diff options
Diffstat (limited to 'var')
27 files changed, 1160 insertions, 193 deletions
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py new file mode 100644 index 0000000000..b3e5994e30 --- /dev/null +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -0,0 +1,67 @@ +############################################################################## +# 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 Armadillo(Package): + """Armadillo is a high quality linear algebra library (matrix maths) + for the C++ language, aiming towards a good balance between speed and + ease of use.""" + + homepage = "http://arma.sourceforge.net/" + url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + + version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') + + variant('hdf5', default=False, description='Include HDF5 support') + + depends_on('arpack') + depends_on('blas') + depends_on('lapack') + depends_on('superlu@5.2:') + depends_on('hdf5', when='+hdf5') + + def install(self, spec, prefix): + cmake_args = [ + # ARPACK support + '-DARPACK_LIBRARY={0}/libarpack.a'.format( + spec['arpack'].prefix.lib), + # BLAS support + '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib), + # LAPACK support + '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib), + # SuperLU support + '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include), + '-DSuperLU_LIBRARY={0}/libsuperlu.a'.format( + spec['superlu'].prefix.lib64), + # HDF5 support + '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF') + ] + + cmake_args.extend(std_cmake_args) + cmake('.', *cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/arpack/package.py b/var/spack/repos/builtin/packages/arpack/package.py index 75158776fe..91b5f06a4a 100644 --- a/var/spack/repos/builtin/packages/arpack/package.py +++ b/var/spack/repos/builtin/packages/arpack/package.py @@ -24,12 +24,12 @@ ############################################################################## from spack import * import os -import shutil + class Arpack(Package): """A collection of Fortran77 subroutines designed to solve large scale - eigenvalue problems. - """ + eigenvalue problems.""" + homepage = "http://www.caam.rice.edu/software/ARPACK/" url = "http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz" @@ -39,27 +39,35 @@ class Arpack(Package): depends_on('lapack') def patch(self): - # Filter the cray makefile to make a spack one. - shutil.move('ARMAKES/ARmake.CRAY', 'ARmake.inc') makefile = FileFilter('ARmake.inc') - # Be sure to use Spack F77 wrapper - makefile.filter('^FC.*', 'FC = f77') - makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g') + # Section 1: Paths and Libraries + + # Change the build directory + makefile.filter('^home.*', 'home = %s' % os.getcwd()) + + # Use external BLAS/LAPACK + makefile.filter('^BLASdir.*', + 'BLASdir = %s' % self.spec['blas'].prefix) + makefile.filter('^LAPACKdir.*', + 'LAPACKdir = %s' % self.spec['lapack'].prefix) + + # Do not include the platform in the library name + makefile.filter('^PLAT.*', 'PLAT = ') + makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = $(home)/libarpack.a') - # Set up some variables. - makefile.filter('^PLAT.*', 'PLAT = ') - makefile.filter('^home.*', 'home = %s' % os.getcwd()) - makefile.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix) - makefile.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix) + # Section 2: Compilers - # build the library in our own prefix. - makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = %s/libarpack.a' % os.getcwd()) + # Be sure to use the Spack compiler wrapper + makefile.filter('^FC.*', 'FC = {0}'.format(os.environ['F77'])) + makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g -fPIC') + if not which('ranlib'): + makefile.filter('^RANLIB.*', 'RANLIB = touch') def install(self, spec, prefix): with working_dir('SRC'): make('all') - mkdirp(prefix.lib) + mkdir(prefix.lib) install('libarpack.a', prefix.lib) diff --git a/var/spack/repos/builtin/packages/daal/package.py b/var/spack/repos/builtin/packages/daal/package.py new file mode 100644 index 0000000000..e13dd80e19 --- /dev/null +++ b/var/spack/repos/builtin/packages/daal/package.py @@ -0,0 +1,28 @@ +from spack import * +import os + +from spack.pkg.builtin.intel import IntelInstaller + + +class Daal(IntelInstaller): + """Intel Data Analytics Acceleration Library. + + Note: You will have to add the download file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "https://software.intel.com/en-us/daal" + + version('2016.2.181', 'aad2aa70e5599ebfe6f85b29d8719d46', + url="file://%s/l_daal_2016.2.181.tgz" % os.getcwd()) + version('2016.3.210', 'ad747c0dd97dace4cad03cf2266cad28', + url="file://%s/l_daal_2016.3.210.tgz" % os.getcwd()) + + def install(self, spec, prefix): + + self.intel_prefix = os.path.join(prefix, "pkg") + IntelInstaller.install(self, spec, prefix) + + daal_dir = os.path.join(self.intel_prefix, "daal") + for f in os.listdir(daal_dir): + os.symlink(os.path.join(daal_dir, f), os.path.join(self.prefix, f)) diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 54b6426d36..23ec74abed 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -80,8 +80,8 @@ 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='+petsc+mpi') - depends_on("slepc", when='+slepc+petsc+mpi') + depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501 + depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi') depends_on("trilinos", when='+trilinos+mpi') # developer dependnecies @@ -108,12 +108,11 @@ class Dealii(Package): # of Spack's. Be more specific to avoid this. # Note that both lapack and blas are provided in -DLAPACK_XYZ. '-DLAPACK_FOUND=true', - '-DLAPACK_INCLUDE_DIRS=%s;%s' % - (spec['lapack'].prefix.include, - spec['blas'].prefix.include), - '-DLAPACK_LIBRARIES=%s;%s' % - (spec['lapack'].lapack_shared_lib, - spec['blas'].blas_shared_lib), + '-DLAPACK_INCLUDE_DIRS=%s;%s' % ( + spec['lapack'].prefix.include, spec['blas'].prefix.include), + '-DLAPACK_LIBRARIES=%s;%s' % ( + spec['lapack'].lapack_shared_lib, + spec['blas'].blas_shared_lib), '-DMUPARSER_DIR=%s' % spec['muparser'].prefix, '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, '-DTBB_DIR=%s' % spec['tbb'].prefix, @@ -168,14 +167,14 @@ class Dealii(Package): if '+netcdf' in spec: options.extend([ '-DNETCDF_FOUND=true', - '-DNETCDF_LIBRARIES=%s;%s' % - (join_path(spec['netcdf-cxx'].prefix.lib, - 'libnetcdf_c++.%s' % dsuf), - join_path(spec['netcdf'].prefix.lib, - 'libnetcdf.%s' % dsuf)), - '-DNETCDF_INCLUDE_DIRS=%s;%s' % - (spec['netcdf-cxx'].prefix.include, - spec['netcdf'].prefix.include), + '-DNETCDF_LIBRARIES=%s;%s' % ( + join_path(spec['netcdf-cxx'].prefix.lib, + 'libnetcdf_c++.%s' % dsuf), + join_path(spec['netcdf'].prefix.lib, + 'libnetcdf.%s' % dsuf)), + '-DNETCDF_INCLUDE_DIRS=%s;%s' % ( + spec['netcdf-cxx'].prefix.include, + spec['netcdf'].prefix.include), ]) else: options.extend([ @@ -266,9 +265,9 @@ class Dealii(Package): filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', (''), 'step-40.cc') - filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', + filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 (''), 'step-40.cc') - filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', + filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 (''), 'step-40.cc') filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 filter_file(r'(preconditioner\);)', (''), 'step-40.cc') diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index 63a5560137..447964f286 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -26,20 +26,28 @@ from spack import * import os + class Espresso(Package): """ - QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials - modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + QE is an integrated suite of Open-Source computer codes for + electronic-structure calculations and materials modeling at + the nanoscale. It is based on density-functional theory, plane + waves, and pseudopotentials. """ homepage = 'http://quantum-espresso.org' url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz' + version( + '5.4.0', + '8bb78181b39bd084ae5cb7a512c1cfe7', + url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz' + ) version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3') - variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support') + variant('mpi', default=True, description='Builds with mpi support') variant('openmp', default=False, description='Enables openMP support') variant('scalapack', default=True, description='Enables scalapack support') - variant('elpa', default=True, description='Use elpa as an eigenvalue solver') + variant('elpa', default=True, description='Uses elpa as an eigenvalue solver') depends_on('blas') depends_on('lapack') @@ -47,7 +55,12 @@ class Espresso(Package): depends_on('mpi', when='+mpi') depends_on('fftw~mpi', when='~mpi') depends_on('fftw+mpi', when='+mpi') - depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation + # TODO : + mpi needed to avoid false dependencies installation + depends_on('scalapack', when='+scalapack+mpi') + + # Spurious problems running in parallel the Makefile + # generated by qe configure + parallel = False def check_variants(self, spec): error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active' @@ -93,4 +106,3 @@ class Espresso(Package): install(filename, prefix.bin) else: make('install') - diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py new file mode 100644 index 0000000000..15ddfcee16 --- /dev/null +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -0,0 +1,103 @@ +############################################################################## +# 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 * +import os + + +class Ferret(Package): + """Ferret is an interactive computer visualization and analysis environment + designed to meet the needs of oceanographers and meteorologists + analyzing large and complex gridded data sets.""" + homepage = "http://ferret.noaa.gov/Ferret/" + url = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz" + + version('6.96', '51722027c864369f41bab5751dfff8cc', + url="ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz") + + depends_on("hdf5~mpi~fortran") + depends_on("netcdf~mpi") + depends_on("netcdf-fortran") + depends_on("readline") + depends_on("zlib") + + def patch(self): + hdf5_prefix = self.spec['hdf5'].prefix + netcdff_prefix = self.spec['netcdf-fortran'].prefix + readline_prefix = self.spec['readline'].prefix + libz_prefix = self.spec['zlib'].prefix + + filter_file(r'^BUILDTYPE.+', + 'BUILDTYPE = x86_64-linux', + 'FERRET/site_specific.mk') + filter_file(r'^INSTALL_FER_DIR.+', + 'INSTALL_FER_DIR = %s' % self.spec.prefix, + 'FERRET/site_specific.mk') + filter_file(r'^HDF5_DIR.+', + 'HDF5_DIR = %s' % hdf5_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^NETCDF4_DIR.+', + 'NETCDF4_DIR = %s' % netcdff_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^READLINE_DIR.+', + 'READLINE_DIR = %s' % readline_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^LIBZ_DIR.+', + 'LIBZ_DIR = %s' % libz_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^JAVA_HOME.+', + ' ', + 'FERRET/site_specific.mk') + filter_file(r'-lm', + '-lgfortran -lm', + 'FERRET/platform_specific.mk.x86_64-linux') + + def install(self, spec, prefix): + hdf5_prefix = spec['hdf5'].prefix + netcdff_prefix = spec['netcdf-fortran'].prefix + netcdf_prefix = spec['netcdf'].prefix + libz_prefix = spec['zlib'].prefix + ln = which('ln') + ln('-sf', + hdf5_prefix + '/lib', + hdf5_prefix + '/lib64') + ln('-sf', + netcdff_prefix + '/lib', + netcdff_prefix + '/lib64') + ln('-sf', + netcdf_prefix + '/lib/libnetcdf.a', + netcdff_prefix + '/lib/libnetcdf.a') + ln('-sf', + netcdf_prefix + '/lib/libnetcdf.la', + netcdff_prefix + '/lib/libnetcdf.la') + ln('-sf', + libz_prefix + '/lib', + libz_prefix + '/lib64') + os.environ['LDFLAGS'] = '-lquadmath' + with working_dir('FERRET', create=False): + os.environ['LD_X11'] = '-L/usr/lib/X11 -lX11' + os.environ['HOSTTYPE'] = 'x86_64-linux' + make(parallel=False) + make("install") diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py new file mode 100644 index 0000000000..493ca16417 --- /dev/null +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -0,0 +1,144 @@ +from spack import * +import os +import re + +from spack.pkg.builtin.intel import IntelInstaller, filter_pick, \ + get_all_components + + +class IntelParallelStudio(IntelInstaller): + """Intel Parallel Studio. + + Note: You will have to add the download file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe" + + # TODO: can also try the online installer (will download files on demand) + version('composer.2016.2', '1133fb831312eb519f7da897fec223fa', + url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501 + % os.getcwd()) + version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', + url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501 + version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', + url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501 + version('composer.2016.3', '3208eeabee951fc27579177b593cefe9', + url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501 + % os.getcwd()) + version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3', + url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501 + version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3', + url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501 + + variant('rpath', default=True, description="Add rpath to .cfg files") + variant('newdtags', default=False, + description="Allow use of --enable-new-dtags in MPI wrappers") + variant('all', default=False, + description="Install all files with the requested edition") + variant('mpi', default=True, + description="Install the Intel MPI library and ITAC tool") + variant('mkl', default=True, description="Install the Intel MKL library") + variant('daal', + default=True, description="Install the Intel DAAL libraries") + variant('ipp', default=True, description="Install the Intel IPP libraries") + variant('tools', default=True, description="""Install the Intel Advisor,\ +VTune Amplifier, and Inspector tools""") + + provides('mpi', when='@cluster:+mpi') + provides('mkl', when='+mkl') + provides('daal', when='+daal') + provides('ipp', when='+ipp') + + def install(self, spec, prefix): + + base_components = "ALL" # when in doubt, install everything + mpi_components = "" + mkl_components = "" + daal_components = "" + ipp_components = "" + + if spec.satisfies('+all'): + base_components = "ALL" + else: + all_components = get_all_components() + regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)' + base_components = \ + filter_pick(all_components, re.compile(regex).search) + regex = '(icsxe|imb|mpi|itac|intel-tc|clck)' + mpi_components = \ + filter_pick(all_components, re.compile(regex).search) + mkl_components = \ + filter_pick(all_components, re.compile('(mkl)').search) + daal_components = \ + filter_pick(all_components, re.compile('(daal)').search) + ipp_components = \ + filter_pick(all_components, re.compile('(ipp)').search) + regex = '(gdb|vtune|inspector|advisor)' + tool_components = \ + filter_pick(all_components, re.compile(regex).search) + + components = base_components + if not spec.satisfies('+all'): + if spec.satisfies('+mpi') and 'cluster' in str(spec.version): + components += mpi_components + if spec.satisfies('+mkl'): + components += mkl_components + if spec.satisfies('+daal'): + components += daal_components + if spec.satisfies('+ipp'): + components += ipp_components + if spec.satisfies('+tools') and (spec.satisfies('@cluster') or + spec.satisfies('@professional')): + components += tool_components + + self.intel_components = ';'.join(components) + IntelInstaller.install(self, spec, prefix) + + absbindir = os.path.dirname(os.path.realpath(os.path.join( + self.prefix.bin, "icc"))) + abslibdir = os.path.dirname(os.path.realpath(os.path.join + (self.prefix.lib, "intel64", "libimf.a"))) + + os.symlink(self.global_license_file, os.path.join(absbindir, + "license.lic")) + if spec.satisfies('+tools') and (spec.satisfies('@cluster') or + spec.satisfies('@professional')): + os.mkdir(os.path.join(self.prefix, "inspector_xe/licenses")) + os.symlink(self.global_license_file, os.path.join( + self.prefix, "inspector_xe/licenses", "license.lic")) + os.mkdir(os.path.join(self.prefix, "advisor_xe/licenses")) + os.symlink(self.global_license_file, os.path.join( + self.prefix, "advisor_xe/licenses", "license.lic")) + os.mkdir(os.path.join(self.prefix, "vtune_amplifier_xe/licenses")) + os.symlink(self.global_license_file, os.path.join( + self.prefix, "vtune_amplifier_xe/licenses", "license.lic")) + + if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \ + spec.satisfies('@cluster'): + os.symlink(self.global_license_file, os.path.join( + self.prefix, "itac_latest", "license.lic")) + if spec.satisfies('~newdtags'): + wrappers = ["mpif77", "mpif77", "mpif90", "mpif90", + "mpigcc", "mpigcc", "mpigxx", "mpigxx", + "mpiicc", "mpiicc", "mpiicpc", "mpiicpc", + "mpiifort", "mpiifort"] + wrapper_paths = [] + for root, dirs, files in os.walk(spec.prefix): + for name in files: + if name in wrappers: + wrapper_paths.append(os.path.join(spec.prefix, + root, name)) + for wrapper in wrapper_paths: + filter_file(r'-Xlinker --enable-new-dtags', r' ', + wrapper) + + if spec.satisfies('+rpath'): + for compiler_command in ["icc", "icpc", "ifort"]: + cfgfilename = os.path.join(absbindir, "%s.cfg" % + compiler_command) + with open(cfgfilename, "w") as f: + f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir) + + os.symlink(os.path.join(self.prefix.man, "common", "man1"), + os.path.join(self.prefix.man, "man1")) diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py new file mode 100644 index 0000000000..ec3192380a --- /dev/null +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -0,0 +1,125 @@ +from spack import * +import os +import re + + +def filter_pick(input_list, regex_filter): + """Returns the items in input_list that are found in the regex_filter""" + return [l for l in input_list for m in (regex_filter(l),) if m] + + +def unfilter_pick(input_list, regex_filter): + """Returns the items in input_list that are not found in the + regex_filter""" + return [l for l in input_list for m in (regex_filter(l),) if not m] + + +def get_all_components(): + """Returns a list of all the components associated with the downloaded + Intel package""" + all_components = [] + with open("pset/mediaconfig.xml", "r") as f: + lines = f.readlines() + for line in lines: + if line.find('<Abbr>') != -1: + component = line[line.find('<Abbr>') + 6:line.find('</Abbr>')] + all_components.append(component) + return all_components + + +class IntelInstaller(Package): + """Base package containing common methods for installing Intel software""" + + homepage = "https://software.intel.com/en-us" + intel_components = "ALL" + license_required = True + license_comment = '#' + license_files = ['Licenses/license.lic'] + license_vars = ['INTEL_LICENSE_FILE'] + license_url = \ + 'https://software.intel.com/en-us/articles/intel-license-manager-faq' + + @property + def global_license_file(self): + """Returns the path where a global license file should be stored.""" + if not self.license_files: + return + return join_path(self.global_license_dir, "intel", + os.path.basename(self.license_files[0])) + + def install(self, spec, prefix): + + # Remove the installation DB, otherwise it will try to install into + # location of other Intel builds + if os.path.exists(os.path.join(os.environ["HOME"], "intel", + "intel_sdp_products.db")): + os.remove(os.path.join(os.environ["HOME"], "intel", + "intel_sdp_products.db")) + + if not hasattr(self, "intel_prefix"): + self.intel_prefix = self.prefix + + silent_config_filename = 'silent.cfg' + with open(silent_config_filename, 'w') as f: + f.write(""" +ACCEPT_EULA=accept +PSET_MODE=install +CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes +PSET_INSTALL_DIR=%s +ACTIVATION_LICENSE_FILE=%s +ACTIVATION_TYPE=license_file +PHONEHOME_SEND_USAGE_DATA=no +CONTINUE_WITH_OPTIONAL_ERROR=yes +COMPONENTS=%s +""" % (self.intel_prefix, self.global_license_file, self.intel_components)) + + install_script = which("install.sh") + install_script('--silent', silent_config_filename) + + +class Intel(IntelInstaller): + """Intel Compilers. + + Note: You will have to add the download file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe" + + # TODO: can also try the online installer (will download files on demand) + version('16.0.2', '1133fb831312eb519f7da897fec223fa', + url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501 + % os.getcwd()) + version('16.0.3', '3208eeabee951fc27579177b593cefe9', + url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501 + % os.getcwd()) + + variant('rpath', default=True, description="Add rpath to .cfg files") + + def install(self, spec, prefix): + components = [] + all_components = get_all_components() + regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)' + components = filter_pick(all_components, re.compile(regex).search) + + self.intel_components = ';'.join(components) + IntelInstaller.install(self, spec, prefix) + + absbindir = os.path.split(os.path.realpath(os.path.join( + self.prefix.bin, "icc")))[0] + abslibdir = os.path.split(os.path.realpath(os.path.join( + self.prefix.lib, "intel64", "libimf.a")))[0] + + # symlink or copy? + os.symlink(self.global_license_file, os.path.join(absbindir, + "license.lic")) + + if spec.satisfies('+rpath'): + for compiler_command in ["icc", "icpc", "ifort"]: + cfgfilename = os.path.join(absbindir, "%s.cfg" % + compiler_command) + with open(cfgfilename, "w") as f: + f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir) + + os.symlink(os.path.join(self.prefix.man, "common", "man1"), + os.path.join(self.prefix.man, "man1")) diff --git a/var/spack/repos/builtin/packages/ipp/package.py b/var/spack/repos/builtin/packages/ipp/package.py new file mode 100644 index 0000000000..2bd931d5bd --- /dev/null +++ b/var/spack/repos/builtin/packages/ipp/package.py @@ -0,0 +1,26 @@ +from spack import * +import os + +from spack.pkg.builtin.intel import IntelInstaller + + +class Ipp(IntelInstaller): + """Intel Integrated Performance Primitives. + + Note: You will have to add the download file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "https://software.intel.com/en-us/intel-ipp" + + version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3', + url="file://%s/l_ipp_9.0.3.210.tgz" % os.getcwd()) + + def install(self, spec, prefix): + + self.intel_prefix = os.path.join(prefix, "pkg") + IntelInstaller.install(self, spec, prefix) + + ipp_dir = os.path.join(self.intel_prefix, "ipp") + for f in os.listdir(ipp_dir): + os.symlink(os.path.join(ipp_dir, f), os.path.join(self.prefix, f)) diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py new file mode 100644 index 0000000000..454e78d29c --- /dev/null +++ b/var/spack/repos/builtin/packages/mkl/package.py @@ -0,0 +1,28 @@ +from spack import * +import os + +from spack.pkg.builtin.intel import IntelInstaller + + +class Mkl(IntelInstaller): + """Intel Math Kernel Library. + + Note: You will have to add the download file to a + mirror so that Spack can find it. For instructions on how to set up a + mirror, see http://software.llnl.gov/spack/mirrors.html""" + + homepage = "https://software.intel.com/en-us/intel-mkl" + + version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65', + url="file://%s/l_mkl_11.3.2.181.tgz" % os.getcwd()) + version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34', + url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd()) + + def install(self, spec, prefix): + + self.intel_prefix = os.path.join(prefix, "pkg") + IntelInstaller.install(self, spec, prefix) + + mkl_dir = os.path.join(self.intel_prefix, "mkl") + for f in os.listdir(mkl_dir): + os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f)) diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 22e49daaa7..d09ebd6739 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -48,6 +48,13 @@ class Openblas(Package): patch('make.patch') def install(self, spec, prefix): + # As of 06/2016 there is no mechanism to specify that packages which + # depends on Blas/Lapack need C or/and Fortran symbols. For now + # require both. + if self.compiler.f77 is None: + raise InstallError('OpenBLAS requires both C and Fortran ', + 'compilers!') + # Configure fails to pick up fortran from FC=/abs/path/to/f77, but # works fine with FC=/abs/path/to/gfortran. # When mixing compilers make sure that diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 0638628a6c..be3d1342fc 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -121,6 +121,13 @@ class Openmpi(Package): return 'verbs' def install(self, spec, prefix): + # As of 06/2016 there is no mechanism to specify that packages which + # depends on MPI need C or/and Fortran implementation. For now + # require both. + if (self.compiler.f77 is None) or (self.compiler.fc is None): + raise InstallError('OpenMPI requires both C and Fortran ', + 'compilers!') + config_args = ["--prefix=%s" % prefix, "--with-hwloc=%s" % spec['hwloc'].prefix, "--enable-shared", diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 6456a1aabf..8dd1d8d2b9 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -28,13 +28,16 @@ from spack import * class Petsc(Package): """ - PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications - modeled by partial differential equations. + PETSc is a suite of data structures and routines for the scalable + (parallel) solution of scientific applications modeled by partial + differential equations. """ homepage = "http://www.mcs.anl.gov/petsc/index.html" url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34') + version('3.6.4', '7632da2375a3df35b8891c9526dbdde7') version('3.6.3', '91dd3522de5a5ef039ff8f50800db606') version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f') version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13') @@ -69,10 +72,12 @@ class Petsc(Package): depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('parmetis', when='+metis+mpi') # Hypre does not support complex numbers. - # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers - # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py + # Also PETSc prefer to build it without internal superlu, likely due to + # conflict in headers see + # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py # NOQA: ignore=E501 depends_on('hypre~internal-superlu', when='+hypre+mpi~complex') - depends_on('superlu-dist', when='+superlu-dist+mpi') + depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi') + depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi') depends_on('mumps+mpi', when='+mumps+mpi') depends_on('scalapack', when='+mumps+mpi') @@ -80,17 +85,17 @@ class Petsc(Package): if '~mpi' in self.spec: compiler_opts = [ '--with-cc=%s' % os.environ['CC'], - '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), - '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), + '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), # NOQA: ignore=E501 + '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), # NOQA: ignore=E501 '--with-mpi=0' ] - error_message_fmt = '\t{library} support requires "+mpi" to be activated' + error_message_fmt = '\t{library} support requires "+mpi" to be activated' # NOQA: ignore=E501 - # If mpi is disabled (~mpi), it's an error to have any of these enabled. - # This generates a list of any such errors. + # If mpi is disabled (~mpi), it's an error to have any of these + # enabled. This generates a list of any such errors. errors = [error_message_fmt.format(library=x) - for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist') - if ('+'+x) in self.spec] + for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist') # NOQA: ignore=E501 + if ('+' + x) in self.spec] if errors: errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) @@ -105,26 +110,31 @@ class Petsc(Package): options = ['--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ - '--with-precision=%s' % ('double' if '+double' in spec else 'single'), - '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), + '--with-precision=%s' % ('double' if '+double' in spec else 'single'), # NOQA: ignore=E501 + '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), # NOQA: ignore=E501 '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), '--with-debugging=%s' % ('1' if '+debug' in spec else '0'), '--with-blas-lapack-dir=%s' % spec['lapack'].prefix ]) # Activates library support if needed - for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'): + for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis', + 'mumps', 'scalapack'): options.append( - '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) + '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) # NOQA: ignore=E501 ) if library in spec: options.append( - '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) + '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) # NOQA: ignore=E501 ) - # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a + # PETSc does not pick up SuperluDist from the dir as they look for + # superlu_dist_4.1.a if 'superlu-dist' in spec: options.extend([ - '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include, - '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'), + '--with-superlu_dist-include=%s' % + spec['superlu-dist'].prefix.include, + '--with-superlu_dist-lib=%s' % + join_path(spec['superlu-dist'].prefix.lib, + 'libsuperlu_dist.a'), '--with-superlu_dist=1' ]) else: diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py index 86875bbcae..a9962777dc 100644 --- a/var/spack/repos/builtin/packages/py-astropy/package.py +++ b/var/spack/repos/builtin/packages/py-astropy/package.py @@ -24,29 +24,38 @@ ############################################################################## from spack import * + class PyAstropy(Package): - """ - The Astropy Project is a community effort to develop a single core + """The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between - Python astronomy packages. - """ + Python astronomy packages.""" + homepage = 'http://www.astropy.org/' + url = 'https://pypi.python.org/packages/source/a/astropy/astropy-1.1.2.tar.gz' + version('1.1.2', 'cbe32023b5b1177d1e2498a0d00cda51') version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d') - def url_for_version(self, version): - return 'https://pypi.python.org/packages/source/a/astropy/astropy-{0}.tar.gz'.format(version) - + # Required dependencies extends('python') + depends_on('py-numpy') - depends_on('cfitsio') - depends_on('expat') + # Optional dependencies depends_on('py-h5py') - depends_on('py-numpy') + depends_on('py-beautifulsoup4') + depends_on('py-pyyaml') depends_on('py-scipy') + depends_on('libxml2') + depends_on('py-matplotlib') + depends_on('py-pytz') + depends_on('py-scikit-image') + depends_on('py-pandas') + + # System dependencies + depends_on('cfitsio') + depends_on('expat') def install(self, spec, prefix): python('setup.py', 'build', '--use-system-cfitsio', - '--use-system-expat') - python('setup.py', 'install', '--prefix=' + prefix) - + '--use-system-expat') + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py new file mode 100644 index 0000000000..64368fe70d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 PyBeautifulsoup4(Package): + """Beautiful Soup is a Python library for pulling data out of HTML and + XML files. It works with your favorite parser to provide idiomatic ways + of navigating, searching, and modifying the parse tree.""" + + homepage = "https://www.crummy.com/software/BeautifulSoup" + url = "https://pypi.python.org/packages/source/b/beautifulsoup4/beautifulsoup4-4.4.1.tar.gz" + + version('4.4.1', '8fbd9a7cac0704645fa20d1419036815') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py new file mode 100644 index 0000000000..d57ef4bd76 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-emcee/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 PyEmcee(Package): + """emcee is an MIT licensed pure-Python implementation of Goodman & Weare's + Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.""" + + homepage = "http://dan.iel.fm/emcee/current/" + url = "https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz" + + version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7') + + extends('python') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index a8eb027ba5..0180b658f5 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -23,23 +23,42 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyH5py(Package): - """The h5py package provides both a high- and low-level interface to the HDF5 library from Python.""" + """The h5py package provides both a high- and low-level interface to the + HDF5 library from Python.""" + homepage = "https://pypi.python.org/pypi/h5py" url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz" - version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758') + version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4') version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74') + version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758') + + variant('mpi', default=False, description='Build with MPI support') - extends('python', ignore=lambda f: re.match(r'bin/cy*', f)) - depends_on('hdf5') - depends_on('py-numpy') - depends_on('py-cython') + extends('python') + + # Build dependencies + depends_on('py-cython@0.19:') + depends_on('pkg-config') + depends_on('hdf5@1.8.4:+mpi', when='+mpi') + depends_on('hdf5@1.8.4:~mpi', when='~mpi') + depends_on('mpi', when='+mpi') + + # Build and runtime dependencies + depends_on('py-numpy@1.6.1:') + + # Runtime dependencies depends_on('py-six') - depends_on('py-pkgconfig') def install(self, spec, prefix): - python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix) - python('setup.py', 'install', '--prefix=%s' % prefix) + python('setup.py', 'configure', + '--hdf5={0}'.format(spec['hdf5'].prefix)) + + if '+mpi' in spec: + env['CC'] = spec['mpi'].mpicc + python('setup.py', 'configure', '--mpi') + + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py new file mode 100644 index 0000000000..47751a702d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-iminuit/package.py @@ -0,0 +1,46 @@ +############################################################################## +# 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 PyIminuit(Package): + """Interactive IPython-Friendly Minimizer based on SEAL Minuit2.""" + + homepage = "https://pypi.python.org/pypi/iminuit" + url = "https://pypi.python.org/packages/source/i/iminuit/iminuit-1.2.tar.gz" + + version('1.2', '4701ec472cae42015e26251703e6e984') + + # Required dependencies + extends('python') + depends_on('py-setuptools') + + # Optional dependencies + depends_on('py-numpy') + depends_on('py-matplotlib') + depends_on('py-cython') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py new file mode 100644 index 0000000000..16506e3eca --- /dev/null +++ b/var/spack/repos/builtin/packages/py-nestle/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 PyNestle(Package): + """Nested sampling algorithms for evaluating Bayesian evidence.""" + + homepage = "http://kbarbary.github.io/nestle/" + url = "https://pypi.python.org/packages/source/n/nestle/nestle-0.1.1.tar.gz" + + version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5') + + # Required dependencies + extends('python') + depends_on('py-numpy') + + # Optional dependencies + depends_on('py-scipy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py new file mode 100644 index 0000000000..82ae2a2e69 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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 PySncosmo(Package): + """SNCosmo is a Python library for high-level supernova cosmology + analysis.""" + + homepage = "http://sncosmo.readthedocs.io/" + url = "https://pypi.python.org/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz" + + version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e') + + # Required dependencies + # py-sncosmo binaries are duplicates of those from py-astropy + extends('python', ignore=r'bin/.*') + depends_on('py-numpy') + depends_on('py-scipy') + depends_on('py-astropy') + + # Recommended dependencies + depends_on('py-matplotlib') + depends_on('py-iminuit') + depends_on('py-emcee') + depends_on('py-nestle') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py new file mode 100644 index 0000000000..b0adbe3658 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-wcsaxes/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 PyWcsaxes(Package): + """WCSAxes is a framework for making plots of Astronomical data + in Matplotlib.""" + + homepage = "http://wcsaxes.readthedocs.io/en/latest/index.html" + url = "https://github.com/astrofrog/wcsaxes/archive/v0.8.tar.gz" + + version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920') + + extends('python', ignore=r'bin/pbr') + depends_on('py-numpy') + depends_on('py-matplotlib') + depends_on('py-astropy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 86c12498e1..b6a62bf742 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -22,9 +22,6 @@ # 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 functools -import glob -import inspect import os import re from contextlib import closing @@ -37,11 +34,10 @@ from spack.util.environment import * class Python(Package): """The Python programming language.""" + homepage = "http://www.python.org" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz" - extendable = True - version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe') version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36') version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True) @@ -49,6 +45,8 @@ class Python(Package): version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') + extendable = True + depends_on("openssl") depends_on("bzip2") depends_on("readline") @@ -64,39 +62,63 @@ class Python(Package): # Rest of install is pretty standard except setup.py needs to # be able to read the CPPFLAGS and LDFLAGS as it scans for the # library and headers to build - configure_args= [ - "--prefix=%s" % prefix, - "--with-threads", - "--enable-shared", - "CPPFLAGS=-I%s/include -I%s/include -I%s/include -I%s/include -I%s/include -I%s/include" % ( - spec['openssl'].prefix, spec['bzip2'].prefix, - spec['readline'].prefix, spec['ncurses'].prefix, - spec['sqlite'].prefix, spec['zlib'].prefix), - "LDFLAGS=-L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib" % ( - spec['openssl'].prefix, spec['bzip2'].prefix, - spec['readline'].prefix, spec['ncurses'].prefix, - spec['sqlite'].prefix, spec['zlib'].prefix) - ] + cppflags = ' -I'.join([ + spec['openssl'].prefix.include, spec['bzip2'].prefix.include, + spec['readline'].prefix.include, spec['ncurses'].prefix.include, + spec['sqlite'].prefix.include, spec['zlib'].prefix.include + ]) + + ldflags = ' -L'.join([ + spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib, + spec['readline'].prefix.lib, spec['ncurses'].prefix.lib, + spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib + ]) + + config_args = [ + "--prefix={0}".format(prefix), + "--with-threads", + "--enable-shared", + "CPPFLAGS=-I{0}".format(cppflags), + "LDFLAGS=-L{0}".format(ldflags) + ] + if spec.satisfies('@3:'): - configure_args.append('--without-ensurepip') - configure(*configure_args) + config_args.append('--without-ensurepip') + + configure(*config_args) + make() make("install") - # Modify compiler paths in configuration files. This is necessary for - # building site packages outside of spack - filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)', - (r'\4\5'), - join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py')) + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} - python3_version = '' + dirname = join_path(prefix.lib, + 'python{0}'.format(self.version.up_to(2))) + + config = 'config' if spec.satisfies('@3:'): - python3_version = '-%d.%dm' % self.version[:2] - makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile') - filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)', - (r'\4\5'), - makefile_filepath) + config = 'config-{0}m'.format(self.version.up_to(2)) + + files = [ + '_sysconfigdata.py', + join_path(config, 'Makefile') + ] + for filename in files: + filter_file(env['CC'], self.compiler.cc, + join_path(dirname, filename), **kwargs) + filter_file(env['CXX'], self.compiler.cxx, + join_path(dirname, filename), **kwargs) # ======================================================================== # Set up environment to make install easy for python extensions. @@ -104,57 +126,59 @@ class Python(Package): @property def python_lib_dir(self): - return os.path.join('lib', 'python%d.%d' % self.version[:2]) - + return join_path('lib', 'python{0}'.format(self.version.up_to(2))) @property def python_include_dir(self): - return os.path.join('include', 'python%d.%d' % self.version[:2]) - + return join_path('include', 'python{0}'.format(self.version.up_to(2))) @property def site_packages_dir(self): - return os.path.join(self.python_lib_dir, 'site-packages') - + return join_path(self.python_lib_dir, 'site-packages') def setup_dependent_environment(self, spack_env, run_env, extension_spec): - # TODO: do this only for actual extensions. + """Set PYTHONPATH to include site-packages dir for the + extension and any other python extensions it depends on.""" - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. python_paths = [] for d in extension_spec.traverse(): if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + python_paths.append(join_path(d.prefix, + self.site_packages_dir)) pythonpath = ':'.join(python_paths) spack_env.set('PYTHONPATH', pythonpath) - # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH + # For run time environment set only the path for + # extension_spec and prepend it to PYTHONPATH if extension_spec.package.extends(self.spec): - run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir)) - + run_env.prepend_path('PYTHONPATH', join_path( + extension_spec.prefix, self.site_packages_dir)) def setup_dependent_package(self, module, ext_spec): - """ - Called before python modules' install() methods. + """Called before python modules' install() methods. In most cases, extensions will only need to have one line:: - python('setup.py', 'install', '--prefix=%s' % prefix) - """ + python('setup.py', 'install', '--prefix={0}'.format(prefix))""" + # Python extension builds can have a global python executable function - if self.version >= Version("3.0.0") and self.version < Version("4.0.0"): - module.python = Executable(join_path(self.spec.prefix.bin, 'python3')) + if Version("3.0.0") <= self.version < Version("4.0.0"): + module.python = Executable(join_path(self.spec.prefix.bin, + 'python3')) else: - module.python = Executable(join_path(self.spec.prefix.bin, 'python')) + module.python = Executable(join_path(self.spec.prefix.bin, + 'python')) # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. - module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) - module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) - module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir) - - # Make the site packages directory for extensions, if it does not exist already. + module.python_lib_dir = join_path(ext_spec.prefix, + self.python_lib_dir) + module.python_include_dir = join_path(ext_spec.prefix, + self.python_include_dir) + module.site_packages_dir = join_path(ext_spec.prefix, + self.site_packages_dir) + + # Make the site packages directory for extensions if ext_spec.package.is_extension: mkdirp(module.site_packages_dir) @@ -167,25 +191,28 @@ class Python(Package): ignore_arg = args.get('ignore', lambda f: False) # Always ignore easy-install.pth, as it needs to be merged. - patterns = [r'easy-install\.pth$'] + patterns = [r'site-packages/easy-install\.pth$'] # Ignore pieces of setuptools installed by other packages. + # Must include directory name or it will remove all site*.py files. if ext_pkg.name != 'py-setuptools': - patterns.append(r'/site[^/]*\.pyc?$') - patterns.append(r'setuptools\.pth') - patterns.append(r'bin/easy_install[^/]*$') - patterns.append(r'setuptools.*egg$') + patterns.extend([ + r'bin/easy_install[^/]*$', + r'site-packages/setuptools[^/]*\.egg$', + r'site-packages/setuptools\.pth$', + r'site-packages/site[^/]*\.pyc?$', + r'site-packages/__pycache__/site[^/]*\.pyc?$' + ]) if ext_pkg.name != 'py-numpy': patterns.append(r'bin/f2py$') return match_predicate(ignore_arg, patterns) - def write_easy_install_pth(self, exts): paths = [] for ext in sorted(exts.values()): - ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir) - easy_pth = "%s/easy-install.pth" % ext_site_packages + ext_site_packages = join_path(ext.prefix, self.site_packages_dir) + easy_pth = join_path(ext_site_packages, "easy-install.pth") if not os.path.isfile(easy_pth): continue @@ -195,15 +222,18 @@ class Python(Package): line = line.rstrip() # Skip lines matching these criteria - if not line: continue - if re.search(r'^(import|#)', line): continue - if (ext.name != 'py-setuptools' and - re.search(r'setuptools.*egg$', line)): continue + if not line: + continue + if re.search(r'^(import|#)', line): + continue + if ((ext.name != 'py-setuptools' and + re.search(r'setuptools.*egg$', line))): + continue paths.append(line) - site_packages = os.path.join(self.prefix, self.site_packages_dir) - main_pth = "%s/easy-install.pth" % site_packages + site_packages = join_path(self.prefix, self.site_packages_dir) + main_pth = join_path(site_packages, "easy-install.pth") if not paths: if os.path.isfile(main_pth): @@ -211,15 +241,22 @@ class Python(Package): else: with closing(open(main_pth, 'w')) as f: - f.write("import sys; sys.__plen = len(sys.path)\n") + f.write(""" +import sys +sys.__plen = len(sys.path) +""") for path in paths: - f.write("%s\n" % path) - f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; " - "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n") - + f.write("{0}\n".format(path)) + f.write(""" +new = sys.path[sys.__plen:] +del sys.path[sys.__plen:] +p = getattr(sys, '__egginsert', 0) +sys.path[p:p] = new +sys.__egginsert = p + len(new) +""") def activate(self, ext_pkg, **args): - ignore=self.python_ignore(ext_pkg, args) + ignore = self.python_ignore(ext_pkg, args) args.update(ignore=ignore) super(Python, self).activate(ext_pkg, **args) @@ -228,12 +265,12 @@ class Python(Package): exts[ext_pkg.name] = ext_pkg.spec self.write_easy_install_pth(exts) - def deactivate(self, ext_pkg, **args): args.update(ignore=self.python_ignore(ext_pkg, args)) super(Python, self).deactivate(ext_pkg, **args) exts = spack.install_layout.extension_map(self.spec) - if ext_pkg.name in exts: # Make deactivate idempotent. + # Make deactivate idempotent + if ext_pkg.name in exts: del exts[ext_pkg.name] self.write_easy_install_pth(exts) diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index c148a579ec..d3739bf6a6 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -34,13 +34,16 @@ class Slepc(Package): homepage = "http://www.grycap.upv.es/slepc" url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz" + version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2') + version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876') version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') - variant('arpack', default=False, description='Enables Arpack wrappers') + variant('arpack', default=True, description='Enables Arpack wrappers') - depends_on('petsc') - depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi') - depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi') + depends_on('petsc@3.7:', when='@3.7.1:') + depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3') + depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') + depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') def install(self, spec, prefix): # set SLEPC_DIR for installation @@ -64,7 +67,7 @@ class Slepc(Package): configure('--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) - #FIXME: + # FIXME: # make('test') make('install') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 6c06b5497c..e51d7224d9 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -25,50 +25,54 @@ from spack import * import glob + class SuperluDist(Package): - """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + """A general purpose library for the direct solution of large, sparse, + nonsymmetric systems of linear equations on high performance machines.""" homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670') - # default to version 4.3 since petsc and trilinos are not tested with 5.0. - version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True) + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') version('4.2', 'ae9fafae161f775fbac6eba11e530a65') version('4.1', '4edee38cc29f687bd0c8eb361096a455') version('4.0', 'c0b98b611df227ae050bc1635c6940e0') - depends_on ('mpi') - depends_on ('blas') - depends_on ('lapack') - depends_on ('parmetis') - depends_on ('metis@5:') + depends_on('mpi') + depends_on('blas') + depends_on('lapack') + depends_on('parmetis') + depends_on('metis@5:') def install(self, spec, prefix): makefile_inc = [] makefile_inc.extend([ 'PLAT = _mac_x', - 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + 'DSuperLUroot = %s' % self.stage.source_path, 'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a', 'BLASDEF = -DUSE_VENDOR_BLAS', - 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names + 'BLASLIB = %s %s' % + (to_link_flags(spec['lapack'].lapack_shared_lib), + to_link_flags(spec['blas'].blas_shared_lib)), 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, 'FLIBS =', - 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', # NOQA: ignore=E501 'ARCH = ar', 'ARCHFLAGS = cr', 'RANLIB = true', - 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names - 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include), + 'CC = %s' % spec['mpi'].mpicc, + 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' % + (spec['parmetis'].prefix.include, + spec['metis'].prefix.include), 'NOOPTS = -fPIC -std=c99', - 'FORTRAN = mpif77', + 'FORTRAN = %s' % spec['mpi'].mpif77, 'F90FLAGS = -O2', - 'LOADER = mpif77', + 'LOADER = %s' % spec['mpi'].mpif77, 'LOADOPTS =', 'CDEFS = -DAdd_' - ]) + ]) - #with working_dir('src'): with open('make.inc', 'w') as fh: fh.write('\n'.join(makefile_inc)) @@ -83,9 +87,10 @@ class SuperluDist(Package): mkdirp(headers_location) mkdirp(prefix.lib) - headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h')) + headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h')) for h in headers: - install(h,headers_location) + install(h, headers_location) - superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') - install(superludist_lib,self.prefix.lib) + superludist_lib = join_path(self.stage.source_path, + 'lib/libsuperlu_dist.a') + install(superludist_lib, self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py new file mode 100644 index 0000000000..c634c1d1ba --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 Superlu(Package): + """SuperLU is a general purpose library for the direct solution of large, + sparse, nonsymmetric systems of linear equations on high performance + machines. SuperLU is designed for sequential machines.""" + + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz" + + version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447') + + depends_on('blas') + + def install(self, spec, prefix): + cmake_args = [ + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON', + # BLAS support + '-Denable_blaslib=OFF', + '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_shared_lib) + ] + + cmake_args.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + cmake('..', *cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index c46425c0d3..573ee38a79 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -24,26 +24,33 @@ ############################################################################## from spack import * + class Tmux(Package): """tmux is a terminal multiplexer. What is a terminal multiplexer? It lets - you switch easily between several programs in one terminal, detach them (they - keep running in the background) and reattach them to a different terminal. And - do a lot more. + you switch easily between several programs in one terminal, detach them + (they keep running in the background) and reattach them to a different + terminal. And do a lot more. """ homepage = "http://tmux.github.io" - url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz" + url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz" version('1.9a', 'b07601711f96f1d260b390513b509a2d') version('2.1', '74a2855695bccb51b6e301383ad4818c') + version('2.2', 'bd95ee7205e489c62c616bb7af040099') depends_on('libevent') depends_on('ncurses') def install(self, spec, prefix): + pkg_config_path = ':'.join([ + spec['libevent'].prefix, + spec['ncurses'].prefix + ]) + configure( "--prefix=%s" % prefix, - "PKG_CONFIG_PATH=%s:%s" % (spec['libevent'].prefix, spec['ncurses'].prefix)) + "PKG_CONFIG_PATH=%s" % pkg_config_path) make() make("install") diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 6913d79dcc..3a53ac5c01 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -45,6 +45,8 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e') + version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9') version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') @@ -89,7 +91,8 @@ class Trilinos(Package): # work at the end. But let's avoid all this by simply using shared libs depends_on('mumps@5.0:+mpi+shared', when='+mumps') depends_on('scalapack', when='+mumps') - depends_on('superlu-dist', when='+superlu-dist') + depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist') + depends_on('superlu-dist', when='@12.6.2:+superlu-dist') depends_on('hypre~internal-superlu', when='+hypre') depends_on('hdf5+mpi', when='+hdf5') depends_on('python', when='+python') |