diff options
Diffstat (limited to 'var')
67 files changed, 1163 insertions, 285 deletions
diff --git a/var/spack/repos/builtin/packages/adios/adios_1100.patch b/var/spack/repos/builtin/packages/adios/adios_1100.patch new file mode 100644 index 0000000000..7a9f857c32 --- /dev/null +++ b/var/spack/repos/builtin/packages/adios/adios_1100.patch @@ -0,0 +1,29 @@ +From 3b21a8a4150962c6938baeceacd04f619cea2fbc Mon Sep 17 00:00:00 2001 +From: Norbert Podhorszki <pnorbert@ornl.gov> +Date: Thu, 1 Sep 2016 16:26:23 -0400 +Subject: [PATCH] ifdef around 'bool' type. hdf5 1.10 defines bool and breaks + compiling bp2h5.c + +--- + utils/bp2h5/bp2h5.c | 8 +++++--- + 1 file changed, 5 insertions(+), 3 deletions(-) + +diff --git a/utils/bp2h5/bp2h5.c b/utils/bp2h5/bp2h5.c +index 9c500c7..fa746bd 100644 +--- a/utils/bp2h5/bp2h5.c ++++ b/utils/bp2h5/bp2h5.c +@@ -43,9 +43,11 @@ + #include "dmalloc.h" + #endif + +-typedef int bool; +-#define false 0 +-#define true 1 ++#ifndef bool ++ typedef int bool; ++# define false 0 ++# define true 1 ++#endif + + bool noindex = false; // do no print array indices with data + bool printByteAsChar = false; // print 8 bit integer arrays as string diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 01834383b8..e240ce0858 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -36,6 +36,8 @@ class Adios(Package): homepage = "http://www.olcf.ornl.gov/center-projects/adios/" url = "https://github.com/ornladios/ADIOS/archive/v1.10.0.tar.gz" + version('develop', git='https://github.com/ornladios/ADIOS.git', + branch='master') version('1.10.0', 'eff450a4c0130479417cfd63186957f3') version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678') @@ -48,14 +50,14 @@ class Adios(Package): variant('mpi', default=True, description='Enable MPI support') variant('infiniband', default=False, description='Enable infiniband support') + # transforms variant('zlib', default=True, description='Enable szip transform support') variant('szip', default=False, description='Enable szip transform support') - variant('hdf5', default=False, description='Enable HDF5 transport support') - variant('netcdf', default=False, description='Enable NetCDF transport support') + # transports and serial file converters + variant('hdf5', default=False, description='Enable parallel HDF5 transport and serial bp2h5 converter') # Lots of setting up here for this package # module swap PrgEnv-intel PrgEnv-$COMP - # module load cray-netcdf/4.3.3.1 # module load cray-hdf5/1.8.14 # module load python/2.7.10 @@ -69,9 +71,13 @@ class Adios(Package): # optional transformations depends_on('zlib', when='+zlib') depends_on('szip', when='+szip') - # optional transports - depends_on('hdf5', when='+hdf5') - depends_on('netcdf', when='+netcdf') + # optional transports & file converters + depends_on('hdf5@1.8:+mpi', when='+hdf5') + + # Fix ADIOS <=1.10.0 compile error on HDF5 1.10+ + # https://github.com/ornladios/ADIOS/commit/3b21a8a41509 + # https://github.com/LLNL/spack/issues/1683 + patch('adios_1100.patch', when='@:1.10.0^hdf5@1.10:') def validate(self, spec): """ @@ -114,9 +120,7 @@ class Adios(Package): if '+szip' in spec: extra_args.append('--with-szip=%s' % spec['szip'].prefix) if '+hdf5' in spec: - extra_args.append('--with-hdf5=%s' % spec['hdf5'].prefix) - if '+netcdf' in spec: - extra_args.append('--with-netcdf=%s' % spec['netcdf'].prefix) + extra_args.append('--with-phdf5=%s' % spec['hdf5'].prefix) sh = which('sh') sh('./autogen.sh') diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py new file mode 100644 index 0000000000..7bb1985003 --- /dev/null +++ b/var/spack/repos/builtin/packages/bamtools/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Bamtools(Package): + """C++ API & command-line toolkit for working with BAM data.""" + + homepage = "https://github.com/pezmaster31/bamtools" + url = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz" + + version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9') + version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc') + version('2.2.3', '6eccd3e45e4ba12a68daa3298998e76d') + + depends_on('cmake', type='build') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py new file mode 100644 index 0000000000..46f3185154 --- /dev/null +++ b/var/spack/repos/builtin/packages/bedtools2/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Bedtools2(Package): + """Collectively, the bedtools utilities are a swiss-army knife of + tools for a wide-range of genomics analysis tasks. The most + widely-used tools enable genome arithmetic: that is, set theory + on the genome.""" + + homepage = "https://github.com/arq5x/bedtools2" + url = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz" + + version('2.26.0', '52227e7efa6627f0f95d7d734973233d') + version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d') + + depends_on('zlib') + + def install(self, spec, prefix): + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index e329e6fd7a..bf49ca9405 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -31,9 +31,9 @@ class Binutils(Package): homepage = "http://www.gnu.org/software/binutils/" url = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" - # 2.26 is incompatible with py-pillow build for some reason. + version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68') version('2.26', '64146a0faa3b411ba774f47d41de239f') - version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True) + version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66') version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b') version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py index ef7f25a7ce..d15030622e 100644 --- a/var/spack/repos/builtin/packages/bpp-suite/package.py +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -34,7 +34,6 @@ class BppSuite(Package): version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4') - # FIXME: Add dependencies if required. depends_on('cmake', type='build') depends_on('texinfo', type='build') depends_on('bpp-core') diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index 716e0103d1..0ce6ec593c 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -39,6 +39,7 @@ class Cereal(Package): homepage = "http://uscilab.github.io/cereal/" url = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz" + version('1.2.1', '64476ed74c19068ee543b53ad3992261') version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b') version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9') version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 0c16adcef7..83a68fda07 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -88,11 +88,13 @@ class Cmake(Package): options = [ '--prefix={0}'.format(prefix), - '--parallel={0}'.format(make_jobs), - # jsoncpp requires CMake to build - # use CMake-provided library to avoid circular dependency - '--no-system-jsoncpp' - ] + '--parallel={0}'.format(make_jobs)] + if spec.satisfies("@3:"): + options.append( + # jsoncpp requires CMake to build + # use CMake-provided library to avoid circular dependency + '--no-system-jsoncpp' + ) if '+ownlibs' in spec: # Build and link to the CMake-provided third-party libraries diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 052c7a971c..785de08d34 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -53,13 +53,13 @@ class Cp2k(Package): depends_on('plumed+shared+mpi', when='+plumed+mpi') depends_on('plumed+shared~mpi', when='+plumed~mpi') depends_on('pexsi', when='+mpi') + depends_on('wannier90', when='+mpi') + depends_on('elpa', when='+mpi') # TODO : add dependency on libint # TODO : add dependency on libsmm, libxsmm - # TODO : add dependency on elpa # TODO : add dependency on CUDA # TODO : add dependency on QUIP - # TODO : add dependency on libwannier90 parallel = False @@ -109,7 +109,8 @@ class Cp2k(Package): # Add required macro cppflags.extend(['-D__PLUMED2']) libs.extend([ - join_path(self.spec['plumed'].prefix.lib, 'libplumed.so') + join_path(self.spec['plumed'].prefix.lib, + 'libplumed.{0}'.format(dso_suffix)) ]) mkf.write('CC = {0.compiler.cc}\n'.format(self)) @@ -143,15 +144,26 @@ class Cp2k(Package): if '+mpi' in self.spec: cppflags.extend([ '-D__parallel', + '-D__WANNIER90', + '-D__ELPA3', '-D__SCALAPACK' ]) fcflags.extend([ + '-I' + join_path( + spec['elpa'].prefix, + 'include', + 'elpa-{0}'.format(str(spec['elpa'].version)), + 'modules' + ), '-I' + join_path(spec['pexsi'].prefix, 'fortran') ]) ldflags.extend([ '-L' + spec['scalapack'].prefix.lib ]) libs.extend([ + join_path(spec['elpa'].prefix.lib, + 'libelpa.{0}'.format(dso_suffix)), + join_path(spec['wannier90'].prefix.lib, 'libwannier.a'), join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'), join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'), @@ -173,7 +185,8 @@ class Cp2k(Package): '-L' + spec['blas'].prefix.lib ]) libs.extend([ - join_path(spec['fftw'].prefix.lib, 'libfftw3.so'), + join_path(spec['fftw'].prefix.lib, + 'libfftw3.{0}'.format(dso_suffix)), spec['lapack'].lapack_shared_lib, spec['blas'].blas_shared_lib ]) diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 4954e435c0..a22ac52714 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -32,6 +32,8 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.50.3', 'bd177fd6deecce00cfa7b5916d831c5e') + version('7.50.2', '6e161179f7af4b9f8b6ea21420132719') version('7.50.1', '015f6a0217ca6f2c5442ca406476920b') version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab') version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 939d8fc013..9e8c639128 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -32,6 +32,7 @@ class Dealii(Package): homepage = "https://www.dealii.org" url = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz" + version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7') version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d') version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00') version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa') @@ -67,11 +68,11 @@ class Dealii(Package): # Boost 1.58 is blacklisted, see # https://github.com/dealii/dealii/issues/1591 # Require at least 1.59 - # +python won't affect @:8.4.1 + # +python won't affect @:8.4.2 depends_on("boost@1.59.0:+thread+system+serialization+iostreams", - when='@:8.4.1~mpi') + when='@:8.4.2~mpi') depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi", - when='@:8.4.1+mpi') + when='@:8.4.2+mpi') # since @8.5.0: (and @develop) python bindings are introduced: depends_on("boost@1.59.0:+thread+system+serialization+iostreams", when='@8.5.0:~mpi~python') @@ -102,8 +103,8 @@ class Dealii(Package): depends_on("netcdf-cxx", when='+netcdf+mpi') depends_on("oce", when='+oce') depends_on("p4est", when='+p4est+mpi') - depends_on("petsc+mpi", when='@8.5.0:+petsc+mpi') - depends_on("slepc", when='@8.5.0:+slepc+petsc+mpi') + depends_on("petsc+mpi", when='@8.4.2:+petsc+mpi') + depends_on("slepc", when='@8.4.2:+slepc+petsc+mpi') depends_on("petsc@:3.6.4+mpi", when='@:8.4.1+petsc+mpi') depends_on("slepc@:3.6.3", when='@:8.4.1+slepc+petsc+mpi') depends_on("trilinos", when='+trilinos+mpi') diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py index f28d63f6c3..ae3f26b3ec 100644 --- a/var/spack/repos/builtin/packages/elpa/package.py +++ b/var/spack/repos/builtin/packages/elpa/package.py @@ -34,8 +34,16 @@ class Elpa(Package): homepage = 'http://elpa.mpcdf.mpg.de/' url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' - version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6', - url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz') + version( + '2016.05.003', + '88a9f3f3bfb63e16509dd1be089dcf2c', + url='http://elpa.mpcdf.mpg.de/html/Releases/2016.05.003/elpa-2016.05.003.tar.gz' + ) + version( + '2015.11.001', + 'de0f35b7ee7c971fd0dca35c900b87e6', + url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' + ) variant('openmp', default=False, description='Activates OpenMP support') @@ -46,7 +54,12 @@ class Elpa(Package): def install(self, spec, prefix): - options = ["--prefix=%s" % prefix] + options = [ + 'CC={0}'.format(self.spec['mpi'].mpicc), + 'FC={0}'.format(self.spec['mpi'].mpifc), + 'CXX={0}'.format(self.spec['mpi'].mpicxx), + '--prefix={0}'.format(self.prefix) + ] if '+openmp' in spec: options.append("--enable-openmp") diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index 3dca1ba187..d2c825513c 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -88,7 +88,7 @@ class Espresso(Package): # Add a list of directories to search search_list = [] - for name, dependency_spec in spec.dependencies.iteritems(): + for dependency_spec in spec.dependencies(): search_list.extend([dependency_spec.prefix.lib, dependency_spec.prefix.lib64]) diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py index bed27e6e02..311156378a 100644 --- a/var/spack/repos/builtin/packages/fontconfig/package.py +++ b/var/spack/repos/builtin/packages/fontconfig/package.py @@ -34,6 +34,7 @@ class Fontconfig(Package): depends_on('freetype') depends_on('libxml2') + depends_on('pkg-config', type='build') def install(self, spec, prefix): configure("--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index a14e166ed4..f90e4e7ff0 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -41,9 +41,18 @@ class Gdb(Package): version('7.9', '8f8ced422fe462a00e0135a643544f17') version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc') + variant('python', default=True, description='Compile with Python support') + + # Required dependency depends_on('texinfo', type='build') + # Optional dependency + depends_on('python', when='+python') + def install(self, spec, prefix): - configure('--prefix=%s' % prefix) + options = ['--prefix=%s' % prefix] + if '+python' in spec: + options.extend(['--with-python']) + configure(*options) make() make("install") diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py index a080660721..25e440ff6d 100644 --- a/var/spack/repos/builtin/packages/git-lfs/package.py +++ b/var/spack/repos/builtin/packages/git-lfs/package.py @@ -26,17 +26,28 @@ from spack import * class GitLfs(Package): - """Tool for managing large files with Git.""" + """Git LFS is a system for managing and versioning large files in + association with a Git repository. Instead of storing the large files + within the Git repository as blobs, Git LFS stores special "pointer + files" in the repository, while storing the actual file contents on a + Git LFS server.""" homepage = "https://git-lfs.github.com" - url = "https://github.com/github/git-lfs/archive/v1.4.1.tar.gz" + git_url = "https://github.com/github/git-lfs.git" - version('1.4.1', 'c62a314d96d3a30af4d98fa3305ad317') + version('1.4.1', git=git_url, tag='v1.4.1') + version('1.3.1', git=git_url, tag='v1.3.1') + + # TODO: Implement this by following the instructions at this location: + # https://github.com/github/git-lfs/blob/master/CONTRIBUTING.md#building + # variant('test', default=True, description='Build and run tests as part of the build.') # NOQA: E501 depends_on('go@1.5:', type='build') depends_on('git@1.8.2:', type='run') def install(self, spec, prefix): - bootstrap = Executable('./scripts/bootstrap') - bootstrap() - install('bin/git-lfs', prefix.bin) + bootstrap_script = Executable(join_path('script', 'bootstrap')) + bootstrap_script() + + mkdirp(prefix.bin) + install(join_path('bin', 'git-lfs'), prefix.bin) diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index ed058e0a68..a687b2bb35 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -54,25 +54,27 @@ class Git(Package): # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') - depends_on("openssl") depends_on("autoconf", type='build') depends_on("curl") depends_on("expat") depends_on("gettext") - depends_on("zlib") + depends_on("libiconv") + depends_on("openssl") depends_on("pcre") depends_on("perl") + depends_on("zlib") def install(self, spec, prefix): env['LDFLAGS'] = "-L%s" % spec['gettext'].prefix.lib + " -lintl" configure_args = [ "--prefix=%s" % prefix, - "--with-libpcre=%s" % spec['pcre'].prefix, - "--with-openssl=%s" % spec['openssl'].prefix, - "--with-zlib=%s" % spec['zlib'].prefix, "--with-curl=%s" % spec['curl'].prefix, "--with-expat=%s" % spec['expat'].prefix, + "--with-iconv=%s" % spec['libiconv'].prefix, + "--with-libpcre=%s" % spec['pcre'].prefix, + "--with-openssl=%s" % spec['openssl'].prefix, "--with-perl=%s" % join_path(spec['perl'].prefix.bin, 'perl'), + "--with-zlib=%s" % spec['zlib'].prefix, ] which('autoreconf')('-i') diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py index b0e2109fd3..d48c7c9756 100644 --- a/var/spack/repos/builtin/packages/go-bootstrap/package.py +++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py @@ -1,3 +1,27 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## import os import shutil import glob @@ -17,25 +41,37 @@ class GoBootstrap(Package): extendable = True - # temporary fix until tags are pulled correctly + # NOTE: Go@1.4.2 is the only supported bootstrapping compiler because all + # later versions require a Go compiler to build. + # See: https://golang.org/doc/install/source version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2') - variant('test', - default=True, - description="Run tests as part of build, a good idea but quite" - " time consuming") + variant('test', default=True, description='Build and run tests as part of the build.') provides('golang@:1.4.2') - depends_on('git') + depends_on('git', type='alldeps') + + # NOTE: Older versions of Go attempt to download external files that have + # since been moved while running the test suite. This patch modifies the + # test files so that these tests don't cause false failures. + # See: https://github.com/golang/go/issues/15694 + @when('@:1.4.3') + def patch(self): + test_suite_file = FileFilter(join_path('src', 'run.bash')) + test_suite_file.filter( + r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$', + r'# \1\2\3', + ) + + @when('@1.5.0:') + def patch(self): + pass def install(self, spec, prefix): bash = which('bash') with working_dir('src'): - if '+test' in spec: - bash('all.bash') - else: - bash('make.bash') + bash('{0}.bash'.format('all' if '+test' in spec else 'make')) try: os.makedirs(prefix) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 259498c145..5fa3017ab5 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -1,3 +1,27 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## import os import shutil import glob @@ -12,28 +36,39 @@ class Go(Package): extendable = True - version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4') version('1.6.2', git='https://go.googlesource.com/go', tag='go1.6.2') + version('1.5.4', git='https://go.googlesource.com/go', tag='go1.5.4') + version('1.4.2', git='https://go.googlesource.com/go', tag='go1.4.2') - variant('test', - default=True, - description="Run tests as part of build, a good idea but quite" - " time consuming") + variant('test', default=True, description='Build and run tests as part of the build.') provides('golang') - # to-do, make non-c self-hosting compilers feasible without backflips + depends_on('git', type='alldeps') + # TODO: Make non-c self-hosting compilers feasible without backflips # should be a dep on external go compiler depends_on('go-bootstrap', type='build') - depends_on('git', type='alldeps') + + # NOTE: Older versions of Go attempt to download external files that have + # since been moved while running the test suite. This patch modifies the + # test files so that these tests don't cause false failures. + # See: https://github.com/golang/go/issues/15694 + @when('@:1.4.3') + def patch(self): + test_suite_file = FileFilter(join_path('src', 'run.bash')) + test_suite_file.filter( + r'^(.*)(\$GOROOT/src/cmd/api/run.go)(.*)$', + r'# \1\2\3', + ) + + @when('@1.5.0:') + def patch(self): + pass def install(self, spec, prefix): bash = which('bash') with working_dir('src'): - if '+test' in spec: - bash('all.bash') - else: - bash('make.bash') + bash('{0}.bash'.format('all' if '+test' in spec else 'make')) try: os.makedirs(prefix) diff --git a/var/spack/repos/builtin/packages/grackle/Make.mach.template b/var/spack/repos/builtin/packages/grackle/Make.mach.template new file mode 100644 index 0000000000..83abaa26d1 --- /dev/null +++ b/var/spack/repos/builtin/packages/grackle/Make.mach.template @@ -0,0 +1,71 @@ +MACH_TEXT = Generic Linux +MACH_VALID = 1 +MACH_FILE = Make.mach.@ARCHITECTURE + +#----------------------------------------------------------------------- +# Install paths (local variables) +#----------------------------------------------------------------------- + +LOCAL_HDF5_INSTALL = @HDF5_ROOT + +#----------------------------------------------------------------------- +# Compiler settings +#----------------------------------------------------------------------- + +MACH_CC_NOMPI = @CC # C compiler +MACH_CXX_NOMPI = @CXX # C++ compiler +MACH_FC_NOMPI = @F77 # Fortran 77 +MACH_F90_NOMPI = @FC # Fortran 90 +MACH_LD_NOMPI = @FC # Linker +@LINK_VARIABLES_DEFINITION + +#----------------------------------------------------------------------- +# Machine-dependent defines +#----------------------------------------------------------------------- + +MACH_DEFINES = -DLINUX -DH5_USE_16_API -fPIC + +#----------------------------------------------------------------------- +# Compiler flag settings +#----------------------------------------------------------------------- + +MACH_CPPFLAGS = -P -traditional +MACH_CFLAGS = +MACH_CXXFLAGS = +MACH_FFLAGS = -fno-second-underscore -ffixed-line-length-132 +MACH_F90FLAGS = -fno-second-underscore +MACH_LDFLAGS = @STDCXX_LIB + +#----------------------------------------------------------------------- +# Optimization flags +#----------------------------------------------------------------------- + +MACH_OPT_WARN = -Wall -g +MACH_OPT_DEBUG = -g +MACH_OPT_HIGH = -O2 +MACH_OPT_AGGRESSIVE = -O3 -g + +#----------------------------------------------------------------------- +# Includes +#----------------------------------------------------------------------- + +LOCAL_INCLUDES_HDF5 = -I@HDF5_ROOT/include # HDF5 includes + +MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5) + +#----------------------------------------------------------------------- +# Libraries +#----------------------------------------------------------------------- + +LOCAL_LIBS_HDF5 = -L@HDF5_ROOT/lib -lhdf5 # HDF5 libraries +LOCAL_LIBS_MACH = # Machine-dependent libraries + +MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH) + +#----------------------------------------------------------------------- +# Installation +#----------------------------------------------------------------------- + +MACH_INSTALL_PREFIX = @PREFIX +MACH_INSTALL_LIB_DIR = +MACH_INSTALL_INCLUDE_DIR = diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py new file mode 100644 index 0000000000..7e3777158f --- /dev/null +++ b/var/spack/repos/builtin/packages/grackle/package.py @@ -0,0 +1,89 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import os.path +import shutil +import inspect + +from spack import * + + +class Grackle(Package): + """Grackle is a chemistry and radiative cooling library for astrophysical + simulations with interfaces for C, C++, and Fortran codes. It is a + generalized and trimmed down version of the chemistry network of the Enzo + simulation code + """ + homepage = 'http://grackle.readthedocs.io/en/grackle-2.2/' + url = 'https://bitbucket.org/grackle/grackle/get/grackle-2.0.1.tar.bz2' + + version('2.2', 'ec49ed1db5a42db21f478285150c2ba3') + version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d') + + depends_on('libtool', when='@2.2') + + depends_on('mpi') + depends_on('hdf5+mpi') + + parallel = False + + def install(self, spec, prefix): + template_name = '{0.architecture}-{0.compiler.name}' + grackle_architecture = template_name.format(spec) + link_variables = 'MACH_AR = ar' if spec.version < Version(2.2) else 'MACH_LIBTOOL = libtool' # NOQA: ignore=E501 + substitutions = { + '@ARCHITECTURE': grackle_architecture, + '@CC': spec['mpi'].mpicc, + '@CXX': spec['mpi'].mpicxx, + '@FC': spec['mpi'].mpifc, + '@F77': spec['mpi'].mpif77, + '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs), + '@HDF5_ROOT': spec['hdf5'].prefix, + '@PREFIX': prefix, + '@LINK_VARIABLES_DEFINITION': link_variables + } + + template = join_path( + os.path.dirname(inspect.getmodule(self).__file__), + 'Make.mach.template' + ) + makefile = join_path( + self.stage.source_path, + 'src', + 'clib', + 'Make.mach.{0}'.format(grackle_architecture) + ) + shutil.copy(template, makefile) + for key, value in substitutions.items(): + filter_file(key, value, makefile) + + configure() + with working_dir('src/clib'): + make('clean') + make('machine-{0}'.format(grackle_architecture)) + make('opt-high') + make('show-config') + make() + mkdirp(prefix.lib) + make('install') diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py new file mode 100644 index 0000000000..1501384493 --- /dev/null +++ b/var/spack/repos/builtin/packages/h5hut/package.py @@ -0,0 +1,70 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +from spack import * + + +class H5hut(Package): + """H5hut (HDF5 Utility Toolkit) + High-Performance I/O Library for Particle-based Simulations + """ + + homepage = "https://amas.psi.ch/H5hut/" + url = "https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/H5hut-1.99.13.tar.gz" + + version("1.99.13", "2a07a449afe50534de006ac6954a421a") + + variant("fortran", default=True, description="Enable Fortran support") + variant("mpi", default=False, description="Enable MPI support") + + depends_on("autoconf @2.60:", type="build") + depends_on("automake", type="build") + depends_on("hdf5 +mpi", when="+mpi") + depends_on("hdf5 @1.8:") + # h5hut +mpi uses the obsolete function H5Pset_fapl_mpiposix: + depends_on("hdf5 @:1.8.12", when="+mpi") + depends_on("libtool", type="build") + depends_on("mpi", when="+mpi") + + def install(self, spec, prefix): + autogen = Executable("./autogen.sh") + autogen() + configopts = ["--prefix={0}".format(prefix)] + if "+fortran" in spec: + if not self.compiler.fc: + raise RuntimeError( + "Cannot build Fortran variant without a Fortran compiler") + configopts.append("--enable-fortran") + if "+mpi" in spec: + configopts.extend([ + "--enable-parallel", + "CC=%s" % spec["mpi"].mpicc, + "CXX=%s" % spec["mpi"].mpicxx]) + if "+fortran" in spec: + configopts.append("FC=%s" % spec["mpi"].mpifc) + configure(*configopts) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py index aafb345be6..9a44184256 100644 --- a/var/spack/repos/builtin/packages/hdf/package.py +++ b/var/spack/repos/builtin/packages/hdf/package.py @@ -38,13 +38,12 @@ class Hdf(Package): variant('szip', default=False, description="Enable szip support") - depends_on("jpeg") - depends_on("szip", when='+szip') - depends_on("zlib") + depends_on('jpeg') + depends_on('szip', when='+szip') + depends_on('zlib') - def url_for_version(self, version): - return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str( - version) + "/src/hdf-" + str(version) + ".tar.gz" + depends_on('bison', type='build') + depends_on('flex', type='build') def install(self, spec, prefix): config_args = [ @@ -66,4 +65,5 @@ class Hdf(Package): configure(*config_args) make() - make("install") + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index aedaf18218..5984e50f42 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -43,6 +43,7 @@ class Hdf5(Package): version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') + version('1.8.12', 'd804802feb99b87fc668a90e6fa34411') variant('debug', default=False, description='Builds a debug version of the library') @@ -52,7 +53,7 @@ class Hdf5(Package): variant('cxx', default=True, description='Enable C++ support') variant('fortran', default=True, description='Enable Fortran support') - variant('mpi', default=False, description='Enable MPI support') + variant('mpi', default=True, description='Enable MPI support') variant('szip', default=False, description='Enable szip support') variant('threadsafe', default=False, description='Enable thread-safe capabilities') diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index c163628840..111c424b22 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -42,6 +42,7 @@ class Hwloc(Package): list_url = "http://www.open-mpi.org/software/hwloc/" list_depth = 3 + version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d') version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f') version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23') version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc') diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/icu/package.py index b8d366b905..bf24067879 100644 --- a/var/spack/repos/builtin/packages/icu/package.py +++ b/var/spack/repos/builtin/packages/icu/package.py @@ -31,8 +31,8 @@ class Icu(Package): Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms.""" - # FIXME: add a proper url for your package's homepage here. - homepage = "http://www.example.com" + + homepage = "http://site.icu-project.org/" url = "http://download.icu-project.org/files/icu4c/54.1/icu4c-54_1-src.tgz" version('54.1', 'e844caed8f2ca24c088505b0d6271bc0') diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 63bf6514cb..bab0920434 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -68,3 +68,9 @@ class Jdk(Package): def install(self, spec, prefix): distutils.dir_util.copy_tree(".", prefix) + + def setup_environment(self, spack_env, run_env): + run_env.set('JAVA_HOME', self.spec.prefix) + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('JAVA_HOME', self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 6ccaa11c90..c7c701175e 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -37,9 +37,11 @@ class Julia(Package): git='https://github.com/JuliaLang/julia.git', branch='master') version('release-0.5', git='https://github.com/JuliaLang/julia.git', branch='release-0.5') + version('0.5.0', 'b61385671ba74767ab452363c43131fb', preferred=True) version('release-0.4', git='https://github.com/JuliaLang/julia.git', branch='release-0.4') - version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True) + version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078') + version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d') version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6') version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac') @@ -162,7 +164,7 @@ class Julia(Package): # Configure Julia with open(join_path(prefix, "etc", "julia", "juliarc.jl"), "a") as juliarc: - if "@master" in spec or "@release-0.5" in spec: + if "@master" in spec or "@release-0.5" in spec or "@0.5:" in spec: # This is required for versions @0.5: juliarc.write( '# Point package manager to working certificates\n') diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index acfdebb972..6329adf8f3 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -40,18 +40,33 @@ class Libgd(Package): homepage = "https://github.com/libgd/libgd" url = "https://github.com/libgd/libgd/archive/gd-2.1.1.tar.gz" + version('2.2.3', 'a67bd15fa33d4aac0a1c7904aed19f49') version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e') + # Build dependencies + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('gettext', type='build') + depends_on('pkg-config', type='build') + depends_on('libpng') - depends_on('cmake', type='build') + depends_on('libtiff') + depends_on('fontconfig') def install(self, spec, prefix): - - with working_dir('spack-build', create=True): - cmake('..', - '-DENABLE_JPEG:BOOL=ON', - '-DENABLE_PNG:BOOL=ON', - '-DENABLE_TIFF:BOOL=ON', - *std_cmake_args) - make() - make("install") + autoreconf("--install", "--force", + "-I", "m4", + "-I", join_path(spec['gettext'].prefix, + "share", "aclocal"), + "-I", join_path(spec['pkg-config'].prefix, + "share", "aclocal"), + "-I", join_path(spec['automake'].prefix, + "share", "aclocal"), + "-I", join_path(spec['libtool'].prefix, + "share", "aclocal") + ) + configure('--prefix={0}'.format(prefix)) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index 1afe4911e6..c3a595d12d 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -30,6 +30,7 @@ class Libpng(Package): homepage = "http://www.libpng.org/pub/png/libpng.html" url = "http://download.sourceforge.net/libpng/libpng-1.6.16.tar.gz" + version('1.6.24', '65213080dd30a9b16193d9b83adc1ee9') version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d') version('1.6.15', '829a256f3de9307731d4f52dc071916d') version('1.6.14', '2101b3de1d5f348925990f9aa8405660') @@ -37,9 +38,10 @@ class Libpng(Package): version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330') version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee') - depends_on('zlib') + depends_on('zlib@1.0.4:') # 1.2.5 or later recommended def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() + make("check") make("install") diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py index 553f0dddb8..b8f6b1cc3a 100644 --- a/var/spack/repos/builtin/packages/libuuid/package.py +++ b/var/spack/repos/builtin/packages/libuuid/package.py @@ -27,7 +27,7 @@ from spack import * class Libuuid(Package): """Portable uuid C library""" - # FIXME: add a proper url for your package's homepage here. + homepage = "http://sourceforge.net/projects/libuuid/" url = "http://downloads.sourceforge.net/project/libuuid/libuuid-1.0.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Flibuuid%2F&ts=1433881396&use_mirror=iweb" @@ -36,6 +36,5 @@ class Libuuid(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) - # FIXME: Add logic to build and install here make() make("install") diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 61ea8daac4..7582faeb92 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -22,9 +22,10 @@ # 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 +from spack import * + class Llvm(Package): """The LLVM Project is a collection of modular and reusable compiler and @@ -37,9 +38,11 @@ class Llvm(Package): homepage = 'http://llvm.org/' url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz' + family = 'compiler' # Used by lmod + # currently required by mesa package version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', - url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') + url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package variant('debug', default=False, description="Build a debug version of LLVM, this increases " diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py index e1a42c0d9a..493ea59f0b 100644 --- a/var/spack/repos/builtin/packages/mbedtls/package.py +++ b/var/spack/repos/builtin/packages/mbedtls/package.py @@ -35,6 +35,7 @@ class Mbedtls(Package): homepage = "https://tls.mbed.org" url = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz" + version('2.3.0', '98158e1160a0825a3e8db38881a177a0') version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be') version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942') version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae') diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 9f8ed5c9e8..ca48a47817 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -43,16 +43,12 @@ class Metis(Package): version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5') version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10') - variant('shared', default=True, - description='Enables the build of shared libraries') - variant('debug', default=False, - description='Builds the library in debug mode') - variant('gdb', default=False, description='Enables gdb support') + variant('shared', default=True, description='Enables the build of shared libraries.') + 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('real64', default=False, - description='Use double precision floating point types') + variant('idx64', default=False, description='Sets the bit width of METIS\'s index type to 64.') + variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.') depends_on('cmake@2.8:', when='@5:', type='build') @@ -63,12 +59,37 @@ class Metis(Package): return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version) @when('@:4') + def patch(self): + pass + + @when('@5:') + def patch(self): + source_path = self.stage.source_path + metis_header = FileFilter(join_path(source_path, 'include', 'metis.h')) + + metis_header.filter( + r'(\b)(IDXTYPEWIDTH )(\d+)(\b)', + r'\1\2{0}\4'.format('64' if '+idx64' in self.spec else '32'), + ) + metis_header.filter( + r'(\b)(REALTYPEWIDTH )(\d+)(\b)', + r'\1\2{0}\4'.format('64' if '+real64' in self.spec else '32'), + ) + + # Make clang 7.3 happy. + # Prevents "ld: section __DATA/__thread_bss extends beyond end of file" + # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059 + # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb + if self.spec.satisfies('%clang@7.3.0'): + filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', + join_path(source_path, 'GKlib', 'error.c')) + + @when('@:4') def install(self, spec, prefix): # Process library spec and options - unsupp_vars = [v for v in ('+gdb', '+idx64', '+real64') if v in spec] - if unsupp_vars: - msg = 'Given variants %s are unsupported by METIS 4!' % unsupp_vars - raise InstallError(msg) + if any('+{0}'.format(v) in spec for v in ['gdb', 'idx64', 'real64']): + raise InstallError('METIS@:4 does not support the following ' + 'variants: gdb, idx64, real64.') options = ['COPTIONS=-fPIC'] if '+debug' in spec: @@ -118,49 +139,48 @@ class Metis(Package): join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'), '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm') - test_bin = lambda testname: join_path(prefix.bin, testname) - test_graph = lambda graphname: join_path(prefix.share, graphname) - - graph = test_graph('4elt.graph') - os.system('%s %s' % (test_bin('mtest'), graph)) - os.system('%s %s 40' % (test_bin('kmetis'), graph)) - os.system('%s %s' % (test_bin('onmetis'), graph)) - graph = test_graph('test.mgraph') - os.system('%s %s 2' % (test_bin('pmetis'), graph)) - os.system('%s %s 2' % (test_bin('kmetis'), graph)) - os.system('%s %s 5' % (test_bin('kmetis'), graph)) - graph = test_graph('metis.mesh') - os.system('%s %s 10' % (test_bin('partnmesh'), graph)) - os.system('%s %s 10' % (test_bin('partdmesh'), graph)) - os.system('%s %s' % (test_bin('mesh2dual'), graph)) - - # FIXME: The following code should replace the testing code in the - # block above since it causes installs to fail when one or more of the - # Metis tests fail, but it currently doesn't work because the 'mtest', - # 'onmetis', and 'partnmesh' tests return error codes that trigger - # false positives for failure. - """ - Executable(test_bin('mtest'))(test_graph('4elt.graph')) - Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40') - Executable(test_bin('onmetis'))(test_graph('4elt.graph')) - - Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2') - Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2') - Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5') - - Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10') - Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10') - Executable(test_bin('mesh2dual'))(test_graph('metis.mesh')) - """ + if self.run_tests: + test_bin = lambda testname: join_path(prefix.bin, testname) + test_graph = lambda graphname: join_path(prefix.share, graphname) + + graph = test_graph('4elt.graph') + os.system('%s %s' % (test_bin('mtest'), graph)) + os.system('%s %s 40' % (test_bin('kmetis'), graph)) + os.system('%s %s' % (test_bin('onmetis'), graph)) + graph = test_graph('test.mgraph') + os.system('%s %s 2' % (test_bin('pmetis'), graph)) + os.system('%s %s 2' % (test_bin('kmetis'), graph)) + os.system('%s %s 5' % (test_bin('kmetis'), graph)) + graph = test_graph('metis.mesh') + os.system('%s %s 10' % (test_bin('partnmesh'), graph)) + os.system('%s %s 10' % (test_bin('partdmesh'), graph)) + os.system('%s %s' % (test_bin('mesh2dual'), graph)) + + # FIXME: The following code should replace the testing code in the + # block above since it causes installs to fail when one or more of + # the Metis tests fail, but it currently doesn't work because the + # 'mtest', 'onmetis', and 'partnmesh' tests return error codes that + # trigger false positives for failure. + """ + Executable(test_bin('mtest'))(test_graph('4elt.graph')) + Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40') + Executable(test_bin('onmetis'))(test_graph('4elt.graph')) + + Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2') + Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2') + Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5') + + Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10') + Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10') + Executable(test_bin('mesh2dual'))(test_graph('metis.mesh')) + """ @when('@5:') def install(self, spec, prefix): - options = [] - options.extend(std_cmake_args) - - build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path + build_directory = join_path(source_directory, 'build') + options = std_cmake_args[:] options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory) options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) @@ -172,26 +192,24 @@ class Metis(Package): if '+gdb' in spec: options.append('-DGDB:BOOL=ON') - metis_header = join_path(source_directory, 'include', 'metis.h') - if '+idx64' in spec: - filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header) - if '+real64' in spec: - filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header) - - # Make clang 7.3 happy. - # Prevents "ld: section __DATA/__thread_bss extends beyond end of file" - # See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059 - # and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb - if spec.satisfies('%clang@7.3.0'): - filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', - join_path(source_directory, 'GKlib', 'error.c')) - with working_dir(build_directory, create=True): cmake(source_directory, *options) make() make('install') - # now run some tests: + # install GKlib headers, which will be needed for ParMETIS + GKlib_dist = join_path(prefix.include, 'GKlib') + mkdirp(GKlib_dist) + hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h')) + for hfile in hfiles: + install(hfile, GKlib_dist) + + if self.run_tests: + # FIXME: On some systems, the installed binaries for METIS cannot + # be executed without first being read. + ls = which('ls') + ls('-a', '-l', prefix.bin) + for f in ['4elt', 'copter2', 'mdual']: graph = join_path(source_directory, 'graphs', '%s.graph' % f) Executable(join_path(prefix.bin, 'graphchk'))(graph) @@ -202,10 +220,3 @@ class Metis(Package): Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2') graph = join_path(source_directory, 'graphs', 'metis.mesh') Executable(join_path(prefix.bin, 'mpmetis'))(graph, '2') - - # install GKlib headers, which will be needed for ParMETIS - GKlib_dist = join_path(prefix.include, 'GKlib') - mkdirp(GKlib_dist) - hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h')) - for hfile in hfiles: - install(hfile, GKlib_dist) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index a123830185..06678bf08b 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -28,14 +28,12 @@ from spack import * class Mvapich2(Package): """MVAPICH2 is an MPI implementation for Infiniband networks.""" homepage = "http://mvapich.cse.ohio-state.edu/" - url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2rc2.tar.gz" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz" - version('2.2rc2', 'f9082ffc3b853ad1b908cf7f169aa878') - version('2.2b', '5651e8b7a72d7c77ca68da48f3a5d108') - version('2.2a', 'b8ceb4fc5f5a97add9b3ff1b9cbe39d2') - version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6') - version('2.0', '9fbb68a4111a8b6338e476dc657388b4') - version('1.9', '5dc58ed08fd3142c260b70fe297e127c') + version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e') + version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6') + version('2.0', '9fbb68a4111a8b6338e476dc657388b4') + version('1.9', '5dc58ed08fd3142c260b70fe297e127c') patch('ad_lustre_rwcontig_open_source.patch', when='@1.9') @@ -95,6 +93,7 @@ class Mvapich2(Package): ########## # FIXME : CUDA support is missing + depends_on('bison') depends_on('libpciaccess') def url_for_version(self, version): diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index aaacbac7b1..e4fd5bf269 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -50,7 +50,10 @@ class Ncurses(Package): "--enable-widec", "--enable-overwrite", "--disable-lib-suffixes", - "--without-ada"] + "--without-ada", + "--enable-pc-files", + "--with-pkg-config-libdir={0}/lib/pkgconfig".format(prefix) + ] configure(*opts) make() make("install") diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index f61e6984b5..4abc09deb0 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -34,6 +34,7 @@ class Ncview(Package): depends_on("netcdf") depends_on("udunits2") + depends_on("libpng") # OS Dependencies # Ubuntu: apt-get install libxaw7-dev diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py index ab40c14340..5dc686c907 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf/package.py @@ -50,12 +50,18 @@ class Netcdf(Package): # Required for NetCDF-4 support depends_on("zlib") - depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi') - depends_on('hdf5+mpi', when='@4.4.1:+mpi') - depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi') - depends_on('hdf5~mpi', when='@4.4.1:~mpi') + depends_on('hdf5') + + # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later + # https://github.com/Unidata/netcdf-c/issues/250 + depends_on('hdf5@:1.8', when='@:4.4.0') def install(self, spec, prefix): + # Workaround until variant forwarding works properly + if '+mpi' in spec and spec.satisfies('^hdf5~mpi'): + raise RuntimeError('Invalid spec. Package netcdf requires ' + 'hdf5+mpi, but spec asked for hdf5~mpi.') + # Environment variables CPPFLAGS = [] LDFLAGS = [] diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 08c94a5c9b..93d64fb466 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -36,6 +36,7 @@ class NetlibLapack(Package): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + version('3.6.1', '421b2cb72e15f237e144428f9c460ee0') version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 49b8633209..13e932e176 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -41,12 +41,14 @@ class NetlibScalapack(Package): variant('shared', default=True, description='Build the shared library version') - variant('fpic', default=False, description="Build with -fpic compiler option") + variant('fpic', default=False, + description="Build with -fpic compiler option") provides('scalapack') depends_on('mpi') depends_on('lapack') + depends_on('blas') depends_on('cmake', when='@2.0.0:', type='build') def install(self, spec, prefix): @@ -54,18 +56,18 @@ class NetlibScalapack(Package): "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'), "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else - 'ON'), - # forces scalapack to use find_package(LAPACK): - "-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", + 'ON') ] # Make sure we use Spack's Lapack: options.extend([ '-DLAPACK_FOUND=true', - '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include, '-DLAPACK_LIBRARIES=%s' % ( spec['lapack'].lapack_shared_lib if '+shared' in spec else spec['lapack'].lapack_static_lib), + '-DBLAS_LIBRARIES=%s' % ( + spec['blas'].blas_shared_lib if '+shared' in spec else + spec['blas'].blas_static_lib) ]) if '+fpic' in spec: diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 37f7a7005d..23c7b02daf 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -32,6 +32,7 @@ class Openblas(Package): homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.19', '28c998054fd377279741c6f0b9ea7941') version('0.2.18', '805e7f660877d588ea7e3792cda2ee65') version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 67bf6f3713..bb356aaccc 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -65,6 +65,7 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('2.0.1', '6f78155bd7203039d2448390f3b51c96') version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674') version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 8d9049a8f7..40c8b1b9f1 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -36,24 +36,18 @@ class Openssl(Package): homepage = "http://www.openssl.org" url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz" - version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') - version('1.0.1r', '1abd905e079542ccae948af37e393d28') - version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1') - version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') - version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') - version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') - version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0') + version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa') + version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d') + version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5') + version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a') + version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1') + version('1.0.1r', '1abd905e079542ccae948af37e393d28') + version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') depends_on("zlib") parallel = False - def url_for_version(self, version): - if '@system' in self.spec: - return '@system (reserved version for system openssl)' - else: - return super(Openssl, self).url_for_version(self.version) - def handle_fetch_error(self, error): tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has " "been updated, and the version in your instance of Spack is " diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 8afae91af1..74e00cc9e0 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -38,11 +38,9 @@ class Parmetis(Package): version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628') version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce') - variant('shared', default=True, - description='Enables the build of shared libraries') - variant('debug', default=False, - description='Builds the library in debug mode') - variant('gdb', default=False, description='Enables gdb support') + variant('shared', default=True, description='Enables the build of shared libraries.') + variant('debug', default=False, description='Builds the library in debug mode.') + variant('gdb', default=False, description='Enables gdb support.') depends_on('cmake@2.8:', type='build') depends_on('mpi') @@ -50,9 +48,9 @@ class Parmetis(Package): patch('enable_external_metis.patch') # bug fixes from PETSc developers - # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ + # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ # NOQA: E501 patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch') - # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ + # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ # NOQA: E501 patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') def url_for_version(self, version): @@ -60,12 +58,10 @@ class Parmetis(Package): return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version) def install(self, spec, prefix): - options = [] - options.extend(std_cmake_args) - - build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path + build_directory = join_path(source_directory, 'build') + options = std_cmake_args[:] options.extend([ '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include, '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix, diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 73091bb182..1f1b9adffd 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -90,6 +90,8 @@ class Petsc(Package): def mpi_dependent_options(self): if '~mpi' in self.spec: compiler_opts = [ + '--with-cpp=cpp', + '--with-cxxcpp=cpp', '--with-cc=%s' % os.environ['CC'], '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), @@ -111,6 +113,8 @@ class Petsc(Package): raise RuntimeError('\n'.join(errors)) else: compiler_opts = [ + '--with-cpp=cpp', + '--with-cxxcpp=cpp', '--with-mpi=1', '--with-mpi-dir=%s' % self.spec['mpi'].prefix, ] diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py index 64368fe70d..d3a260bd7f 100644 --- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py +++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py @@ -37,5 +37,7 @@ class PyBeautifulsoup4(Package): extends('python') + depends_on('py-setuptools', type='build') + def install(self, spec, prefix): python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index 1d8b3faa6f..211e3b4199 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -32,7 +32,7 @@ class PyPillow(Package): capabilities.""" homepage = "https://python-pillow.org/" - url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz" + url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz" # TODO: This version should be deleted once the next release comes out. # TODO: It fixes a bug that prevented us from linking to Tk/Tcl. diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py new file mode 100644 index 0000000000..2835bfcca8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-proj/package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by David Beckingsale, david@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +from spack import * + + +class PyProj(Package): + """Python interface to the PROJ.4 Library.""" + homepage = "http://jswhit.github.io/pyproj/" + url = "https://github.com/jswhit/pyproj/tarball/v1.9.5.1rel" + + # This is not a tagged release of pyproj. + # The changes in this "version" fix some bugs, especially with Python3 use. + version('1.9.5.1.1', 'd035e4bc704d136db79b43ab371b27d2', + url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f') + + version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835') + + extends('python') + + depends_on('py-cython', type='build') + depends_on('py-setuptools', type='build') + + # NOTE: py-proj does NOT depends_on('proj'). + # The py-proj git repo actually includes the correct version of PROJ.4, + # which is built internally as part of the py-proj build. + # Adding depends_on('proj') will cause mysterious build errors. + + def install(self, spec, prefix): + setup_py('install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index a79c2e477b..97632493af 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -27,9 +27,10 @@ from spack import Package class PyPy2neo(Package): - """FIXME: put a proper description of your package here.""" - # FIXME: add a proper url for your package's homepage here. - homepage = "http://www.example.com" + """Py2neo is a client library and toolkit for working with Neo4j from + within Python applications and from the command line.""" + + homepage = "http://py2neo.org/" url = "https://github.com/nigelsmall/py2neo/archive/py2neo-2.0.8.tar.gz" version('2.0.8', 'e3ec5172a9e006515ef4155688a05a55') diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index cab516e1df..83a69c5682 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -28,7 +28,7 @@ from spack import * class PyScipy(Package): """Scientific Library for Python.""" homepage = "http://www.scipy.org/" - url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" + url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224') version('0.15.1', 'be56cd8e60591d6332aac792a5880110') @@ -36,6 +36,8 @@ class PyScipy(Package): extends('python') depends_on('py-nose', type='build') + # Known not to work with 2.23, 2.25 + depends_on('binutils@2.26:', type='build') depends_on('py-numpy+blas+lapack', type=nolink) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py new file mode 100644 index 0000000000..646bd4db2f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-yt/package.py @@ -0,0 +1,78 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +from spack import * + + +class PyYt(Package): + """Volumetric Data Analysis + + yt is a python package for analyzing and visualizing + volumetric, multi-resolution data from astrophysical + simulations, radio telescopes, and a burgeoning + interdisciplinary community. + """ + homepage = "http://yt-project.org" + url = "https://bitbucket.org/yt_analysis/yt" + + version("3.3.1", hg="https://bitbucket.org/yt_analysis/yt", + tag="yt-3.3.1", commit="9bc3d0e9b750c923d44d73c447df64fc431f5838") + version("3.2.3", hg="https://bitbucket.org/yt_analysis/yt", + tag="yt-3.2.3", commit="83d2c1e9313e7d83eb5b96888451ff2646fd8ff3") + version("3.1.0", hg="https://bitbucket.org/yt_analysis/yt", + tag="yt-3.1.0", commit="fd7cdc4836188a3badf81adb477bcc1b9632e485") + version("3.0.2", hg="https://bitbucket.org/yt_analysis/yt", + tag="yt-3.0.2", commit="511887af4c995a78fe606e58ce8162c88380ecdc") + version("2.6.3", hg="https://bitbucket.org/yt_analysis/yt", + tag="yt-2.6.3", commit="816186f16396a16853810ac9ebcde5057d8d5b1a") + version("development", hg="https://bitbucket.org/yt_analysis/yt", + branch="yt") + + variant("astropy", default=True, description="enable astropy support") + variant("h5py", default=True, description="enable h5py support") + variant("scipy", default=True, description="enable scipy support") + + extends("python") + + depends_on("py-astropy", type="nolink", when="+astropy") + depends_on("py-cython", type="nolink") + depends_on("py-h5py", type="nolink", when="+h5py") + depends_on("py-ipython", type="nolink") + depends_on("py-matplotlib", type="nolink") + depends_on("py-numpy", type="nolink") + depends_on("py-scipy", type="nolink", when="+scipy") + depends_on("py-setuptools", type="build") + depends_on("py-sympy", type="nolink") + depends_on("python @2.7:2.999,3.4:") + + def install(self, spec, prefix): + setup_py("install", "--prefix=%s" % prefix) + self.check_install(spec, prefix) + + def check_install(self, spec, prefix): + # The Python interpreter path can be too long for this + # yt = Executable(join_path(prefix.bin, "yt")) + # yt("--help") + python(join_path(prefix.bin, "yt"), "--help") diff --git a/var/spack/repos/builtin/packages/python/ncurses.patch b/var/spack/repos/builtin/packages/python/ncurses.patch new file mode 100644 index 0000000000..9054c03e7b --- /dev/null +++ b/var/spack/repos/builtin/packages/python/ncurses.patch @@ -0,0 +1,11 @@ +--- a/setup.py 2016-08-30 15:39:59.334926574 -0500 ++++ b/setup.py 2016-08-30 15:46:57.227946339 -0500 +@@ -745,8 +745,6 @@ + # use the same library for the readline and curses modules. + if 'curses' in readline_termcap_library: + curses_library = readline_termcap_library +- elif self.compiler.find_library_file(lib_dirs, 'ncursesw'): +- curses_library = 'ncursesw' + elif self.compiler.find_library_file(lib_dirs, 'ncurses'): + curses_library = 'ncurses' + elif self.compiler.find_library_file(lib_dirs, 'curses'): diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 57783b0542..f3380cf75d 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -74,6 +74,8 @@ class Python(Package): depends_on("tk", when="+tk") depends_on("tcl", when="+tk") + patch('ncurses.patch') + @when('@2.7,3.4:') def patch(self): # NOTE: Python's default installation procedure makes it possible for a @@ -110,6 +112,8 @@ class Python(Package): 'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)), 'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)), ] + if spec.satisfies("platform=darwin") and ('%gcc' in spec): + config_args.append('--disable-toolbox-glue') if '+ucs4' in spec: if spec.satisfies('@:2.7'): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 3032e81f78..639875d29d 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -48,6 +48,7 @@ class Qt(Package): variant('krellpatch', default=False, description="Build with openspeedshop based patch.") variant('mesa', default=False, description="Depend on mesa.") variant('gtk', default=False, description="Build with gtkplus.") + variant('examples', default=False, description="Build examples.") variant('dbus', default=False, description="Build with D-Bus support.") patch('qt3krell.patch', when='@3.3.8b+krellpatch') @@ -165,6 +166,9 @@ class Qt(Package): '-no-nis' ] + if '~examples' in self.spec: + config_args.extend(['-nomake', 'examples']) + if '@4' in self.spec: config_args.append('-no-phonon') diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch deleted file mode 100644 index 0c15eab386..0000000000 --- a/var/spack/repos/builtin/packages/qthreads/ldflags.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/configure -+++ b/configure -@@ -40456,7 +40456,7 @@ - hwloc_saved_LDFLAGS="$LDFLAGS" - if test "x$with_hwloc" != x; then - CPPFLAGS="-I$with_hwloc/include $CPPFLAGS" -- LDFLAGS="-L$with_hwloc/lib $CPPFLAGS" -+ LDFLAGS="-L$with_hwloc/lib $LDFLAGS" - fi - - diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py index 8d5cc87062..c68d8dba6c 100644 --- a/var/spack/repos/builtin/packages/qthreads/package.py +++ b/var/spack/repos/builtin/packages/qthreads/package.py @@ -38,28 +38,15 @@ class Qthreads(Package): attain either state.""" homepage = "http://www.cs.sandia.gov/qthreads/" - # Google Code has stopped serving tarballs - # We assume the tarballs will soon be available on Github instead - # url = "https://qthreads.googlecode.com/files/qthread-1.10.tar.bz2" - # version('1.10', '5af8c8bbe88c2a6d45361643780d1671') + url = "https://github.com/Qthreads/qthreads/releases/download/1.10/qthread-1.10.tar.bz2" + version("1.10", "d1cf3cf3f30586921359f7840171e551") - # Temporarily install from a git branch - url = "https://github.com/Qthreads/qthreads" - version("1.10", - git="https://github.com/Qthreads/qthreads", - branch="release-1.10") - - # patch("ldflags.patch") patch("restrict.patch") patch("trap.patch") - depends_on("autoconf", type="build") - depends_on("automake", type="build") depends_on("hwloc") def install(self, spec, prefix): - autogen = Executable("./autogen.sh") - autogen() configure("--prefix=%s" % prefix, "--enable-guard-pages", "--with-topology=hwloc", diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index 6b0b224785..b82a7e55d6 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -42,7 +42,8 @@ class Samtools(Package): def install(self, spec, prefix): if self.spec.version >= Version('1.3.1'): - configure('--prefix={0}'.format(prefix), '--with-ncurses') + configure('--prefix={0}'.format(prefix), '--with-ncurses', + 'CURSES_LIB=-lncurses') make() make('install') else: diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index 5113c88bdf..691d53a9f1 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -41,7 +41,8 @@ class Silo(Package): variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') - depends_on('hdf5') + # silo uses the obsolete function H5Pset_fapl_mpiposix: + depends_on("hdf5 @:1.8.12") depends_on('qt', when='+silex') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py index 8c4663c524..eae4971ace 100644 --- a/var/spack/repos/builtin/packages/stat/package.py +++ b/var/spack/repos/builtin/packages/stat/package.py @@ -34,8 +34,8 @@ class Stat(Package): version('2.2.0', '26bd69dd57a15afdd5d0ebdb0b7fb6fc') version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91') version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b') - version('3.0.0b', '8851912ba40e31cf7be6dde3be8e702c', - url='https://github.com/LLNL/STAT/files/427762/STAT-3.0.0b.tar.gz') + version('3.0.0', 'a97cb235c266371c4a26329112de48a2', + url='https://github.com/LLNL/STAT/releases/download/v3.0.0/STAT-3.0.0.tar.gz') # TODO: dysect requires Dyninst patch for version 3.0.0b variant('dysect', default=False, description="enable DySectAPI") diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py new file mode 100644 index 0000000000..b1b7dada6f --- /dev/null +++ b/var/spack/repos/builtin/packages/uberftp/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Uberftp(Package): + """UberFTP is an interactive (text-based) client for GridFTP""" + + homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php" + url = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz" + + version('2_8', 'bc7a159955a9c4b9f5f42f3d2b8fc830') + version('2_7', 'faaea2d6e1958c1105cfc9147824e03c') + version('2_6', '784210976f259f9d19c0798c19778d34') + + depends_on('globus_toolkit') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py index d88caeb00a..5d2ab24cc5 100644 --- a/var/spack/repos/builtin/packages/visit/package.py +++ b/var/spack/repos/builtin/packages/visit/package.py @@ -31,13 +31,15 @@ class Visit(Package): homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/" url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz" - version('2.10.1', '3cbca162fdb0249f17c4456605c4211e') + version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b') version('2.10.2', '253de0837a9d69fb689befc98ea4d068') + version('2.10.1', '3cbca162fdb0249f17c4456605c4211e') depends_on("vtk@6.1.0~opengl2") depends_on("qt@4.8.6") depends_on("python") depends_on("silo+shared") + depends_on("hdf5~mpi") def install(self, spec, prefix): with working_dir('spack-build', create=True): @@ -46,6 +48,7 @@ class Visit(Package): feature_args.extend([ "-DVTK_MAJOR_VERSION=6", "-DVTK_MINOR_VERSION=1", + "-DVISIT_USE_GLEW=OFF", "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec[ 'qt'].prefix.bin, "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec[ diff --git a/var/spack/repos/builtin/packages/vtk/gcc.patch b/var/spack/repos/builtin/packages/vtk/gcc.patch new file mode 100644 index 0000000000..37ba5ac45a --- /dev/null +++ b/var/spack/repos/builtin/packages/vtk/gcc.patch @@ -0,0 +1,21 @@ +--- old/CMake/vtkCompilerExtras.cmake ++++ new/CMake/vtkCompilerExtras.cmake +@@ -26,6 +26,8 @@ + execute_process(COMMAND ${CMAKE_C_COMPILER} --version + OUTPUT_VARIABLE _gcc_version_info + ERROR_VARIABLE _gcc_version_info) ++ ++ string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}") + + string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]" + _gcc_version "${_gcc_version_info}") +--- old/CMake/GenerateExportHeader.cmake ++++ new/CMake/GenerateExportHeader.cmake +@@ -166,6 +166,7 @@ + execute_process(COMMAND ${CMAKE_C_COMPILER} --version + OUTPUT_VARIABLE _gcc_version_info + ERROR_VARIABLE _gcc_version_info) ++ string (REPLACE ";" "" _gcc_version_info "${_gcc_version_info}") + string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" + _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 087c0e93eb..f7015904b0 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -40,6 +40,8 @@ class Vtk(Package): version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') + patch("gcc.patch") + depends_on('cmake', type='build') depends_on("qt") diff --git a/var/spack/repos/builtin/packages/wannier90/make.sys b/var/spack/repos/builtin/packages/wannier90/make.sys new file mode 100644 index 0000000000..f96fa23fb2 --- /dev/null +++ b/var/spack/repos/builtin/packages/wannier90/make.sys @@ -0,0 +1,7 @@ +F90 = @F90 +COMMS=mpi +MPIF90=@MPIF90 +FCOPTS=-O2 -fpic +LDOPTS=-O2 -fpic + +LIBS = @LIBS diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py new file mode 100644 index 0000000000..189e568cdc --- /dev/null +++ b/var/spack/repos/builtin/packages/wannier90/package.py @@ -0,0 +1,117 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import inspect +import os.path +import shutil + +from spack import * + + +class Wannier90(Package): + """Wannier90 calculates maximally-localised Wannier functions (MLWFs). + + Wannier90 is released under the GNU General Public License. + """ + homepage = 'http://wannier.org' + url = 'http://wannier.org/code/wannier90-2.0.1.tar.gz' + + version('2.0.1', '4edd742506eaba93317249d33261fb22') + + depends_on('mpi') + depends_on('lapack') + depends_on('blas') + + parallel = False + + def install(self, spec, prefix): + + substitutions = { + '@F90': spack_fc, + '@MPIF90': self.spec['mpi'].mpifc, + '@LIBS': ' '.join([ + self.spec['lapack'].lapack_shared_lib, + self.spec['lapack'].blas_shared_lib + ]) + } + ####### + # TODO : this part is replicated in PEXSI + # TODO : and may be a common pattern for Editable Makefiles + # TODO : see #1186 + template = join_path( + os.path.dirname(inspect.getmodule(self).__file__), + 'make.sys' + ) + makefile = join_path( + self.stage.source_path, + 'make.sys' + ) + + shutil.copy(template, makefile) + for key, value in substitutions.items(): + filter_file(key, value, makefile) + ###### + + make('wannier') + mkdirp(self.prefix.bin) + install( + join_path(self.stage.source_path, 'wannier90.x'), + join_path(self.prefix.bin, 'wannier90.x') + ) + + make('post') + install( + join_path(self.stage.source_path, 'postw90.x'), + join_path(self.prefix.bin, 'postw90.x') + ) + + make('lib') + mkdirp(self.prefix.lib) + install( + join_path(self.stage.source_path, 'libwannier.a'), + join_path(self.prefix.lib, 'libwannier.a') + ) + + make('w90chk2chk') + install( + join_path(self.stage.source_path, 'w90chk2chk.x'), + join_path(self.prefix.bin, 'w90chk2chk.x') + ) + + make('w90vdw') + install( + join_path(self.stage.source_path, 'utility', 'w90vdw', 'w90vdw.x'), + join_path(self.prefix.bin, 'w90vdw.x') + ) + + make('w90pov') + install( + join_path(self.stage.source_path, 'utility', 'w90pov', 'w90pov'), + join_path(self.prefix.bin, 'w90pov') + ) + + install_tree( + join_path(self.stage.source_path, 'pseudo'), + join_path(self.prefix.bin, 'pseudo') + ) diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py index cd50d46826..3cfc4c2408 100644 --- a/var/spack/repos/builtin/packages/xorg-util-macros/package.py +++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py @@ -28,7 +28,7 @@ from spack import * class XorgUtilMacros(Package): """The m4 macros used by all of the Xorg packages.""" - homepage = "http://www.example.com" + homepage = "https://cgit.freedesktop.org/xorg/util/macros/" url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2" version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1') diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index 0094395968..8d4dd321b0 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -22,10 +22,11 @@ # 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 re import os import glob -from spack import * class Zoltan(Package): @@ -47,23 +48,28 @@ class Zoltan(Package): version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9') version('3.3', '5eb8f00bda634b25ceefa0122bd18d65') - variant('debug', default=False, - description='Builds a debug version of the library') - variant('shared', default=True, - description='Builds a shared version of the library') + variant('debug', default=False, description='Builds a debug version of the library.') + variant('shared', default=True, description='Builds a shared version of the library.') - variant('fortran', default=True, description='Enable Fortran support') - variant('mpi', default=False, description='Enable MPI support') + variant('fortran', default=True, description='Enable Fortran support.') + variant('mpi', default=True, description='Enable MPI support.') depends_on('mpi', when='+mpi') + def url_for_version(self, version): + return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version) + def install(self, spec, prefix): - config_args = [ - '--enable-f90interface' - if '+fortan' in spec else '--disable-f90interface', + # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers + # because of some complicated generic type problem. + if spec.satisfies('@:3.6+fortran+mpi'): + raise RuntimeError(('Cannot build Zoltan v{0} with +fortran and ' + '+mpi; please disable one of these features ' + 'or upgrade versions.').format(self.version)) - '--enable-mpi' - if '+mpi' in spec else '--disable-mpi', + config_args = [ + self.get_config_flag('f90interface', 'fortran'), + self.get_config_flag('mpi', 'mpi'), ] config_cflags = [ '-O0' if '+debug' in spec else '-O3', @@ -71,49 +77,70 @@ class Zoltan(Package): ] if '+shared' in spec: - config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o') config_args.append('RANLIB=echo') + config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o') config_cflags.append('-fPIC') + if spec.satisfies('%gcc'): + config_args.append('--with-libs={0}'.format('-lgfortran')) if '+mpi' in spec: - config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin) - config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin) - config_args.append('--with-mpi=%s' % spec['mpi'].prefix) - config_args.append('--with-mpi-compilers=%s' % - spec['mpi'].prefix.bin) + config_args.append('CC={0}'.format(spec['mpi'].mpicc)) + config_args.append('CXX={0}'.format(spec['mpi'].mpicxx)) + config_args.append('FC={0}'.format(spec['mpi'].mpifc)) + + mpi_libs = ' -l'.join(self.get_mpi_libs()) + config_args.append('--with-mpi={0}'.format(spec['mpi'].prefix)) + config_args.append('--with-mpi-libs=-l{0}'.format(mpi_libs)) # NOTE: Early versions of Zoltan come packaged with a few embedded # library packages (e.g. ParMETIS, Scotch), which messes with Spack's # ability to descend directly into the package's source directory. + source_directory = self.stage.source_path if spec.satisfies('@:3.6'): - cd('Zoltan_v%s' % self.version) - - mkdirp('build') - cd('build') - - config_zoltan = Executable('../configure') - config_zoltan( - '--prefix=%s' % pwd(), - '--with-cflags=%s' % ' '.join(config_cflags), - '--with-cxxflags=%s' % ' '.join(config_cflags), - *config_args) - - make() - make('install') + zoltan_directory = 'Zoltan_v{0}'.format(self.version) + source_directory = join_path(source_directory, zoltan_directory) + + build_directory = join_path(source_directory, 'build') + with working_dir(build_directory, create=True): + config = Executable(join_path(source_directory, 'configure')) + config( + '--prefix={0}'.format(prefix), + '--with-cflags={0}'.format(' '.join(config_cflags)), + '--with-cxxflags={0}'.format(' '.join(config_cflags)), + '--with-fcflags={0}'.format(' '.join(config_cflags)), + *config_args + ) + + # NOTE: Earlier versions of Zoltan cannot be built in parallel + # because they contain nested Makefile dependency bugs. + make(parallel=not spec.satisfies('@:3.6+fortran')) + make('install') # NOTE: Unfortunately, Zoltan doesn't provide any configuration # options for the extension of the output library files, so this # script must change these extensions as a post-processing step. if '+shared' in spec: - for libpath in glob.glob('lib/*.a'): - libdir, libname = (os.path.dirname(libpath), - os.path.basename(libpath)) - move(libpath, os.path.join( - libdir, re.sub(r'\.a$', '.so', libname))) - - mkdirp(prefix) - move('include', prefix) - move('lib', prefix) - - def url_for_version(self, version): - return '%s/zoltan_distrib_v%s.tar.gz' % (Zoltan.base_url, version) + for lib_path in glob.glob(join_path(prefix, 'lib', '*.a')): + lib_static_name = os.path.basename(lib_path) + lib_shared_name = re.sub(r'\.a$', '.{0}'.format(dso_suffix), + lib_static_name) + move(lib_path, join_path(prefix, 'lib', lib_shared_name)) + + def get_config_flag(self, flag_name, flag_variant): + flag_pre = 'en' if '+{0}'.format(flag_variant) in self.spec else 'dis' + return '--{0}able-{1}'.format(flag_pre, flag_name) + + # NOTE: Zoltan assumes that it's linking against an MPI library that can + # be found with '-lmpi,' which isn't the case for many MPI packages. This + # function finds the names of the actual libraries for Zoltan's MPI dep. + def get_mpi_libs(self): + mpi_libs = set() + + for lib_path in glob.glob(join_path(self.spec['mpi'].prefix.lib, '*')): + mpi_lib_match = re.match( + r'^(lib)((\w*)mpi(\w*))\.((a)|({0}))$'.format(dso_suffix), + os.path.basename(lib_path)) + if mpi_lib_match: + mpi_libs.add(mpi_lib_match.group(2)) + + return list(mpi_libs) |