diff options
| author | Kelly (KT) Thompson <kgt@lanl.gov> | 2016-03-30 15:35:46 -0600 |
|---|---|---|
| committer | Kelly (KT) Thompson <kgt@lanl.gov> | 2016-03-30 15:35:46 -0600 |
| commit | be2862ef4ec0f36ec77ed5c2f915f315b9eed238 (patch) | |
| tree | 797d944352ed51b86e9a91a314c8eb73133a1f9a /var | |
| parent | 8bf86178761ed00ca49febf6ae1b23b6f5511c97 (diff) | |
| parent | 4bc6ace201fc682a9a681b73d1096a95edb48c64 (diff) | |
| download | spack-be2862ef4ec0f36ec77ed5c2f915f315b9eed238.tar.gz spack-be2862ef4ec0f36ec77ed5c2f915f315b9eed238.tar.bz2 spack-be2862ef4ec0f36ec77ed5c2f915f315b9eed238.tar.xz spack-be2862ef4ec0f36ec77ed5c2f915f315b9eed238.zip | |
Merge remote-tracking branch 'upstream/develop' into pkg-numdiff
Diffstat (limited to 'var')
71 files changed, 1682 insertions, 319 deletions
diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py new file mode 100644 index 0000000000..c5fed52f53 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/python/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 Python(Package): + """Dummy Python package to demonstrate preferred versions.""" + homepage = "http://www.python.org" + url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" + + extendable = True + + version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') + version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') + version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) + version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') + version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') + version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') + + def install(self, spec, prefix): + pass + diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py new file mode 100644 index 0000000000..8f19c84d22 --- /dev/null +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class AprUtil(Package): + """Apache Portable Runtime Utility""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz' + + version('1.5.4', '866825c04da827c6e5f53daff5569f42') + + depends_on('apr') + + def install(self, spec, prefix): + + # configure, build, install: + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py new file mode 100644 index 0000000000..8a440766ec --- /dev/null +++ b/var/spack/repos/builtin/packages/apr/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Apr(Package): + """Apache portable runtime.""" + homepage = 'https://apr.apache.org/' + url = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz' + + version('1.5.2', '98492e965963f852ab29f9e61b2ad700') + + def install(self, spec, prefix): + options = ['--prefix=%s' % prefix] + configure(*options) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 0b49d14202..dd86b17a53 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -35,6 +35,10 @@ class ArpackNg(Package): 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') @@ -46,7 +50,10 @@ class ArpackNg(Package): options = ['--prefix=%s' % prefix] if '+mpi' in spec: - options.append('--enable-mpi') + options.extend([ + '--enable-mpi', + 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + ]) if '~shared' in spec: options.append('--enable-shared=no') 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/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py new file mode 100644 index 0000000000..7260fd74a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -0,0 +1,17 @@ +from spack import * +import os + +class Astyle(Package): + """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.""" + homepage = "http://astyle.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz" + + version('2.04', '30b1193a758b0909d06e7ee8dd9627f6') + + def install(self, spec, prefix): + + with working_dir('src'): + make('-f', + join_path(self.stage.source_path,'build','clang','Makefile'), + parallel=False) + install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index fc683363a7..b5504122b7 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -1,31 +1,36 @@ from spack import * from spack.util.executable import Executable -import os +import os.path class Atlas(Package): """ - Automatically Tuned Linear Algebra Software, generic shared - ATLAS is an approach for the automatic generation and optimization of - numerical software. Currently ATLAS supplies optimized versions for the - complete set of linear algebra kernels known as the Basic Linear Algebra - Subroutines (BLAS), and a subset of the linear algebra routines in the - LAPACK library. + Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and + optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear + algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines + in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" + version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', + url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + resource(name='lapack', + url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', + md5='b1d3e3e425b2e44a06760ff173104bdf', + destination='spack-resource-lapack', + when='@3:') + version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') - version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2') - # TODO: make this provide BLAS once it works better. Create a way - # TODO: to mark "beta" packages and require explicit invocation. + variant('shared', default=True, description='Builds shared library') - # provides('blas') + provides('blas') + provides('lapack') + parallel = False def patch(self): - # Disable thraed check. LLNL's environment does not allow + # Disable thread check. LLNL's environment does not allow # disabling of CPU throttling in a way that ATLAS actually # understands. filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);', @@ -33,26 +38,21 @@ class Atlas(Package): # TODO: investigate a better way to add the check back in # TODO: using, say, MSRs. Or move this to a variant. - @when('@:3.10') def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs") - make() - make('check') - make('ptcheck') - make('time') - make("install") + options = [] + if '+shared' in spec: + options.append('--shared') - def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--incdir=%s' % prefix.include, - '--libdir=%s' % prefix.lib, - '--cc=cc', - "--shared") + # Lapack resource + lapack_stage = self.stage[1] + lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) + lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) + options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path) + with working_dir('spack-build', create=True): + configure = Executable('../configure') + configure('--prefix=%s' % prefix, *options) make() make('check') make('ptcheck') diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index fb1f5daee7..f889da21f2 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -1,5 +1,9 @@ from spack import * import spack +import sys + +import os +import sys class Boost(Package): """Boost provides free peer-reviewed portable C++ source @@ -45,34 +49,34 @@ class Boost(Package): version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5') version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0') - default_install_libs = set(['atomic', - 'chrono', - 'date_time', - 'filesystem', + default_install_libs = set(['atomic', + 'chrono', + 'date_time', + 'filesystem', 'graph', 'iostreams', 'locale', 'log', - 'math', + 'math', 'program_options', - 'random', - 'regex', - 'serialization', - 'signals', - 'system', - 'test', - 'thread', + '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 + # 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), + 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') @@ -124,9 +128,9 @@ class Boost(Package): 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, + 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')) @@ -155,7 +159,7 @@ class Boost(Package): linkTypes = ['static'] if '+shared' in spec: linkTypes.append('shared') - + threadingOpts = [] if '+multithreaded' in spec: threadingOpts.append('multi') @@ -163,28 +167,38 @@ class Boost(Package): 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=%s' % ','.join(linkTypes), '--layout=tagged']) - + return threadingOpts def install(self, spec, prefix): + # On Darwin, Boost expects the Darwin libtool. However, one of the + # dependencies may have pulled in Spack's GNU libtool, and these two are + # not compatible. We thus create a symlink to Darwin's libtool and add + # it at the beginning of PATH. + if sys.platform == 'darwin': + newdir = os.path.abspath('darwin-libtool') + mkdirp(newdir) + force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool')) + env['PATH'] = newdir + ':' + env['PATH'] + 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 + # 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'] = './' @@ -207,4 +221,7 @@ class Boost(Package): # Boost.MPI if the threading options are not separated. for threadingOpt in threadingOpts: b2('install', 'threading=%s' % threadingOpt, *b2_options) - + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index cc93c7067c..91a4e3b415 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -30,6 +30,7 @@ class Cmake(Package): homepage = 'https://www.cmake.org' url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' + version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') version('3.4.0', 'cd3034e0a44256a0917e254167217fc8') @@ -38,10 +39,12 @@ class Cmake(Package): version('2.8.10.2', '097278785da7182ec0aea8769d06860c') variant('ncurses', default=True, description='Enables the build of the ncurses gui') + variant('openssl', default=True, description="Enables CMake's OpenSSL features") 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('openssl', when='+openssl') depends_on('qt', when='+qt') depends_on('python@2.7.11:', when='+doc') depends_on('py-sphinx', when='+doc') @@ -77,8 +80,9 @@ class Cmake(Package): options.append('--sphinx-html') options.append('--sphinx-man') - options.append('--') - options.append('-DCMAKE_USE_OPENSSL=ON') + if '+openssl' in spec: + options.append('--') + options.append('-DCMAKE_USE_OPENSSL=ON') configure(*options) make() diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 1693c4b160..bc83cb2b65 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -8,8 +8,8 @@ class Cryptopp(Package): 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" + homepage = "http://www.cryptopp.com" + base_url = "http://www.cryptopp.com" version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') @@ -25,7 +25,5 @@ class Cryptopp(Package): 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) + version_string = str(version).replace('.', '') + return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 294b0de54e..422f5a19eb 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -13,6 +13,7 @@ class Dbus(Package): homepage = "http://dbus.freedesktop.org/" url = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz" + version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b') version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36') version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43') version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index e40046b452..8d6e672f86 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -48,7 +48,7 @@ class Eigen(Package): depends_on('metis', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') - depends_on('SuiteSparse', when='+suitesparse') + 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') diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index a2bf58f585..59f362ab46 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -32,6 +32,10 @@ class Espresso(Package): if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): raise RuntimeError(error.format(variant='elpa')) + def setup_environment(self, spack_env, run_env): + # Espresso copies every executable in prefix without creating sub-folders + run_env.prepend_path('PATH', self.prefix) + def install(self, spec, prefix): self.check_variants(spec) diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 new file mode 100644 index 0000000000..444e292786 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 @@ -0,0 +1,42 @@ +diff --git a/gcc/configure b/gcc/configure +index 9523773..52b0bf7 100755 +--- a/gcc/configure ++++ b/gcc/configure +@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then : + else + gcc_cv_as_ix86_filds=no + if test x$gcc_cv_as != x; then +- $as_echo 'filds mem; fists mem' > conftest.s ++ $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then : + else + gcc_cv_as_ix86_fildq=no + if test x$gcc_cv_as != x; then +- $as_echo 'fildq mem; fistpq mem' > conftest.s ++ $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s + if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5' + { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5 + (eval $ac_try) 2>&5 +diff --git a/gcc/configure.ac b/gcc/configure.ac +index 68b0ee8..bd53978 100644 +--- a/gcc/configure.ac ++++ b/gcc/configure.ac +@@ -3869,13 +3869,13 @@ foo: nop + + gcc_GAS_CHECK_FEATURE([filds and fists mnemonics], + gcc_cv_as_ix86_filds,,, +- [filds mem; fists mem],, ++ [filds (%ebp); fists (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDS, 1, + [Define if your assembler uses filds and fists mnemonics.])]) + + gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics], + gcc_cv_as_ix86_fildq,,, +- [fildq mem; fistpq mem],, ++ [fildq (%ebp); fistpq (%ebp)],, + [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1, + [Define if your assembler uses fildq and fistq mnemonics.])]) + diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 new file mode 100644 index 0000000000..b065997f45 --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 @@ -0,0 +1,28 @@ +From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001 +From: Iain Sandoe <iain@codesourcery.com> +Date: Sat, 21 Dec 2013 00:30:18 +0000 +Subject: [PATCH] don't try to mark local symbols as no-dead-strip + +--- + gcc/config/darwin.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c +index 40804b8..0080299 100644 +--- a/gcc/config/darwin.c ++++ b/gcc/config/darwin.c +@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED) + void + darwin_mark_decl_preserved (const char *name) + { ++ /* Actually we shouldn't mark any local symbol this way, but for now ++ this only happens with ObjC meta-data. */ ++ if (darwin_label_is_anonymous_local_objc_name (name)) ++ return; ++ + fprintf (asm_out_file, "\t.no_dead_strip "); + assemble_name (asm_out_file, name); + fputc ('\n', asm_out_file); +-- +2.2.1 + diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index f8958ee290..6043b62279 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -26,6 +26,8 @@ from spack import * from contextlib import closing from glob import glob +import sys +import os class Gcc(Package): """The GNU Compiler Collection includes front ends for C, C++, @@ -47,24 +49,33 @@ class Gcc(Package): version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4') version('4.5.4', '27e459c2566b8209ab064570e1b378f7') - variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO") + variant('binutils', default=sys.platform != 'darwin', + description="Build via binutils") + variant('gold', default=sys.platform != 'darwin', + description="Build the gold linker plugin for ld-based LTO") depends_on("mpfr") depends_on("gmp") 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') + depends_on("binutils~libiberty", when='+binutils ~gold') + depends_on("binutils~libiberty+gold", when='+binutils +gold') + # TODO: integrate these libraries. #depends_on("ppl") #depends_on("cloog") + if sys.platform == 'darwin': + patch('darwin/gcc-4.9.patch1', when='@4.9.3') + patch('darwin/gcc-4.9.patch2', when='@4.9.3') def install(self, spec, prefix): # libjava/configure needs a minor fix to install into spack paths. - filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True) + filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', + string=True) enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc')) - if spec.satisfies("@4.7.1:"): + + if spec.satisfies("@4.7.1:") and sys.platform != 'darwin': enabled_languages.add('go') # Generic options to compile GCC @@ -72,32 +83,40 @@ class Gcc(Package): "--libdir=%s/lib64" % prefix, "--disable-multilib", "--enable-languages=" + ','.join(enabled_languages), - "--with-mpc=%s" % spec['mpc'].prefix, - "--with-mpfr=%s" % spec['mpfr'].prefix, - "--with-gmp=%s" % spec['gmp'].prefix, + "--with-mpc=%s" % spec['mpc'].prefix, + "--with-mpfr=%s" % spec['mpfr'].prefix, + "--with-gmp=%s" % spec['gmp'].prefix, "--enable-lto", - "--with-gnu-ld", - "--with-gnu-as", "--with-quad"] # Binutils - static_bootstrap_flags = "-static-libstdc++ -static-libgcc" - binutils_options = ["--with-sysroot=/", - "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-boot-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags), - "--with-ld=%s/bin/ld" % spec['binutils'].prefix, - "--with-as=%s/bin/as" % spec['binutils'].prefix] - options.extend(binutils_options) + if spec.satisfies('+binutils'): + static_bootstrap_flags = "-static-libstdc++ -static-libgcc" + binutils_options = ["--with-sysroot=/", + "--with-stage1-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), + "--with-boot-ldflags=%s %s" % + (self.rpath_args, static_bootstrap_flags), + "--with-gnu-ld", + "--with-ld=%s/bin/ld" % spec['binutils'].prefix, + "--with-gnu-as", + "--with-as=%s/bin/as" % spec['binutils'].prefix] + options.extend(binutils_options) # Isl if 'isl' in spec: isl_options = ["--with-isl=%s" % spec['isl'].prefix] options.extend(isl_options) + if sys.platform == 'darwin' : + darwin_options = [ "--with-build-config=bootstrap-debug" ] + options.extend(darwin_options) + build_dir = join_path(self.stage.path, 'spack-build') configure = Executable( join_path(self.stage.source_path, 'configure') ) with working_dir(build_dir, create=True): # Rest of install is straightforward. configure(*options) - make() + if sys.platform == 'darwin' : make("bootstrap") + else: make() make("install") self.write_rpath_specs() @@ -114,7 +133,8 @@ class Gcc(Package): """Generate a spec file so the linker adds a rpath to the libs the compiler used to build the executable.""" if not self.spec_dir: - tty.warn("Could not install specs for %s." % self.spec.format('$_$@')) + tty.warn("Could not install specs for %s." % + self.spec.format('$_$@')) return gcc = Executable(join_path(self.prefix.bin, 'gcc')) @@ -124,5 +144,6 @@ class Gcc(Package): for line in lines: out.write(line + "\n") if line.startswith("*link:"): - out.write("-rpath %s/lib:%s/lib64 \\\n"% (self.prefix, self.prefix)) + out.write("-rpath %s/lib:%s/lib64 \\\n" % + (self.prefix, self.prefix)) set_install_permissions(specs_file) diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py new file mode 100644 index 0000000000..4f1f1ec2dd --- /dev/null +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -0,0 +1,69 @@ +from spack import * + +class Gdal(Package): + """ + GDAL is a translator library for raster and vector geospatial + data formats that is released under an X/MIT style Open Source + license by the Open Source Geospatial Foundation. As a library, + it presents a single raster abstract data model and vector + abstract data model to the calling application for all supported + formats. It also comes with a variety of useful command line + utilities for data translation and processing + """ + + homepage = "http://www.gdal.org/" + url = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz" + list_url = "http://download.osgeo.org/gdal/" + list_depth = 2 + + version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5') + + extends('python') + + variant('hdf5', default=False, description='Enable HDF5 support') + variant('hdf', default=False, description='Enable HDF4 support') + variant('openjpeg', default=False, description='Enable JPEG2000 support') + variant('geos', default=False, description='Enable GEOS support') + variant('kea', default=False, description='Enable KEA support') + variant('netcdf', default=False, description='Enable netcdf support') + + depends_on('swig') + depends_on("hdf5", when='+hdf5') + depends_on("hdf", when='+hdf') + depends_on("openjpeg", when='+openjpeg') + depends_on("geos", when='+geos') + depends_on("kealib", when='+kea') + depends_on("netcdf", when='+netcdf') + depends_on("libtiff") + depends_on("libpng") + depends_on("zlib") + depends_on("proj") + depends_on("py-numpy") + + parallel = False + + def install(self, spec, prefix): + args = [] + args.append("--prefix=%s" % prefix) + args.append("--with-liblzma=yes") + args.append("--with-zlib=%s" % spec['zlib'].prefix) + args.append("--with-python=%s" % spec['python'].prefix.bin + "/python") + args.append("--without-libtool") + + if '+geos' in spec: + args.append('--with-geos=yes') + if '+hdf' in spec: + args.append('--with-hdf4=%s' % spec['hdf'].prefix) + if '+hdf5' in spec: + args.append('--with-hdf5=%s' % spec['hdf5'].prefix) + if '+openjpeg' in spec: + args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix) + if '+kea' in spec: + args.append('--with-kea=yes') + if '+netcdf' in spec: + args.append('--with-netcdf=%s' % spec['netcdf'].prefix) + + configure(*args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py index 4a2657e32f..030703f286 100644 --- a/var/spack/repos/builtin/packages/geos/package.py +++ b/var/spack/repos/builtin/packages/geos/package.py @@ -1,4 +1,5 @@ from spack import * +import os class Geos(Package): """GEOS (Geometry Engine - Open Source) is a C++ port of the Java @@ -10,6 +11,10 @@ class Geos(Package): homepage = "http://trac.osgeo.org/geos/" url = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2" + # Verison 3.5.0 supports Autotools and CMake + version('3.5.0', '136842690be7f504fba46b3c539438dd') + + # Versions through 3.4.2 have CMake, but only Autotools is supported version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae') version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e') version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488') @@ -21,11 +26,22 @@ class Geos(Package): version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1') version('3.3.3', '8454e653d7ecca475153cc88fd1daa26') - extends('python') - depends_on('swig') +# # Python3 is not supported. +# variant('python', default=False, description='Enable Python support') + +# extends('python', when='+python') +# depends_on('python', when='+python') +# depends_on('swig', when='+python') def install(self, spec, prefix): - configure("--prefix=%s" % prefix, - "--enable-python") + args = ["--prefix=%s" % prefix] +# if '+python' in spec: +# os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin', +# 'python' if spec['python'].version[:1][0] <= 2 else 'python3') +# os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig') +# +# args.append("--enable-python") + + configure(*args) make() make("install") diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py new file mode 100644 index 0000000000..05712d7392 --- /dev/null +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -0,0 +1,30 @@ +from spack import * + +class Gettext(Package): + """GNU internationalization (i18n) and localization (l10n) library.""" + homepage = "https://www.gnu.org/software/gettext/" + url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" + + version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + + def install(self, spec, prefix): + options = ['--disable-dependency-tracking', + '--disable-silent-rules', + '--disable-debug', + '--prefix=%s' % prefix, + '--with-included-gettext', + '--with-included-glib', + '--with-included-libcroco', + '--with-included-libunistring', + '--with-emacs', + '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, + '--disable-java', + '--disable-csharp', + '--without-git', # Don't use VCS systems to create these archives + '--without-cvs', + '--without-xz'] + + configure(*options) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py new file mode 100644 index 0000000000..663b758747 --- /dev/null +++ b/var/spack/repos/builtin/packages/googletest/package.py @@ -0,0 +1,24 @@ +from spack import * + +class Googletest(Package): + """Google test framework for C++. Also called gtest.""" + homepage = "https://github.com/google/googletest" + url = "https://github.com/google/googletest/tarball/release-1.7.0" + + version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4') + + depends_on("cmake") + + def install(self, spec, prefix): + which('cmake')('.', *std_cmake_args) + + make() + + # Google Test doesn't have a make install + # We have to do our own install here. + install_tree('include', prefix.include) + + mkdirp(prefix.lib) + install('./libgtest.a', '%s' % prefix.lib) + install('./libgtest_main.a', '%s' % prefix.lib) + diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 242ee100d7..4b915daa68 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -1,5 +1,5 @@ from spack import * -import os +import os, sys class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -12,7 +12,10 @@ class Hypre(Package): version('2.10.1', 'dc048c4cabb3cd549af72591474ad674') version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') - variant('shared', default=True, description="Build shared library version (disables static library)") + # hypre does not know how to build shared libraries on Darwin + variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") + # SuperluDist have conflicting headers with those in Hypre + variant('internal-superlu', default=True, description="Use internal Superlu routines") depends_on("mpi") depends_on("blas") @@ -37,6 +40,12 @@ class Hypre(Package): if '+shared' in self.spec: configure_args.append("--enable-shared") + if '~internal-superlu' in self.spec: + configure_args.append("--without-superlu") + # MLI and FEI do not build without superlu on Linux + configure_args.append("--without-mli") + configure_args.append("--without-fei") + # Hypre's source is staged under ./src so we'll have to manually # cd into it. with working_dir("src"): diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py new file mode 100644 index 0000000000..475d21e1d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -0,0 +1,35 @@ +from spack import * + +class Kealib(Package): + """An HDF5 Based Raster File Format + + KEALib provides an implementation of the GDAL data model. + The format supports raster attribute tables, image pyramids, + meta-data and in-built statistics while also handling very + large files and compression throughout. + + Based on the HDF5 standard, it also provides a base from which + other formats can be derived and is a good choice for long + term data archiving. An independent software library (libkea) + provides complete access to the KEA image format and a GDAL + driver allowing KEA images to be used from any GDAL supported software. + + Development work on this project has been funded by Landcare Research. + """ + homepage = "http://kealib.org/" + url = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz" + + version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d') + + depends_on("hdf5") + + def install(self, spec, prefix): + with working_dir('trunk', create=False): + cmake_args = [] + cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix) + cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include) + cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib) + cmake('.', *cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 9f16708af5..29bc21b65c 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,8 +38,6 @@ 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/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 280e400f69..1d25d59e50 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -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') @@ -133,6 +133,21 @@ class Llvm(Package): } }, { + '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' : { diff --git a/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch new file mode 100644 index 0000000000..b182b167b9 --- /dev/null +++ b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch @@ -0,0 +1,22 @@ +# HG changeset patch +# User Sean Farley <sean@mcs.anl.gov> +# Date 1332269671 18000 +# Tue Mar 20 13:54:31 2012 -0500 +# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e +# Parent 88049269953c67c3fdcc4309bf901508a875f0dc +cmake: add gklib headers to install into include + +diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt +Index: libmetis/CMakeLists.txt +=================================================================== +--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500 ++++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500 +@@ -12,6 +12,8 @@ endif() + if(METIS_INSTALL) + install(TARGETS metis + LIBRARY DESTINATION lib + RUNTIME DESTINATION lib + ARCHIVE DESTINATION lib) ++ install(FILES gklib_defs.h DESTINATION include) ++ install(FILES gklib_rename.h DESTINATION include) + endif() diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index bbfc4de7d1..9301135f9f 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -24,7 +24,7 @@ ############################################################################## from spack import * - +import glob,sys class Metis(Package): """ @@ -49,6 +49,8 @@ class Metis(Package): depends_on('gdb', when='+gdb') + patch('install_gklib_defs_rename.patch') + def install(self, spec, prefix): options = [] @@ -80,4 +82,15 @@ class Metis(Package): with working_dir(build_directory, create=True): cmake(source_directory, *options) make() - make("install")
\ No newline at end of file + make("install") + + # install GKlib headers, which will be needed for ParMETIS + GKlib_dist = join_path(prefix.include,'GKlib') + mkdirp(GKlib_dist) + fs = glob.glob(join_path(source_directory,'GKlib',"*.h")) + for f in fs: + install(f, GKlib_dist) + + # The shared library is not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index c4d9940bb7..b20dc8dd60 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -54,7 +54,7 @@ class Mpich(Package): env.set('MPICH_F90', spack_f90) env.set('MPICH_FC', spack_fc) - def setup_dependent_python_module(self, module, spec, dep_spec): + 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') diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc index 2e6a041878..22d8f5518a 100644 --- a/var/spack/repos/builtin/packages/mumps/Makefile.inc +++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc @@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH) IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH) PLAT = -LIBEXT = .a -OUTC = -o +OUTC = -o OUTF = -o RM = /bin/rm -f -AR = ar vr -RANLIB = ranlib INCSEQ = -I$(topdir)/libseq LIBSEQ = -L$(topdir)/libseq -lmpiseq diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 44a37903cc..26440ab7c8 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -1,6 +1,5 @@ from spack import * -import os - +import os, sys class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -19,11 +18,12 @@ class Mumps(Package): 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') + variant('shared', default=True, description='Build shared libraries') + - depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') - depends_on('metis', when='~parmetis+metis') + depends_on('metis', when='+metis') depends_on('parmetis', when="+parmetis") depends_on('blas') depends_on('lapack') @@ -38,11 +38,11 @@ class Mumps(Package): 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( @@ -54,18 +54,25 @@ class Mumps(Package): if '+ptscotch' in self.spec: orderings.append('-Dptscotch') - if '+parmetis' in self.spec or '+metis' in self.spec: + 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[libname].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)]) + ["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') - if '+parmetis' in self.spec: - orderings.append('-Dparmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) + # when building shared libs need -fPIC, otherwise + # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC + fpic = '-fPIC' if '+shared' in self.spec else '' # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers if '+idx64' in self.spec: @@ -73,14 +80,14 @@ class Mumps(Package): # 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']) + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O -DINTSIZE64' % fpic]) else: makefile_conf.extend( - ['OPTF = -O -DALLOW_NON_INIT', - 'OPTL = -O ', - 'OPTC = -O ']) + ['OPTF = %s -O -DALLOW_NON_INIT' % fpic, + 'OPTL = %s -O ' % fpic, + 'OPTC = %s -O ' % fpic]) if '+mpi' in self.spec: @@ -101,12 +108,33 @@ class Mumps(Package): # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER makefile_conf.append("CDEFS = -DAdd_") - + if '+shared' in self.spec: + if sys.platform == 'darwin': + # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + makefile_conf.extend([ + 'LIBEXT=.dylib', + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT=.so', + 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, + 'RANLIB=echo' + ]) + else: + makefile_conf.extend([ + 'LIBEXT = .a', + 'AR = ar vr', + 'RANLIB = ranlib' + ]) + + 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) @@ -117,7 +145,7 @@ class Mumps(Package): def install(self, spec, prefix): make_libs = [] - # the coice to compile ?examples is to have kind of a sanity + # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: make_libs.append('sexamples') @@ -130,10 +158,25 @@ class Mumps(Package): make_libs.append('zexamples') self.write_makefile_inc() - - make(*make_libs) + + # Build fails in parallel + make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) if '~mpi' in spec: - install('libseq/libmpiseq.a', prefix.lib) + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' + install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) + + # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI + # FIXME: use something like numdiff to compare blessed output with the current + with working_dir('examples'): + if '+float' in spec: + os.system('./ssimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./csimpletest < input_simpletest_real') + if '+double' in spec: + os.system('./dsimpletest < input_simpletest_real') + if '+complex' in spec: + os.system('./zsimpletest < input_simpletest_cmplx') diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py new file mode 100644 index 0000000000..19ca8ce287 --- /dev/null +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Muparser(Package): + """C++ math expression parser library.""" + homepage = "http://muparser.beltoforion.de/" + url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz" + + version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7') + + def install(self, spec, prefix): + options = ['--disable-debug', + '--disable-dependency-tracking', + '--prefix=%s' % prefix] + + configure(*options) + + make(parallel=False) + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py new file mode 100644 index 0000000000..5334dfb853 --- /dev/null +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -0,0 +1,15 @@ +from spack import * + +class NetcdfCxx(Package): + """C++ compatibility bindings for NetCDF""" + homepage = "http://www.unidata.ucar.edu/software/netcdf" + url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz" + + version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c') + + depends_on('netcdf') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index 227362399a..b60a2c4e9a 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -43,6 +43,13 @@ class Netcdf(Package): "--enable-dap" ] + # Make sure Netcdf links against Spack's curl + # Otherwise it may pick up system's curl, which could lead to link errors: + # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0' + LIBS.append("-lcurl") + CPPFLAGS.append("-I%s" % spec['curl'].prefix.include) + LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib) + if '+mpi' in spec: config_args.append('--enable-parallel4') diff --git a/var/spack/repos/builtin/packages/netlib-blas/package.py b/var/spack/repos/builtin/packages/netlib-blas/package.py deleted file mode 100644 index 85e97323d3..0000000000 --- a/var/spack/repos/builtin/packages/netlib-blas/package.py +++ /dev/null @@ -1,46 +0,0 @@ -from spack import * -import os - - -class NetlibBlas(Package): - """Netlib reference BLAS""" - homepage = "http://www.netlib.org/lapack/" - url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" - - version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') - - variant('fpic', default=False, description="Build with -fpic compiler option") - - # virtual dependency - provides('blas') - - # Doesn't always build correctly in parallel - parallel = False - - def patch(self): - os.symlink('make.inc.example', 'make.inc') - - mf = FileFilter('make.inc') - mf.filter('^FORTRAN.*', 'FORTRAN = f90') - mf.filter('^LOADER.*', 'LOADER = f90') - mf.filter('^CC =.*', 'CC = cc') - - if '+fpic' in self.spec: - mf.filter('^OPTS.*=.*', 'OPTS = -O2 -frecursive -fpic') - mf.filter('^CFLAGS =.*', 'CFLAGS = -O3 -fpic') - - - def install(self, spec, prefix): - make('blaslib') - - # Tests that blas builds correctly - make('blas_testing') - - # No install provided - mkdirp(prefix.lib) - install('librefblas.a', prefix.lib) - - # Blas virtual package should provide blas.a and libblas.a - with working_dir(prefix.lib): - symlink('librefblas.a', 'blas.a') - symlink('librefblas.a', 'libblas.a') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 741f4af421..c4b7ce3b04 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -1,16 +1,15 @@ from spack import * + class NetlibLapack(Package): """ - LAPACK version 3.X is a comprehensive FORTRAN library that does - linear algebra operations including matrix inversions, least - squared solutions to linear sets of equations, eigenvector - analysis, singular value decomposition, etc. It is a very - comprehensive and reputable package that has found extensive - use in the scientific community. + LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix + inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value + decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the + scientific community. """ homepage = "http://www.netlib.org/lapack/" - url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') @@ -19,42 +18,34 @@ class NetlibLapack(Package): version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70') version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') - variant('shared', default=False, description="Build shared library version") + variant('debug', default=False, description='Activates the Debug build type') + variant('shared', default=True, description="Build shared library version") + variant('external-blas', default=False, description='Build lapack with an external blas') + + variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface') # virtual dependency + provides('blas', when='~external-blas') provides('lapack') - # blas is a virtual dependency. - depends_on('blas') - depends_on('cmake') - - # Doesn't always build correctly in parallel - parallel = False - - @when('^netlib-blas') - def get_blas_libs(self): - 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')] - + depends_on('blas', when='+external-blas') 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') - - cmake_args += std_cmake_args - - cmake(*cmake_args) - make() - make("install") - + cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] + if '+external-blas' in spec: + # TODO : the mechanism to specify the library should be more general, + # TODO : but this allows to have an hook to an external blas + cmake_args.extend([ + '-DUSE_OPTIMIZED_BLAS:BOOL=ON', + '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a') + ]) + + cmake_args.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + 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 index 62abfcc48e..d59f8e41fe 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" @@ -11,16 +12,16 @@ class NetlibScalapack(Package): 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): + + 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'), @@ -40,10 +41,16 @@ class NetlibScalapack(Package): make() make("install") - def setup_dependent_python_module(self, module, spec, dependent_spec): + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) + + + 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['scalapack'] else '.a' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' - spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib - spec['scalapack'].cc_link = spec['scalapack'].fc_link - spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)] + 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/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py new file mode 100644 index 0000000000..4d5081ac9d --- /dev/null +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -0,0 +1,51 @@ +from spack import * +import platform, sys + +class Oce(Package): + """ + Open CASCADE Community Edition: + patches/improvements/experiments contributed by users over the official Open CASCADE library. + """ + homepage = "https://github.com/tpaviot/oce" + url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" + + version('0.17.1', '36c67b87093c675698b483454258af91') + version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') + version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.15' , '7ec541a1c350ca8a684f74980e48801c') + + depends_on('cmake@2.8:') + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + options.extend([ + '-DOCE_INSTALL_PREFIX=%s' % prefix, + '-DOCE_BUILD_SHARED_LIB:BOOL=ON', + '-DOCE_BUILD_TYPE:STRING=Release', + '-DOCE_DATAEXCHANGE:BOOL=ON', + '-DOCE_DISABLE_X11:BOOL=ON', + '-DOCE_DRAW:BOOL=OFF', + '-DOCE_MODEL:BOOL=ON', + '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb + '-DOCE_OCAF:BOOL=ON', + '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', + '-DOCE_VISUALISATION:BOOL=OFF', + '-DOCE_WITH_FREEIMAGE:BOOL=OFF', + '-DOCE_WITH_GL2PS:BOOL=OFF', + '-DOCE_WITH_OPENCL:BOOL=OFF' + ]) + + if platform.system() == 'Darwin': + options.extend([ + '-DOCE_OSX_USE_COCOA:BOOL=ON', + ]) + + cmake('.', *options) + + make("install/strip") + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin'): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 38b355159d..6e99c23652 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -62,7 +62,7 @@ class Octave(Package): depends_on('qrupdate', when='+qrupdate') #depends_on('qscintilla', when='+qscintilla) # TODO: add package depends_on('qt', when='+qt') - depends_on('SuiteSparse', when='+suitesparse') + depends_on('suite-sparse',when='+suitesparse') depends_on('zlib', when='+zlib') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 781a1e2ec8..1d10f217c4 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -6,6 +6,7 @@ class Openblas(Package): homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') @@ -14,7 +15,14 @@ class Openblas(Package): provides('lapack') def install(self, spec, prefix): - make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') + extra=[] + if spec.satisfies('@0.2.16'): + extra.extend([ + 'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_ + ]) + + make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra) + make("tests") make('install', "PREFIX='%s'" % prefix) lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py new file mode 100644 index 0000000000..afec197d11 --- /dev/null +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -0,0 +1,26 @@ +from spack import * + +class Openjpeg(Package): + """ + OpenJPEG is an open-source JPEG 2000 codec written in C language. + It has been developed in order to promote the use of JPEG 2000, a + still-image compression standard from the Joint Photographic + Experts Group (JPEG). + Since April 2015, it is officially recognized by ISO/IEC and + ITU-T as a JPEG 2000 Reference Software. + """ + homepage = "https://github.com/uclouvain/openjpeg" + url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz" + + version('2.1' , '3e1c451c087f8462955426da38aa3b3d') + version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') + version('2.0' , 'cdf266530fee8af87454f15feb619609') + version('1.5.2', '545f98923430369a6b046ef3632ef95c') + version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py new file mode 100644 index 0000000000..1e2969fe64 --- /dev/null +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -0,0 +1,34 @@ +from spack import * + +class P4est(Package): + """Dynamic management of a collection (a forest) of adaptive octrees in parallel""" + homepage = "http://www.p4est.org" + url = "http://p4est.github.io/release/p4est-1.1.tar.gz" + + version('1.1', '37ba7f4410958cfb38a2140339dbf64f') + + # disable by default to make it work on frontend of clusters + variant('tests', default=False, description='Run small tests') + + depends_on('mpi') + + def install(self, spec, prefix): + options = ['--enable-mpi', + '--enable-shared', + '--disable-vtk-binary', + '--without-blas', + 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', + 'CFLAGS=-O2', + 'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers + 'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + 'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + 'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + ] + + configure('--prefix=%s' % prefix, *options) + + make() + if '+tests' in self.spec: + make("check") + + make("install") 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..e4f2729483 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -0,0 +1,71 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ca945dd..aff8b5f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -23,7 +23,7 @@ else() + set(ParMETIS_LIBRARY_TYPE STATIC) + endif() + +-include(${GKLIB_PATH}/GKlibSystem.cmake) ++include_directories(${GKLIB_PATH}) + + # List of paths that the compiler will search for header files. + # i.e., the -I equivalent +@@ -33,7 +33,7 @@ include_directories(${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) ++find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib) + add_subdirectory(include) + add_subdirectory(libparmetis) + add_subdirectory(programs) +diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt +index 9cfc8a7..e0c4de7 100644 +--- a/libparmetis/CMakeLists.txt ++++ b/libparmetis/CMakeLists.txt +@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c) + # Create libparmetis + add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources}) + # Link with metis and MPI libraries. +-target_link_libraries(parmetis metis ${MPI_LIBRARIES}) ++target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES}) ++if(UNIX) ++ target_link_libraries(parmetis m) ++endif() + set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + + install(TARGETS parmetis +diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h +index c1daeeb..07511f6 100644 +--- a/libparmetis/parmetislib.h ++++ b/libparmetis/parmetislib.h +@@ -20,13 +20,12 @@ + + #include <parmetis.h> + +-#include "../metis/libmetis/gklib_defs.h" ++#include <gklib_defs.h> + +-#include <mpi.h> ++#include <mpi.h> + + #include <rename.h> + #include <defs.h> + #include <struct.h> + #include <macros.h> + #include <proto.h> +- +diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h +index e26cd2d..d156480 100644 +--- a/programs/parmetisbin.h ++++ b/programs/parmetisbin.h +@@ -19,7 +19,7 @@ + #include <GKlib.h> + #include <parmetis.h> + +-#include "../metis/libmetis/gklib_defs.h" ++#include <gklib_defs.h> + #include "../libparmetis/rename.h" + #include "../libparmetis/defs.h" + #include "../libparmetis/struct.h" diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c897dec7e4..ff4370aa4b 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -24,10 +24,7 @@ ############################################################################## 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 - +import sys 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=spec['metis'].prefix.include), + '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix), '-DCMAKE_C_COMPILER:STRING=mpicc', '-DCMAKE_CXX_COMPILER:STRING=mpicxx']) @@ -78,18 +79,11 @@ 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) + + # The shared library is not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/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 efe172fc08..5c1fc6cc92 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -17,14 +17,18 @@ class Petsc(Package): 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('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('complex', default=False, description='Build with complex numbers') + variant('debug', default=False, description='Compile in debug mode') - 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') + 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 (only parallel)') + variant('mumps', default=True, description='Activates support for MUMPS (only parallel)') + variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)') # Virtual dependencies depends_on('blas') @@ -40,7 +44,13 @@ class Petsc(Package): depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('parmetis', when='+metis+mpi') - depends_on('hypre', when='+hypre+mpi') + # Hypre does not support complex numbers. + # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers + # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py + depends_on('hypre~internal-superlu', when='+hypre+mpi~complex') + depends_on('superlu-dist', when='+superlu-dist+mpi') + depends_on('mumps+mpi', when='+mumps+mpi') + depends_on('scalapack', when='+mumps+mpi') def mpi_dependent_options(self): if '~mpi' in self.spec: @@ -55,7 +65,7 @@ class Petsc(Package): # 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') + for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist') if ('+'+x) in self.spec] if errors: errors = ['incompatible variants given'] + errors @@ -68,15 +78,17 @@ class Petsc(Package): return compiler_opts def install(self, spec, prefix): - options = [] + options = ['--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ '--with-precision=%s' % ('double' if '+double' in spec else 'single'), + '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), + '--with-debugging=%s' % ('1' if '+debug' 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'): + for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'): options.append( '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) ) @@ -84,9 +96,24 @@ class Petsc(Package): options.append( '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) ) + # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a + if 'superlu-dist' in spec: + options.extend([ + '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include, + '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'), + '--with-superlu_dist=1' + ]) + else: + options.append( + '--with-superlu_dist=0' + ) configure('--prefix=%s' % prefix, *options) # PETSc has its own way of doing parallel make. make('MAKE_NP=%s' % make_jobs, parallel=False) make("install") + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up PETSC_DIR for everyone using PETSc package + spack_env.set('PETSC_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py new file mode 100644 index 0000000000..0aa4208b4d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyBottleneck(Package): + """Bottleneck is a collection of fast NumPy array functions written in Cython.""" + homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0" + url = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz" + + version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') + + extends('python', ignore=r'bin/f2py$') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py index 68eb735ad9..072355026e 100644 --- a/var/spack/repos/builtin/packages/py-cython/package.py +++ b/var/spack/repos/builtin/packages/py-cython/package.py @@ -3,10 +3,14 @@ from spack import * class PyCython(Package): """The Cython compiler for writing C extensions for the Python language.""" homepage = "https://pypi.python.org/pypi/cython" - url = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz" + url = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz" - version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') + version('0.23.5', '66b62989a67c55af016c916da36e7514') + version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e') + + # These versions contain illegal Python3 code... version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6') + version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') extends('python') diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py index 0a17f2f2d2..b67e91ace6 100644 --- a/var/spack/repos/builtin/packages/py-dateutil/package.py +++ b/var/spack/repos/builtin/packages/py-dateutil/package.py @@ -7,6 +7,7 @@ class PyDateutil(Package): version('2.4.0', '75714163bb96bedd07685cdb2071b8bc') version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2') + version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py deleted file mode 100644 index 59005428e4..0000000000 --- a/var/spack/repos/builtin/packages/py-libxml2/package.py +++ /dev/null @@ -1,15 +0,0 @@ -from spack import * - -class PyLibxml2(Package): - """A Python wrapper around libxml2.""" - homepage = "https://xmlsoft.org/python.html" - url = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz" - - version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3') - - extends('python') - depends_on('libxml2') - depends_on('libxslt') - - def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 2167735fb8..45e77dd631 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -12,7 +12,7 @@ class PyMatplotlib(Package): variant('gui', default=False, description='Enable GUI') variant('ipython', default=False, description='Enable ipython support') - extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') + extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$') depends_on('py-pyside', when='+gui') depends_on('py-ipython', when='+ipython') diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py new file mode 100644 index 0000000000..7faa15ad25 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-netcdf/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyNetcdf(Package): + """Python interface to the netCDF Library.""" + homepage = "http://unidata.github.io/netcdf4-python" + url = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel" + + version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af') + + extends('python') + depends_on('py-numpy') + depends_on('py-cython') + depends_on('netcdf') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index 4fee99098e..c2c2b52e03 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -10,6 +10,7 @@ class PyNose(Package): version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') + version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b') extends('python', ignore=r'bin/nosetests.*$') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 89f8a525b1..081a79dec6 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -7,8 +7,9 @@ class PyNumexpr(Package): url = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz" version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd') + version('2.5', '84f66cced45ba3e30dcf77a937763aaa') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 0354811186..40988fb44a 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -1,24 +1,44 @@ from spack import * class PyNumpy(Package): - """array processing for numbers, strings, records, and objects.""" - homepage = "https://pypi.python.org/pypi/numpy" + """NumPy is the fundamental package for scientific computing with Python. + It contains among other things: a powerful N-dimensional array object, + sophisticated (broadcasting) functions, tools for integrating C/C++ and + Fortran code, and useful linear algebra, Fourier transform, and random + number capabilities""" + homepage = "http://www.numpy.org/" url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" - version('1.9.1', '78842b73560ec378142665e712ae4ad9') - version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b') + version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad') + version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.9.1', '78842b73560ec378142665e712ae4ad9') - variant('blas', default=True) + + variant('blas', default=True) + variant('lapack', default=True) extends('python') depends_on('py-nose') - depends_on('netlib-blas+fpic', when='+blas') - depends_on('netlib-lapack+shared', when='+blas') + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') def install(self, spec, prefix): + libraries = [] + library_dirs = [] + if '+blas' in spec: + libraries.append('blas') + library_dirs.append(spec['blas'].prefix.lib) + if '+lapack' in spec: + libraries.append('lapack') + library_dirs.append(spec['lapack'].prefix.lib) + + if '+blas' in spec or '+lapack' in spec: with open('site.cfg', 'w') as f: f.write('[DEFAULT]\n') - f.write('libraries=lapack,blas\n') - f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix)) + f.write('libraries=%s\n' % ','.join(libraries)) + f.write('library_dirs=%s\n' % ':'.join(library_dirs)) + python('setup.py', 'install', '--prefix=%s' % prefix) + diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 5b9997faa9..2320b1f92f 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -8,18 +8,15 @@ class PyPandas(Package): version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') + version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - extends('python') + extends('python', ignore=r'bin/f2py$') depends_on('py-dateutil') depends_on('py-numpy') - depends_on('py-matplotlib') - depends_on('py-scipy') depends_on('py-setuptools') depends_on('py-pytz') - depends_on('libdrm') - depends_on('libpciaccess') - depends_on('llvm') - depends_on('mesa') + depends_on('py-numexpr') + depends_on('py-bottleneck') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py index da6311a784..060cf0cde4 100644 --- a/var/spack/repos/builtin/packages/py-pytz/package.py +++ b/var/spack/repos/builtin/packages/py-pytz/package.py @@ -7,6 +7,7 @@ class PyPytz(Package): version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7') version('2015.4', '417a47b1c432d90333e42084a605d3d8') + version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29') extends('python') diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index 3a1124cc15..c2161c90c4 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -2,11 +2,12 @@ from spack import * class PyScipy(Package): """Scientific Library for Python.""" - homepage = "https://pypi.python.org/pypi/scipy" + homepage = "http://www.scipy.org/" url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" - version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') + version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224') version('0.15.1', 'be56cd8e60591d6332aac792a5880110') + version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') extends('python') depends_on('py-nose') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 26c048bfd4..c6d9be1add 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -9,6 +9,7 @@ class PySetuptools(Package): version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') version('19.2', '78353b1f80375ca5e088f4b4627ffe03') + version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') extends('python') diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py index 05c5bd00a9..df277100f7 100644 --- a/var/spack/repos/builtin/packages/py-six/package.py +++ b/var/spack/repos/builtin/packages/py-six/package.py @@ -6,6 +6,7 @@ class PySix(Package): url = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz" version('1.9.0', '476881ef4012262dfc8adc645ee786c4') + version('1.10.0', '34eed507548117b2ab523ab14b2f8b55') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py new file mode 100644 index 0000000000..984b4196b1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -0,0 +1,19 @@ +from spack import * + +class PyTuiview(Package): + """ + TuiView is a lightweight raster GIS with powerful raster attribute + table manipulation abilities. + """ + homepage = "https://bitbucket.org/chchrsc/tuiview" + url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" + + version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30') + + extends("python") + depends_on("py-pyqt") + depends_on("py-numpy") + depends_on("gdal") + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py index 037a6fc59f..09303d37b4 100644 --- a/var/spack/repos/builtin/packages/py-virtualenv/package.py +++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py @@ -8,6 +8,7 @@ class PyVirtualenv(Package): version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49') version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db') + version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc') extends('python') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 4f55bc803e..f5237c3b57 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -105,10 +105,13 @@ class Python(Package): pythonpath = ':'.join(python_paths) spack_env.set('PYTHONPATH', pythonpath) - run_env.set('PYTHONPATH', pythonpath) + # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH + if extension_spec.package.extends(self.spec): + run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir)) - def modify_module(self, module, spec, ext_spec): + + def setup_dependent_package(self, module, ext_spec): """ Called before python modules' install() methods. @@ -118,17 +121,18 @@ class Python(Package): """ # Python extension builds can have a global python executable function if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): - module.python = Executable(join_path(spec.prefix.bin, 'python3')) + module.python = Executable(join_path(self.spec.prefix.bin, 'python3')) else: - module.python = Executable(join_path(spec.prefix.bin, 'python')) + module.python = Executable(join_path(self.spec.prefix.bin, 'python')) # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir) - # Make the site packages directory if it does not exist already. - mkdirp(module.site_packages_dir) + # Make the site packages directory for extensions, if it does not exist already. + if ext_spec.package.is_extension: + mkdirp(module.site_packages_dir) # ======================================================================== # Handle specifics of activating and deactivating python modules. diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 7ff1898ce9..e13677e4d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -30,7 +30,7 @@ class Ruby(Package): # The actual installation path for this gem spack_env.set('GEM_HOME', extension_spec.prefix) - def modify_module(self, module, spec, ext_spec): + def setup_dependent_package(self, module, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -39,5 +39,5 @@ class Ruby(Package): gem('install', '<gem-name>.gem') """ # 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')) + module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby')) + module.gem = Executable(join_path(self.spec.prefix.bin, 'gem')) diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index d1aed78e0e..b7894e4d2b 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -5,24 +5,35 @@ class Silo(Package): 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" + base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo" + version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8') + version('4.9', 'a83eda4f06761a86726e918fc55e782a') version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') variant('fortran', default=True, description='Enable Fortran support') + variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') - depends_on("hdf5") + depends_on('hdf5') + depends_on('qt', when='+silex') def install(self, spec, prefix): config_args = [ '--enable-fortran' if '+fortran' in spec else '--disable-fortran', + '--enable-silex' if '+silex' in spec else '--disable-silex', ] + if '+silex' in spec: + config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix) + 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), + '--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") + make('install') + + def url_for_version(self, version): + return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version) diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py new file mode 100644 index 0000000000..8b5f24394f --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -0,0 +1,49 @@ +import os +from spack import * + + +class Slepc(Package): + """ + Scalable Library for Eigenvalue Computations. + """ + + homepage = "http://www.grycap.upv.es/slepc" + url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz" + + version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') + + variant('arpack', default=False, description='Enables Arpack wrappers') + + depends_on('petsc') + depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi') + depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi') + + def install(self, spec, prefix): + # set SLEPC_DIR for installation + os.environ['SLEPC_DIR'] = self.stage.source_path + + options = [] + + if '+arpack' in spec: + options.extend([ + '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib, + ]) + if 'arpack-ng~mpi' in spec: + options.extend([ + '--with-arpack-flags=-larpack' + ]) + else: + options.extend([ + '--with-arpack-flags=-lparpack,-larpack' + ]) + + configure('--prefix=%s' % prefix, *options) + + make('MAKE_NP=%s' % make_jobs, parallel=False) + #FIXME: + # make('test') + make('install') + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up SLEPC_DIR for everyone using SLEPc package + spack_env.set('SLEPC_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py new file mode 100644 index 0000000000..5db1c3eb92 --- /dev/null +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -0,0 +1,77 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +#import os + +class Subversion(Package): + """Apache Subversion - an open source version control system.""" + homepage = 'https://subversion.apache.org/' + url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz' + + version('1.8.13', '8065b3698d799507fb72dd7926ed32b6') + version('1.9.3', 'a92bcfaec4e5038f82c74a7b5bbd2f46') + + depends_on('apr') + depends_on('apr-util') + depends_on('zlib') + depends_on('sqlite') + + # Optional: We need swig if we want the Perl, Python or Ruby + # bindings. + #depends_on('swig') + #depends_on('python') + #depends_on('perl') + #depends_on('ruby') + + def install(self, spec, prefix): + + # configure, build, install: + # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html + options = ['--prefix=%s' % prefix] + options.append('--with-apr=%s' % spec['apr'].prefix) + options.append('--with-apr-util=%s' % spec['apr-util'].prefix) + options.append('--with-zlib=%s' % spec['zlib'].prefix) + options.append('--with-sqlite=%s' % spec['sqlite'].prefix) + #options.append('--with-swig=%s' % spec['swig'].prefix) + + configure(*options) + make() + make('install') + + # python bindings + #make('swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + #make('install-swig-py', + # 'swig-pydir=/usr/lib/python2.7/site-packages/libsvn', + # 'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn') + + # perl bindings + #make('swig-pl') + #make('install-swig-pl') + + # ruby bindings + #make('swig-rb') + #make('isntall-swig-rb') diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 6e130d118f..c2196dcec4 100644 --- a/var/spack/repos/builtin/packages/SuiteSparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -1,7 +1,7 @@ from spack import * -class Suitesparse(Package): +class SuiteSparse(Package): """ SuiteSparse is a suite of sparse matrix algorithms """ @@ -23,5 +23,14 @@ class Suitesparse(Package): # FIXME : this actually uses the current workaround # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') + make('install', 'INSTALL=%s' % prefix, + # inject Spack compiler wrappers + 'AUTOCC=no', + 'CC=cc', + 'CXX=c++', + 'F77=f77', + + # BLAS arguments require path to libraries + 'BLAS=-lblas', + 'LAPACK=-llapack') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index c4c76909b3..ddcb7f9225 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -1,4 +1,5 @@ from spack import * +import glob class SuperluDist(Package): """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" @@ -52,12 +53,13 @@ class SuperluDist(Package): # system "make" # need to install by hand - headers_location = join_path(self.prefix.include,'superlu_dist') + headers_location = self.prefix.include 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) + mkdirp(prefix.lib) + + headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h')) + for h in headers: + install(h,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/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py new file mode 100644 index 0000000000..56ffe4c27c --- /dev/null +++ b/var/spack/repos/builtin/packages/tbb/package.py @@ -0,0 +1,79 @@ +from spack import * +import os +import glob + +class Tbb(Package): + """Widely used C++ template library for task parallelism. + Intel Threading Building Blocks (Intel TBB) lets you easily write parallel + C++ programs that take full advantage of multicore performance, that are + portable and composable, and that have future-proof scalability. + """ + homepage = "http://www.threadingbuildingblocks.org/" + + # Only version-specific URL's work for TBB + version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz') + + def coerce_to_spack(self,tbb_build_subdir): + for compiler in ["icc","gcc","clang"]: + fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler )) + for f in fs: + lines = open(f).readlines() + of = open(f,"w") + for l in lines: + if l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CPLUS = $(CXX)\n") + elif l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CONLY = $(CC)\n") + else: + of.write(l); + + def install(self, spec, prefix): + # + # we need to follow TBB's compiler selection logic to get the proper build + link flags + # but we still need to use spack's compiler wrappers + # to accomplish this, we do two things: + # + # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile + # + # * patch tbb's build system to use the compiler wrappers (CC, CXX) for + # icc, gcc, clang + # (see coerce_to_spack()) + # + self.coerce_to_spack("build") + + if spec.satisfies('%clang'): + tbb_compiler = "clang" + elif spec.satisfies('%intel'): + tbb_compiler = "icc" + else: + tbb_compiler = "gcc" + + + mkdirp(prefix) + mkdirp(prefix.lib) + + # + # tbb does not have a configure script or make install target + # we simply call make, and try to put the pieces together + # + make("compiler=%s" %(tbb_compiler)) + + # install headers to {prefix}/include + install_tree('include',prefix.include) + + # install libs to {prefix}/lib + tbb_lib_names = ["libtbb", + "libtbbmalloc", + "libtbbmalloc_proxy"] + + for lib_name in tbb_lib_names: + # install release libs + fs = glob.glob(join_path("build","*release",lib_name + ".*")) + for f in fs: + install(f, prefix.lib) + # install debug libs if they exist + fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*")) + for f in fs: + install(f, prefix.lib) diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index edc40476e3..6223848c68 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -1,15 +1,22 @@ from spack import * +import os, sys, glob - +# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it: +# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111 +# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package +# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh +# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb +# and some relevant documentation/examples: +# https://github.com/trilinos/Trilinos/issues/175 class Trilinos(Package): - """ - The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented + """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. """ homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') version('12.0.1', 'bd99741d047471e127b8296b2ec08017') @@ -17,8 +24,16 @@ class Trilinos(Package): version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds a debug version of the libraries') + variant('metis', default=True, description='Compile with METIS and ParMETIS') + variant('mumps', default=True, description='Compile with support for MUMPS solvers') + variant('superlu-dist', default=True, description='Compile with SuperluDist solvers') + variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('hdf5', default=True, description='Compile with HDF5') + variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers') + # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors + variant('python', default=False, description='Build python wrappers') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds a debug version of the libraries') # Everything should be compiled with -fpic depends_on('blas') @@ -27,28 +42,205 @@ class Trilinos(Package): depends_on('matio') depends_on('glm') depends_on('swig') + depends_on('metis',when='+metis') + depends_on('suite-sparse',when='+suite-sparse') # MPI related dependencies depends_on('mpi') depends_on('netcdf+mpi') + depends_on('parmetis',when='+metis') + # Trilinos' Tribits config system is limited which makes it + # very tricky to link Amesos with static MUMPS, see + # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html + # One could work it out by getting linking flags from mpif90 --showme:link (or alike) + # and adding results to -DTrilinos_EXTRA_LINK_FLAGS + # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and + # it may work at the end. But let's avoid all this by simply using shared libs + depends_on('mumps@5.0:+mpi+shared',when='+mumps') + depends_on('scalapack',when='+mumps') + depends_on('superlu-dist',when='+superlu-dist') + depends_on('hypre~internal-superlu',when='+hypre') + depends_on('hdf5+mpi',when='+hdf5') + + depends_on('python',when='+python') - depends_on('python') # Needs py-numpy activated + patch('umfpack_from_suitesparse.patch') + + # check that the combination of variants makes sense + def variants_check(self): + if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'): + # For Trilinos v11 we need to force SuperLUDist=OFF, + # since only the deprecated SuperLUDist v3.3 together with an Amesos patch + # is working. + raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:') def install(self, spec, prefix): + self.variants_check() + + cxx_flags = [] options = [] options.extend(std_cmake_args) + mpi_bin = spec['mpi'].prefix.bin options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', + '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON', + '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF', '-DTrilinos_ENABLE_TESTS:BOOL=OFF', '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', - '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'), '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'), - '-DTPL_ENABLE_MPI:STRING=ON', - '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, - '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix + '-DTPL_ENABLE_MPI:BOOL=ON', + '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix, + '-DTPL_ENABLE_BLAS=ON', + '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names + '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib, + '-DTPL_ENABLE_LAPACK=ON', + '-DLAPACK_LIBRARY_NAMES=lapack', + '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix, + '-DTPL_ENABLE_Boost:BOOL=ON', + '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include, + '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib, + '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON', + '-DTrilinos_ENABLE_CXX11:BOOL=ON', + '-DTPL_ENABLE_Netcdf:BOOL=ON', + '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'), + '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'), ]) + # Fortran lib + libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read()) + options.extend([ + '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran, + '-DTrilinos_ENABLE_Fortran=ON' + ]) + + # for build-debug only: + #options.extend([ + # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE' + #]) + + # suite-sparse related + if '+suite-sparse' in spec: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file? + #'-DTPL_ENABLE_Cholmod:BOOL=ON', + #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DTPL_ENABLE_UMFPACK:BOOL=ON', + '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib, + '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include, + '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig' + ]) + else: + options.extend([ + '-DTPL_ENABLE_Cholmod:BOOL=OFF', + '-DTPL_ENABLE_UMFPACK:BOOL=OFF', + ]) + + # metis / parmetis + if '+metis' in spec: + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=ON', + '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib, + '-DMETIS_LIBRARY_NAMES=metis', + '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include, + '-DTPL_ENABLE_ParMETIS:BOOL=ON', + '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib), + '-DParMETIS_LIBRARY_NAMES=parmetis;metis', + '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include + ]) + else: + options.extend([ + '-DTPL_ENABLE_METIS:BOOL=OFF', + '-DTPL_ENABLE_ParMETIS:BOOL=OFF', + ]) + + # mumps / scalapack + if '+mumps' in spec: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=ON', + '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib, + '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important! + '-DTPL_ENABLE_SCALAPACK:BOOL=ON', + '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64 + ]) + # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS + cxx_flags.extend([ + '-DMUMPS_5_0' + ]) + else: + options.extend([ + '-DTPL_ENABLE_MUMPS:BOOL=OFF', + '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', + ]) + + # superlu-dist: + if '+superlu-dist' in spec: + # Amesos, conflicting types of double and complex SLU_D + # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html + # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html + options.extend([ + '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF', + '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF' + ]) + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=ON', + '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib, + '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include + ]) + if spec.satisfies('^superlu-dist@4.0:'): + options.extend([ + '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON' + ]) + else: + options.extend([ + '-DTPL_ENABLE_SuperLUDist:BOOL=OFF', + ]) + + + # python + if '+python' in spec: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON' + ]) + else: + options.extend([ + '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF' + ]) + + # collect CXX flags: + options.extend([ + '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)), + ]) + + # disable due to compiler / config errors: + options.extend([ + '-DTrilinos_ENABLE_SEACAS=OFF', + '-DTrilinos_ENABLE_Pike=OFF', + '-DTrilinos_ENABLE_STK=OFF' + ]) + if sys.platform == 'darwin': + options.extend([ + '-DTrilinos_ENABLE_FEI=OFF' + ]) + + with working_dir('spack-build', create=True): cmake('..', *options) make() make('install') + + # When trilinos is built with Python, libpytrilinos is included through + # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake + # contains pytrilinos. This leads to a run-time error: + # Symbol not found: _PyBool_Type + # and prevents Trilinos to be used in any C++ code, which links executable + # against the libraries listed in Trilinos_LIBRARIES. + # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509 + # A workaround it to remove PyTrilinos from the COMPONENTS_LIST : + if '+python' in self.spec: + filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib) + + # The shared libraries are not installed correctly on Darwin; correct this + if (sys.platform == 'darwin') and ('+shared' in spec): + fix_darwin_install_name(prefix.lib) diff --git a/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch new file mode 100644 index 0000000000..9defc55527 --- /dev/null +++ b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch @@ -0,0 +1,12 @@ +diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake +index 963eb71..998cd02 100644 +--- a/cmake/TPLs/FindTPLUMFPACK.cmake ++++ b/cmake/TPLs/FindTPLUMFPACK.cmake +@@ -55,6 +55,6 @@ + + + TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK +- REQUIRED_HEADERS umfpack.h amd.h UFconfig.h ++ REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h + REQUIRED_LIBS_NAMES umfpack amd + ) |