options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame... + '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix), '-DCMAKE_C_COMPILER:STRING=mpicc', '-DCMAKE_CXX_COMPILER:STRING=mpicxx']) @@ -78,18 +79,7 @@ class Parmetis(Package): if '+gdb' in spec: options.append('-DGDB:BOOL=ON') - metis_header = join_path(metis_source, 'include', 'metis.h') - - if '+idx64' in spec: - filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header) - - if '+double' in spec: - filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header) - with working_dir(build_directory, create=True): cmake(source_directory, *options) make() make("install") - # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required - # metis header either - install(metis_header, self.prefix.include) diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch new file mode 100644 index 0000000000..e6b8056c21 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch @@ -0,0 +1,77 @@ +From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001 +From: Jed Brown <jed@59A2.org> +Date: Fri, 12 Oct 2012 15:45:10 -0500 +Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint + #133631] + +''' +I have also reported to to Karypis but have received zero +response and he hasn't released any updates to the original release +either. At least he approved my forum posting so that other people +can see the bug and the fix. +http://glaros.dtc.umn.edu/gkhome/node/837 +''' + +Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4 +--- + libparmetis/xyzpart.c | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 3a2c289..63abfcb 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + for (i=0; i<nbins; i++) + emarkers[i] = gmin + (gmax-gmin)*i/nbins; +- emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON); + + /* get into a iterative backet boundary refinement */ + for (l=0; l<5; l++) { +@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + } + } + nemarkers[0] = gmin; +- nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON); + rcopy(nbins+1, nemarkers, emarkers); + } + +@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + emarkers[0] = gmin; + emarkers[1] = gsum/gnvtxs; +- emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON); + cnbins = 2; + + /* get into a iterative backet boundary refinement */ +@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + iset(cnbins, 0, lcounts); + rset(cnbins, 0, lsums); + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + lcounts[j]++; + lsums[j] += cand[i].key; + i++; +@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + rsorti(cnbins, nemarkers); + rcopy(cnbins, nemarkers, emarkers); +- emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON); + } + + /* assign the coordinate to the appropriate bin */ + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + bxyz[cand[i].val*ndims+k] = j; + i++; + } +-- +2.1.1.1.g1fb337f + diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch new file mode 100644 index 0000000000..9651d55347 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch @@ -0,0 +1,35 @@ +From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001 +From: Sean Farley <sean@mcs.anl.gov> +Date: Tue, 20 Mar 2012 11:59:44 -0500 +Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart + +Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2 +--- + libparmetis/xyzpart.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 307aed9..3a2c289 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + /* determine bucket counts */ + iset(nbins, 0, lcounts); + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + lcounts[j]++; + i++; + } +@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + /* assign the coordinate to the appropriate bin */ + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + bxyz[cand[i].val*ndims+k] = j; + i++; + } +-- +2.1.1.1.g1fb337f + diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 87f700629d..7239baaf7f 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -1,39 +1,101 @@ +import os from spack import * + class Petsc(Package): - """PETSc is a suite of data structures and routines for the - scalable (parallel) solution of scientific applications modeled by - partial differential equations.""" + """ + PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications + modeled by partial differential equations. + """ homepage = "http://www.mcs.anl.gov/petsc/index.html" - url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + version('3.6.3', '91dd3522de5a5ef039ff8f50800db606') version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f') version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13') version('3.5.1', 'a557e029711ebf425544e117ffa44d8f') + version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d') + + variant('shared', default=True, description='Enables the build of shared libraries') + variant('mpi', default=True, description='Activates MPI support') + variant('double', default=True, description='Switches between single and double precision') + + variant('metis', default=True, description='Activates support for metis and parmetis') + variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)') + variant('boost', default=True, description='Activates support for Boost') + variant('hypre', default=True, description='Activates support for Hypre') + + # Virtual dependencies + depends_on('blas') + depends_on('lapack') + depends_on('mpi', when='+mpi') - depends_on("python @2.6:2.9") # requires Python for building + # Build dependencies + depends_on('python @2.6:2.7') - depends_on("boost") - depends_on("blas") - depends_on("lapack") - depends_on("hypre") - depends_on("parmetis") - depends_on("metis") - depends_on("hdf5+mpi") - depends_on("mpi") + # Other dependencies + depends_on('boost', when='+boost') + depends_on('metis', when='+metis') + + depends_on('hdf5+mpi', when='+hdf5+mpi') + depends_on('parmetis', when='+metis+mpi') + depends_on('hypre', when='+hypre+mpi') + + def mpi_dependent_options(self): + if '~mpi' in self.spec: + compiler_opts = [ + '--with-cc=%s' % os.environ['CC'], + '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), + '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), + '--with-mpi=0' + ] + error_message_fmt = '\t{library} support requires "+mpi" to be activated' + + # If mpi is disabled (~mpi), it's an error to have any of these enabled. + # This generates a list of any such errors. + errors = [error_message_fmt.format(library=x) + for x in ('hdf5', 'hypre', 'parmetis') + if ('+'+x) in self.spec] + if errors: + 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, + ] + return compiler_opts def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--with-blas-lib=%s/libblas.a" % spec['blas'].prefix.lib, - "--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib, - "--with-boost-dir=%s" % spec['boost'].prefix, - "--with-hypre-dir=%s" % spec['hypre'].prefix, - "--with-parmetis-dir=%s" % spec['parmetis'].prefix, - "--with-metis-dir=%s" % spec['metis'].prefix, - "--with-hdf5-dir=%s" % spec['hdf5'].prefix, - "--with-mpi-dir=%s" % spec['mpi'].prefix, - "--with-shared-libraries=0") + options = ['--with-debugging=0', + '--with-ssl=0'] + options.extend(self.mpi_dependent_options()) + options.extend([ + '--with-precision=%s' % ('double' if '+double' in spec else 'single'), + '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), + '--with-blas-lapack-dir=%s' % spec['lapack'].prefix + ]) + # Activates library support if needed + for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'): + options.append( + '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) + ) + if library in spec: + options.append( + '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) + ) + + configure('--prefix=%s' % prefix, *options) # PETSc has its own way of doing parallel make. make('MAKE_NP=%s' % make_jobs, parallel=False) diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py new file mode 100644 index 0000000000..797772f4f6 --- /dev/null +++ b/var/spack/repos/builtin/packages/proj/package.py @@ -0,0 +1,20 @@ +from spack import * + +class Proj(Package): + """Cartographic Projections""" + homepage = "https://github.com/OSGeo/proj.4/wiki" + url = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz" + + version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9') + version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c') + version('4.8.0', 'd815838c92a29179298c126effbb1537') + version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd') + version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493') + + # No dependencies + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py index 8001689a18..f599205644 100644 --- a/var/spack/repos/builtin/packages/py-mpi4py/package.py +++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py @@ -5,7 +5,9 @@ class PyMpi4py(Package): homepage = "https://pypi.python.org/pypi/mpi4py" url = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz" + version('2.0.0', '4f7d8126d7367c239fd67615680990e3') version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c') + extends('python') depends_on('py-setuptools') depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e7c6cf0264..4fee99098e 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,11 +1,12 @@ from spack import * + class PyNose(Package): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" homepage = "https://pypi.python.org/pypi/nose" - url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" + url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py new file mode 100644 index 0000000000..6d10fea74f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-phonopy/package.py @@ -0,0 +1,18 @@ +from spack import * + +class PyPhonopy(Package): + """Phonopy is an open source package for phonon + calculations at harmonic and quasi-harmonic levels.""" + homepage = "http://atztogo.github.io/phonopy/index.html" + url = "http://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz" + + version('1.10.0', '973ed1bcea46e21b9bf747aab9061ff6') + + extends('python') + depends_on('py-numpy') + depends_on('py-scipy') + depends_on('py-matplotlib') + depends_on('py-pyyaml') + + def install(self, spec, prefix): + python('setup.py', 'install', '--home=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py new file mode 100644 index 0000000000..cae42f6e59 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPyyaml(Package): + """PyYAML is a YAML parser and emitter for Python.""" + homepage = "http://pyyaml.org/wiki/PyYAML" + url = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz" + + version('3.11', 'f50e08ef0fe55178479d3a618efe21db') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py new file mode 100644 index 0000000000..3118e74519 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-wheel/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyWheel(Package): + """A built-package format for Python.""" + + homepage = "https://pypi.python.org/pypi/wheel" + url = "https://pypi.python.org/packages/source/w/wheel/wheel-0.26.0.tar.gz" + + version('0.26.0', '4cfc6e7e3dc7377d0164914623922a10') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index a1ce06feb0..4f55bc803e 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -1,11 +1,14 @@ +import functools +import glob +import inspect import os import re from contextlib import closing -from llnl.util.lang import match_predicate -from spack.util.environment import * -from spack import * import spack +from llnl.util.lang import match_predicate +from spack import * +from spack.util.environment import * class Python(Package): @@ -34,8 +37,9 @@ class Python(Package): env['PYTHONHOME'] = prefix env['MACOSX_DEPLOYMENT_TARGET'] = '10.6' - # Rest of install is pretty standard except setup.py needs to be able to read the CPPFLAGS - # and LDFLAGS as it scans for the library and headers to build + # Rest of install is pretty standard except setup.py needs to + # be able to read the CPPFLAGS and LDFLAGS as it scans for the + # library and headers to build configure_args= [ "--prefix=%s" % prefix, "--with-threads", @@ -55,6 +59,20 @@ class Python(Package): make() make("install") + # Modify compiler paths in configuration files. This is necessary for + # building site packages outside of spack + filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)', + (r'\4\5'), + join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py')) + + python3_version = '' + if spec.satisfies('@3:'): + python3_version = '-%d.%dm' % self.version[:2] + makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile') + filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)', + (r'\4\5'), + makefile_filepath) + # ======================================================================== # Set up environment to make install easy for python extensions. @@ -75,12 +93,28 @@ class Python(Package): return os.path.join(self.python_lib_dir, 'site-packages') - def setup_dependent_environment(self, module, spec, ext_spec): - """Called before python modules' install() methods. + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # TODO: do this only for actual extensions. + + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. + python_paths = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + + pythonpath = ':'.join(python_paths) + spack_env.set('PYTHONPATH', pythonpath) + run_env.set('PYTHONPATH', pythonpath) + + + def modify_module(self, module, spec, ext_spec): + """ + Called before python modules' install() methods. In most cases, extensions will only need to have one line:: - python('setup.py', 'install', '--prefix=%s' % prefix) + python('setup.py', 'install', '--prefix=%s' % prefix) """ # Python extension builds can have a global python executable function if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): @@ -96,15 +130,6 @@ class Python(Package): # Make the site packages directory if it does not exist already. mkdirp(module.site_packages_dir) - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. - python_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - os.environ['PYTHONPATH'] = ':'.join(python_paths) - - # ======================================================================== # Handle specifics of activating and deactivating python modules. # ======================================================================== diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py index f6712ced38..8f7c2f31b1 100644 --- a/var/spack/repos/builtin/packages/qhull/package.py +++ b/var/spack/repos/builtin/packages/qhull/package.py @@ -8,20 +8,20 @@ class Qhull(Package): implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and - approximations to the convex hull. - - Qhull does not support triangulation of non-convex surfaces, - mesh generation of non-convex objects, medium-sized inputs in - 9-D and higher, alpha shapes, weighted Voronoi diagrams, - Voronoi volumes, or constrained Delaunay triangulations.""" + approximations to the convex hull.""" homepage = "http://www.qhull.org" + version('7.2.0', 'e6270733a826a6a7c32b796e005ec3dc', + url="http://www.qhull.org/download/qhull-2015-src-7.2.0.tgz") + version('1.0', 'd0f978c0d8dfb2e919caefa56ea2953c', url="http://www.qhull.org/download/qhull-2012.1-src.tgz") # https://github.com/qhull/qhull/pull/5 - patch('qhull-iterator.patch') + patch('qhull-iterator.patch', when='@1.0') + + depends_on('cmake') def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py new file mode 100644 index 0000000000..5374d02c97 --- /dev/null +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Qrupdate(Package): + """qrupdate is a Fortran library for fast updates of QR and + Cholesky decompositions.""" + + homepage = "http://sourceforge.net/projects/qrupdate/" + url = "https://downloads.sourceforge.net/qrupdate/qrupdate-1.1.2.tar.gz" + + version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4') + + depends_on("blas") + depends_on("lapack") + + def install(self, spec, prefix): + # Build static and dynamic libraries + make("lib", "solib") + make("install", "PREFIX=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index e8d843519d..d08e8e81e1 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -8,6 +8,9 @@ class Qt(Package): 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') @@ -23,6 +26,7 @@ class Qt(Package): version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009', url="http://download.qt.io/archive/qt/3/qt-x11-free-3.3.8b.tar.gz") + 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.") patch('qt3krell.patch', when='@3.3.8b+krellpatch') @@ -48,13 +52,16 @@ class Qt(Package): # depends_on("icu4c") # OpenGL hardware acceleration - depends_on("mesa", when='@4:') + depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def setup_dependent_environment(self, module, spec, dep_spec): - """Dependencies of Qt find it using the QTDIR environment variable.""" - os.environ['QTDIR'] = self.prefix + def setup_environment(self, spack_env, env): + env.set('QTDIR', self.prefix) + + + def setup_dependent_environment(self, spack_env, run_env, dspec): + spack_env.set('QTDIR', self.prefix) def patch(self): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 6b6242362c..7ff1898ce9 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -1,9 +1,8 @@ from spack import * -import spack -import os + class Ruby(Package): - """A dynamic, open source programming language with a focus on + """A dynamic, open source programming language with a focus on simplicity and productivity.""" homepage = "https://www.ruby-lang.org/" @@ -15,11 +14,23 @@ class Ruby(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") - def setup_dependent_environment(self, module, spec, ext_spec): + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # TODO: do this only for actual extensions. + # Set GEM_PATH to include dependent gem directories + ruby_paths = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + ruby_paths.append(d.prefix) + + spack_env.set_path('GEM_PATH', ruby_paths) + + # The actual installation path for this gem + spack_env.set('GEM_HOME', extension_spec.prefix) + + def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -30,12 +41,3 @@ class Ruby(Package): # Ruby extension builds have global ruby and gem functions module.ruby = Executable(join_path(spec.prefix.bin, 'ruby')) module.gem = Executable(join_path(spec.prefix.bin, 'gem')) - - # Set GEM_PATH to include dependent gem directories - ruby_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - ruby_paths.append(d.prefix) - os.environ['GEM_PATH'] = ':'.join(ruby_paths) - # The actual installation path for this gem - os.environ['GEM_HOME'] = ext_spec.prefix diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index 9eda11df15..d1aed78e0e 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -1,19 +1,28 @@ from spack import * class Silo(Package): - """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.""" + """Silo is a library for reading and writing a wide variety of scientific + data to binary, disk files.""" homepage = "http://wci.llnl.gov/simulation/computer-codes/silo" url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz" - #version('4.9', 'a83eda4f06761a86726e918fc55e782a') version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') - depends_on("hdf5@:1.8.12") + variant('fortran', default=True, description='Enable Fortran support') + + depends_on("hdf5") def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--with-hdf5=%s" %spec['hdf5'].prefix) + config_args = [ + '--enable-fortran' if '+fortran' in spec else '--disable-fortran', + ] + + configure( + "--prefix=%s" % prefix, + "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), + "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), + *config_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py new file mode 100644 index 0000000000..b57f9967c3 --- /dev/null +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -0,0 +1,26 @@ +from spack import * + + +class SuiteSparse(Package): + """ + SuiteSparse is a suite of sparse matrix algorithms + """ + homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' + url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' + + version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + + depends_on('blas') + depends_on('lapack') + + depends_on('metis@5.1.0', when='@4.5.1') + + def install(self, spec, prefix): + # The build system of SuiteSparse is quite old-fashioned + # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) + # with a lot of convoluted logic in it. + # Any kind of customization will need to go through filtering of that file + + # 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') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py new file mode 100644 index 0000000000..c4c76909b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -0,0 +1,63 @@ +from spack import * + +class SuperluDist(Package): + """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" + + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') + version('4.2', 'ae9fafae161f775fbac6eba11e530a65') + version('4.1', '4edee38cc29f687bd0c8eb361096a455') + version('4.0', 'c0b98b611df227ae050bc1635c6940e0') + + depends_on ('mpi') + depends_on ('blas') + depends_on ('lapack') + depends_on ('parmetis') + depends_on ('metis') + + def install(self, spec, prefix): + makefile_inc = [] + makefile_inc.extend([ + 'PLAT = _mac_x', + 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + 'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a', + 'BLASDEF = -DUSE_VENDOR_BLAS', + 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names + 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, + 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, + 'FLIBS =', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + 'ARCH = ar', + 'ARCHFLAGS = cr', + 'RANLIB = true', + 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names + 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include), + 'NOOPTS = -fPIC -std=c99', + 'FORTRAN = mpif77', + 'F90FLAGS = -O2', + 'LOADER = mpif77', + 'LOADOPTS =', + 'CDEFS = -DAdd_' + ]) + + #with working_dir('src'): + with open('make.inc', 'w') as fh: + fh.write('\n'.join(makefile_inc)) + + make("lib", parallel=False) + + # FIXME: + # cd "EXAMPLE" do + # system "make" + + # need to install by hand + headers_location = join_path(self.prefix.include,'superlu_dist') + mkdirp(headers_location) + # FIXME: fetch all headers in the folder automatically + for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: + superludist_header = join_path(self.stage.source_path, 'SRC/',header) + install(superludist_header, headers_location) + + superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') + install(superludist_lib,self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py new file mode 100644 index 0000000000..30c2b76655 --- /dev/null +++ b/var/spack/repos/builtin/packages/tetgen/package.py @@ -0,0 +1,28 @@ +from spack import * + +class Tetgen(Package): + """TetGen is a program and library that can be used to generate tetrahedral + meshes for given 3D polyhedral domains. TetGen generates exact constrained + Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and + Voronoi paritions.""" + + homepage = "http://www.tetgen.org" + url = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz" + + version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18') + + # TODO: Make this a build dependency once build dependencies are supported + # (see: https://github.com/LLNL/spack/pull/378). + depends_on('cmake@2.8.7:', when='@1.5.0:') + + def install(self, spec, prefix): + make('tetgen', 'tetlib') + + mkdirp(prefix.bin) + install('tetgen', prefix.bin) + + mkdirp(prefix.include) + install('tetgen.h', prefix.include) + + mkdirp(prefix.lib) + install('libtet.a', prefix.lib) diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py index a83c10c0c1..6cf8d79072 100644 --- a/var/spack/repos/builtin/packages/texinfo/package.py +++ b/var/spack/repos/builtin/packages/texinfo/package.py @@ -6,7 +6,7 @@ # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. # LLNL-CODE-647188 # -# For details, see https://llnl.github.io/spack +# For details, see https://software.llnl.gov/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 diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 0e15052f64..6430f40e80 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -12,33 +12,44 @@ class Thrift(Package): version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678') - extends("python") - - depends_on("autoconf") - depends_on("automake") - depends_on("bison") - depends_on("boost") - depends_on("flex") - depends_on("jdk") - depends_on("libtool") - depends_on("openssl") - depends_on("python") - - # Compilation fails for most languages, fortunately cpp installs fine - # All other languages (yes, including C) are omitted until someone needs them + # Currently only support for c-family and python + variant('c', default=True, description="Build support for C-family languages") + variant('python', default=True, description="Build support for python") + + depends_on('jdk') + depends_on('autoconf') + depends_on('automake') + depends_on('libtool') + depends_on('boost@1.53:') + depends_on('bison') + depends_on('flex') + depends_on('openssl') + + # Variant dependencies + extends('python', when='+python') + + depends_on('zlib', when='+c') + depends_on('libevent', when='+c') + def install(self, spec, prefix): - env["PY_PREFIX"] = prefix - env["JAVA_PREFIX"] = prefix - - configure("--prefix=%s" % prefix, - "--with-boost=%s" % spec['boost'].prefix, - "--with-c=no", - "--with-go=no", - "--with-python=yes", - "--with-lua=no", - "--with-php=no", - "--with-qt4=no", - "--enable-tests=no") + env['PY_PREFIX'] = prefix + env['JAVA_HOME'] = spec['jdk'].prefix + + # configure options + options = ['--prefix=%s' % prefix] + + options.append('--with-boost=%s' % spec['boost'].prefix) + options.append('--enable-tests=no') + + options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no')) + options.append('--with-python=%s' % ('yes' if '+python' in spec else 'no')) + options.append('--with-java=%s' % ('yes' if '+java' in spec else 'no')) + options.append('--with-go=%s' % ('yes' if '+go' in spec else 'no')) + options.append('--with-lua=%s' % ('yes' if '+lua' in spec else 'no')) + options.append('--with-php=%s' % ('yes' if '+php' in spec else 'no')) + options.append('--with-qt4=%s' % ('yes' if '+qt4' in spec else 'no')) + + configure(*options) make() make("install") diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index 23d36db427..f2067d1366 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -7,10 +7,11 @@ class Tmux(Package): do a lot more. """ - homepage = "http://tmux.sourceforge.net" - url = "http://downloads.sourceforge.net/project/tmux/tmux/tmux-1.9/tmux-1.9a.tar.gz" + homepage = "http://tmux.github.io" + url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz" version('1.9a', 'b07601711f96f1d260b390513b509a2d') + version('2.1', '74a2855695bccb51b6e301383ad4818c') depends_on('libevent') depends_on('ncurses') diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py new file mode 100644 index 0000000000..f65d93776d --- /dev/null +++ b/var/spack/repos/builtin/packages/triangle/package.py @@ -0,0 +1,20 @@ +from spack import * + +class Triangle(Package): + """Triangle is a two-dimensional mesh generator and Delaunay + triangulator. Triangle generates exact Delaunay triangulations, + constrained Delaunay triangulations, conforming Delaunay + triangulations, Voronoi diagrams, and high-quality triangular + meshes.""" + + homepage = "http://www.cs.cmu.edu/~quake/triangle.html" + url = "http://www.netlib.org/voronoi/triangle.zip" + + version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9') + + def install(self, spec, prefix): + make() + mkdirp(prefix.bin) + + install('triangle', prefix.bin) + install('showme', prefix.bin) diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 7c43f796a4..edc40476e3 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -10,40 +10,44 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') version('12.0.1', 'bd99741d047471e127b8296b2ec08017') version('11.14.3', '2f4f83f8333e4233c57d0f01c4b57426') version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('mpi', default=True, description='Add a dependency on MPI and enables MPI dependent packages') + 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') depends_on('lapack') depends_on('boost') - depends_on('netcdf') depends_on('matio') depends_on('glm') depends_on('swig') - depends_on('mpi', when='+mpi') - def install(self, spec, prefix): + # MPI related dependencies + depends_on('mpi') + depends_on('netcdf+mpi') + + depends_on('python') # Needs py-numpy activated - options = [ - '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', - '-DTrilinos_ENABLE_TESTS:BOOL=OFF', - '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', - '-DBUILD_SHARED_LIBS:BOOL=ON', - '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, - '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix - ] - if '+mpi' in spec: - mpi_options = ['-DTPL_ENABLE_MPI:BOOL=ON'] - options.extend(mpi_options) - - # -DCMAKE_INSTALL_PREFIX and all the likes... + def install(self, spec, prefix): + options = [] options.extend(std_cmake_args) + + options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', + '-DTrilinos_ENABLE_TESTS:BOOL=OFF', + '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', + '-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 + ]) + with working_dir('spack-build', create=True): cmake('..', *options) make() diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py new file mode 100644 index 0000000000..9954a733bb --- /dev/null +++ b/var/spack/repos/builtin/packages/udunits2/package.py @@ -0,0 +1,16 @@ +from spack import * + +class Udunits2(Package): + """Automated units conversion""" + + homepage = "http://www.unidata.ucar.edu/software/udunits" + url = "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.20.tar.gz" + + version('2.2.20', '1586b70a49dfe05da5fcc29ef239dce0') + + depends_on('expat') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index ba6c9733a7..fdcac95345 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -8,11 +8,9 @@ class Xz(Package): homepage = "http://tukaani.org/xz/" url = "http://tukaani.org/xz/xz-5.2.0.tar.bz2" - version('5.2.0', '867cc8611760240ebf3440bd6e170bb9', - url = 'http://tukaani.org/xz/xz-5.2.0.tar.bz2') - version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af', - url = 'http://tukaani.org/xz/xz-5.2.2.tar.bz2') - + version('5.2.0', '867cc8611760240ebf3440bd6e170bb9') + version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py new file mode 100644 index 0000000000..620fe9d456 --- /dev/null +++ b/var/spack/repos/builtin/packages/zfp/package.py @@ -0,0 +1,26 @@ +from spack import * + +class Zfp(Package): + """zfp is an open source C library for compressed floating-point arrays that supports + very high throughput read and write random acces, target error bounds or bit rates. + Although bit-for-bit lossless compression is not always possible, zfp is usually + accurate to within machine epsilon in near-lossless mode, and is often orders of + magnitude more accurate than other lossy compressors. + """ + + homepage = "http://computation.llnl.gov/projects/floating-point-compression" + url = "http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.0.tar.gz" + + version('0.5.0', '2ab29a852e65ad85aae38925c5003654') + + def install(self, spec, prefix): + make("shared") + + # No install provided + mkdirp(prefix.lib) + mkdirp(prefix.include) + install('lib/libzfp.so', prefix.lib) + install('inc/zfp.h', prefix.include) + install('inc/types.h', prefix.include) + install('inc/bitstream.h', prefix.include) + install('inc/system.h', prefix.include) |