diff options
Diffstat (limited to 'var')
69 files changed, 2714 insertions, 442 deletions
diff --git a/var/spack/mock_configs/site_spackconfig/compilers.yaml b/var/spack/mock_configs/site_spackconfig/compilers.yaml new file mode 100644 index 0000000000..5f8b38007b --- /dev/null +++ b/var/spack/mock_configs/site_spackconfig/compilers.yaml @@ -0,0 +1,40 @@ +compilers: + all: + clang@3.3: + cc: /path/to/clang + cxx: /path/to/clang++ + f77: None + fc: None + modules: None + strategy: PATH + gcc@4.5.0: + cc: /path/to/gcc + cxx: /path/to/g++ + f77: /path/to/gfortran + fc: /path/to/gfortran + modules: None + strategy: PATH + gcc@5.2.0: + cc: cc + cxx: CC + f77: ftn + fc: ftn + modules: + - PrgEnv-gnu + - gcc/5.2.0 + strategy: MODULES + intel@15.0.1: + cc: cc + ccx: CC + f77: ftn + fc: ftn + modules: + - PrgEnv-intel + - intel/15.0.1 + strategy: MODULES + intel@15.1.2: + cc: /path/to/icc + cxx: /path/to/ic++ + f77: /path/to/ifort + fc: /path/to/ifort + strategy: PATH
\ No newline at end of file diff --git a/var/spack/packages/adios/package.py b/var/spack/packages/adios/package.py new file mode 100644 index 0000000000..260dcbe851 --- /dev/null +++ b/var/spack/packages/adios/package.py @@ -0,0 +1,38 @@ +import os + +from spack import * +class Adios(Package): + """The Adaptable IO System (ADIOS) provides a simple, + flexible way for scientists to describe the + data in their code that may need to be written, + read, or processed outside of the running simulation + """ + + homepage = "http://www.olcf.ornl.gov/center-projects/adios/" + url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz" + + version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76') + + # Lots of setting up here for this package + # module swap PrgEnv-intel PrgEnv-$COMP + # module load cray-netcdf/4.3.3.1 + # module load cray-hdf5/1.8.14 + # module load python/2.7.10 + depends_on('hdf5') + depends_on('mxml') + + def install(self, spec, prefix): + configure_args = ["--prefix=%s" % prefix, + "--with-mxml=%s" % spec['mxml'].prefix, + "--with-hdf5=%s" % spec['hdf5'].prefix, + "--with-netcdf=%s" % os.environ["NETCDF_DIR"], + "--with-infiniband=no", + "MPICC=cc","MPICXX=CC","MPIFC=ftn", + "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"] + + if spec.satisfies('%gcc'): + configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"]) + + configure(*configure_args) + make() + make("install") diff --git a/var/spack/packages/mxml/package.py b/var/spack/packages/mxml/package.py new file mode 100644 index 0000000000..f79251d312 --- /dev/null +++ b/var/spack/packages/mxml/package.py @@ -0,0 +1,26 @@ +import os +from spack import * + +class Mxml(Package): + """Mini-XML is a small XML library that you can use to read and write XML + and XML-like data files in your application without requiring large + non-standard libraries + """ + + homepage = "http://www.msweet.org" + url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz" + + version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19') + version('2.8', 'd85ee6d30de053581242c4a86e79a5d2') + version('2.7', '76f2ae49bf0f5745d5cb5d9507774dc9') + version('2.6', '68977789ae64985dddbd1a1a1652642e') + version('2.5', 'f706377fba630b39fa02fd63642b17e5') + + # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use) + # Case statement to change CC and CXX flags + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static') + make() + make("install") + diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py new file mode 100644 index 0000000000..f7b0da3fd9 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py @@ -0,0 +1,37 @@ + +############################################################################## +# 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 Externalmodule(Package): + homepage = "http://somewhere.com" + url = "http://somewhere.com/module-1.0.tar.gz" + + version('1.0', '1234567890abcdef1234567890abcdef') + + depends_on('externalprereq') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py index def73ad82e..649afa5945 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py @@ -22,8 +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 ############################################################################## +import imp +from llnl.util.filesystem import join_path +from spack.util.naming import mod_to_class from spack import * - +import spack.architecture class Multimethod(Package): """This package is designed for use with Spack's multimethod test. @@ -101,25 +104,26 @@ class Multimethod(Package): # - # Make sure we can switch methods on different architectures + # Make sure we can switch methods on different target # - @when('arch=x86_64') - def different_by_architecture(self): - return 'x86_64' - - @when('arch=ppc64') - def different_by_architecture(self): - return 'ppc64' - - @when('arch=ppc32') - def different_by_architecture(self): - return 'ppc32' - - @when('arch=arm64') - def different_by_architecture(self): - return 'arm64' - - +# for platform_name in ['cray_xc', 'darwin', 'linux']: +# file_path = join_path(spack.platform_path, platform_name) +# platform_mod = imp.load_source('spack.platforms', file_path + '.py') +# cls = getattr(platform_mod, mod_to_class(platform_name)) + +# platform = cls() + platform = spack.architecture.sys_type() + targets = platform.targets.values() + if len(targets) > 1: + targets = targets[:-1] + + for target in targets: + @when('target='+target.name) + def different_by_target(self): + if isinstance(self.spec.architecture.target,basestring): + return self.spec.architecture.target + else: + return self.spec.architecture.target.name # # Make sure we can switch methods on different dependencies # diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 0177fe1a2b..001dde5329 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -22,30 +22,25 @@ # 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 -import spack -from llnl.util.lang import match_predicate from spack import * from spack.util.environment import * class R(Package): - """ - R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a - wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series - analysis, classification, clustering, etc. Please consult the R project homepage for further information. - """ + """R is 'GNU S', a freely available language and environment for + statistical computing and graphics which provides a wide variety of + statistical and graphical techniques: linear and nonlinear modelling, + statistical tests, time series analysis, classification, clustering, etc. + Please consult the R project homepage for further information.""" + homepage = "https://www.r-project.org" url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" - + extendable = True + version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3') @@ -53,7 +48,8 @@ class R(Package): version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') - variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK') + variant('external-lapack', default=False, + description='Links to externally installed BLAS/LAPACK') # Virtual dependencies depends_on('blas', when='+external-lapack') @@ -65,6 +61,7 @@ class R(Package): depends_on('icu') depends_on('glib') depends_on('zlib') + depends_on('bzip2') depends_on('libtiff') depends_on('jpeg') depends_on('cairo') @@ -72,18 +69,21 @@ class R(Package): depends_on('freetype') depends_on('tcl') depends_on('tk') + depends_on('curl') + depends_on('pcre') + depends_on('jdk') def install(self, spec, prefix): rlibdir = join_path(prefix, 'rlib') - options = ['--prefix=%s' % prefix, - '--libdir=%s' % rlibdir, - '--enable-R-shlib', - '--enable-BLAS-shlib', - '--enable-R-framework=no'] + configure_args = ['--prefix=%s' % prefix, + '--libdir=%s' % rlibdir, + '--enable-R-shlib', + '--enable-BLAS-shlib', + '--enable-R-framework=no'] if '+external-lapack' in spec: - options.extend(['--with-blas', '--with-lapack']) + configure_args.extend(['--with-blas', '--with-lapack']) - configure(*options) + configure(*configure_args) make() make('install') @@ -106,25 +106,24 @@ class R(Package): r_libs_path = ':'.join(r_libs_path) spack_env.set('R_LIBS', r_libs_path) - # For run time environment set only the path for extension_spec and prepend it to R_LIBS + # For run time environment set only the path for extension_spec and + # prepend it to R_LIBS if extension_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir)) - + run_env.prepend_path('R_LIBS', os.path.join( + extension_spec.prefix, self.r_lib_dir)) def setup_dependent_package(self, module, ext_spec): - """ - Called before R modules' install() methods. - - In most cases, extensions will only need to have one line:: - - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) - """ + """Called before R modules' install() methods. In most cases, + extensions will only need to have one line: + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % + self.stage.source_path)""" # R extension builds can have a global R executable function module.R = Executable(join_path(self.spec.prefix.bin, 'R')) # Add variable for library directry module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) - # Make the site packages directory for extensions, if it does not exist already. + # Make the site packages directory for extensions, if it does not exist + # already. if ext_spec.package.is_extension: mkdirp(module.r_lib_dir) 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/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py new file mode 100644 index 0000000000..8d7da705e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/bertini/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 Bertini(Package): + """Bertini is a general-purpose solver, written in C, that was created + for research about polynomial continuation. It solves for the numerical + solution of systems of polynomial equations using homotopy continuation.""" + + homepage = "https://bertini.nd.edu/" + url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz" + + version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707') + + variant('mpi', default=True, description='Compile in parallel') + + depends_on('flex') + depends_on('bison') + depends_on('gmp') + depends_on('mpfr') + depends_on('mpi', when='+mpi') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 9e4cc98ae6..5f305abb02 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -30,8 +30,9 @@ class Binutils(Package): url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" + # 2.26 is incompatible with py-pillow build for some reason. version('2.26', '64146a0faa3b411ba774f47d41de239f') - version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66') + version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True) version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b') version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index d833054e33..67294fb9a1 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -132,7 +132,7 @@ class Boost(Package): "/boost/%s/boost_%s.tar.bz2" % (dots, underscores) def determine_toolset(self, spec): - if spec.satisfies("arch=darwin-x86_64"): + if spec.satisfies("platform=darwin"): return 'darwin' toolsets = {'g++': 'gcc', 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 ef6a3ccc7b..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' @@ -87,10 +100,9 @@ class Espresso(Package): configure(*options) make('all') - if spec.architecture.startswith('darwin'): + if spec.satisfies('platform=darwin'): mkdirp(prefix.bin) for filename in glob("bin/*.x"): install(filename, prefix.bin) else: make('install') - diff --git a/var/spack/repos/builtin/packages/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/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py new file mode 100644 index 0000000000..efd5c8bb1d --- /dev/null +++ b/var/spack/repos/builtin/packages/hpl/package.py @@ -0,0 +1,119 @@ +############################################################################## +# 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 +import platform + + +class Hpl(Package): + """HPL is a software package that solves a (random) dense linear system + in double precision (64 bits) arithmetic on distributed-memory computers. + It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + + homepage = "http://www.netlib.org/benchmark/hpl/" + url = "http://www.netlib.org/benchmark/hpl/hpl-2.2.tar.gz" + + version('2.2', '0eb19e787c3dc8f4058db22c9e0c5320') + + variant('openmp', default=False, description='Enable OpenMP support') + + depends_on('mpi@1.1:') + depends_on('blas') + + parallel = False + + def configure(self, spec, arch): + # List of configuration options + # Order is important + config = [] + + # OpenMP support + if '+openmp' in spec: + config.append( + 'OMP_DEFS = {0}'.format(self.compiler.openmp_flag) + ) + + config.extend([ + # Shell + 'SHELL = /bin/sh', + 'CD = cd', + 'CP = cp', + 'LN_S = ln -fs', + 'MKDIR = mkdir -p', + 'RM = /bin/rm -f', + 'TOUCH = touch', + # Platform identifier + 'ARCH = {0}'.format(arch), + # HPL Directory Structure / HPL library + 'TOPdir = {0}'.format(os.getcwd()), + 'INCdir = $(TOPdir)/include', + 'BINdir = $(TOPdir)/bin/$(ARCH)', + 'LIBdir = $(TOPdir)/lib/$(ARCH)', + 'HPLlib = $(LIBdir)/libhpl.a', + # Message Passing library (MPI) + 'MPinc = -I{0}'.format(spec['mpi'].prefix.include), + 'MPlib = -L{0}'.format(spec['mpi'].prefix.lib), + # Linear Algebra library (BLAS or VSIPL) + 'LAinc = {0}'.format(spec['blas'].prefix.include), + 'LAlib = {0}'.format(spec['blas'].blas_shared_lib), + # F77 / C interface + 'F2CDEFS = -DAdd_ -DF77_INTEGER=int -DStringSunStyle', + # HPL includes / libraries / specifics + 'HPL_INCLUDES = -I$(INCdir) -I$(INCdir)/$(ARCH) ' + + '-I$(LAinc) -I$(MPinc)', + 'HPL_LIBS = $(HPLlib) $(LAlib) $(MPlib)', + 'HPL_OPTS = -DHPL_DETAILED_TIMING -DHPL_PROGRESS_REPORT', + 'HPL_DEFS = $(F2CDEFS) $(HPL_OPTS) $(HPL_INCLUDES)', + # Compilers / linkers - Optimization flags + 'CC = {0}'.format(spec['mpi'].mpicc), + 'CCNOOPT = $(HPL_DEFS)', + 'CCFLAGS = $(HPL_DEFS) -O3', + 'LINKER = $(CC)', + 'LINKFLAGS = $(CCFLAGS) $(OMP_DEFS)', + 'ARCHIVER = ar', + 'ARFLAGS = r', + 'RANLIB = echo' + ]) + + # Write configuration options to include file + with open('Make.{0}'.format(arch), 'w') as makefile: + for var in config: + makefile.write('{0}\n'.format(var)) + + def install(self, spec, prefix): + # Arch used for file naming purposes only + arch = '{0}-{1}'.format(platform.system(), platform.processor()) + + # Generate Makefile include + self.configure(spec, arch) + + make('arch={0}'.format(arch)) + + # Manual installation + install_tree(join_path('bin', arch), prefix.bin) + install_tree(join_path('lib', arch), prefix.lib) + install_tree(join_path('include', arch), prefix.include) + install_tree('man', prefix.man) 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/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py index 42e8711a7d..91cef95cec 100644 --- a/var/spack/repos/builtin/packages/libpciaccess/package.py +++ b/var/spack/repos/builtin/packages/libpciaccess/package.py @@ -37,7 +37,7 @@ class Libpciaccess(Package): def install(self, spec, prefix): # libpciaccess does not support OS X - if spec.satisfies('arch=darwin-x86_64'): + if spec.satisfies('platform=darwin'): # create a dummy directory mkdir(prefix.lib) return diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py new file mode 100644 index 0000000000..4bcca43c24 --- /dev/null +++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py @@ -0,0 +1,39 @@ +############################################################################## +# 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 LibpthreadStubs(Package): + """The libpthread-stubs package provides weak aliases for pthread + functions not provided in libc or otherwise available by + default. """ + homepage = "http://xcb.freedesktop.org/" + url = "http://xcb.freedesktop.org/dist/libpthread-stubs-0.1.tar.bz2" + + version('0.3', 'e8fa31b42e13f87e8f5a7a2b731db7ee') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py new file mode 100644 index 0000000000..55816ecdbd --- /dev/null +++ b/var/spack/repos/builtin/packages/libxau/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 Libxau(Package): + """The libXau package contains a library implementing the X11 + Authorization Protocol. This is useful for restricting client + access to the display.""" + homepage = "http://xcb.freedesktop.org/" + url = "http://ftp.x.org/pub/individual/lib/libXau-1.0.8.tar.bz2" + + version('1.0.8', '685f8abbffa6d145c0f930f00703b21b') + + depends_on('xproto') + + def install(self, spec, prefix): + # FIXME: Modify the configure line to suit your build system here. + configure('--prefix=%s' % prefix) + + # FIXME: Add logic to build and install here + make() + make("install") diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index 0f39bb0f1d..746d4567e2 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -35,18 +35,19 @@ class Libxcb(Package): version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') version('1.11.1', '118623c15a96b08622603a71d8789bf3') + depends_on("python") depends_on("xcb-proto") depends_on("pkg-config") - - # depends_on('pthread') # Ubuntu: apt-get install libpthread-stubs0-dev - # depends_on('xau') # Ubuntu: apt-get install libxau-dev + depends_on("libpthread-stubs") + depends_on('libxau') def patch(self): filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h') def install(self, spec, prefix): + env['PKG_CONFIG_PATH'] = env['PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig' configure("--prefix=%s" % prefix) make() diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index c32f66590a..7a6ea7401c 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -267,16 +267,16 @@ class Llvm(Package): if '+all_targets' not in spec: # all is default on cmake targets = ['CppBackend', 'NVPTX', 'AMDGPU'] - if 'x86' in spec.architecture.lower(): + if 'x86' in spec.architecture.target.lower(): targets.append('X86') - elif 'arm' in spec.architecture.lower(): + elif 'arm' in spec.architecture.target.lower(): targets.append('ARM') - elif 'aarch64' in spec.architecture.lower(): + elif 'aarch64' in spec.architecture.target.lower(): targets.append('AArch64') - elif 'sparc' in spec.architecture.lower(): + elif 'sparc' in spec.architecture.target.lower(): targets.append('sparc') - elif ('ppc' in spec.architecture.lower() or - 'power' in spec.architecture.lower()): + elif ('ppc' in spec.architecture.target.lower() or + 'power' in spec.architecture.target.lower()): targets.append('PowerPC') cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets)) diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index 8ce4a7b94d..761932361b 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -57,7 +57,7 @@ class Lua(Package): placement='luarocks') def install(self, spec, prefix): - if spec.satisfies("arch=darwin-i686") or spec.satisfies("arch=darwin-x86_64"): # NOQA: ignore=E501 + if spec.satisfies("platform=darwin"): target = 'macosx' else: target = 'linux' 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/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 164d9db541..ea1844aea0 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -23,15 +23,14 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os class Mpich(Package): """MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.""" homepage = "http://www.mpich.org" - url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" - list_url = "http://www.mpich.org/static/downloads/" + url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" + list_url = "http://www.mpich.org/static/downloads/" list_depth = 2 version('3.2', 'f414cfa77099cd1fa1a5ae4e22db508a') @@ -42,7 +41,8 @@ class Mpich(Package): version('3.1', '5643dd176499bfb7d25079aaff25f2ec') version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') - variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + variant('verbs', default=False, + description='Build support for OpenFabrics verbs.') variant('pmi', default=True, description='Build with PMI support') variant('hydra', default=True, description='Build the hydra process manager') @@ -57,9 +57,9 @@ class Mpich(Package): spack_env.set('MPICH_FC', spack_fc) def setup_dependent_package(self, module, dep_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') def install(self, spec, prefix): @@ -92,7 +92,6 @@ class Mpich(Package): self.filter_compilers() - def filter_compilers(self): """Run after install to make the MPI compilers use the compilers that Spack built the package with. @@ -102,18 +101,20 @@ class Mpich(Package): be bound to whatever compiler they were built with. """ bin = self.prefix.bin - mpicc = os.path.join(bin, 'mpicc') - mpicxx = os.path.join(bin, 'mpicxx') - mpif77 = os.path.join(bin, 'mpif77') - mpif90 = os.path.join(bin, 'mpif90') - - spack_cc = os.environ['CC'] - spack_cxx = os.environ['CXX'] - spack_f77 = os.environ['F77'] - spack_fc = os.environ['FC'] - - kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : True } - filter_file('CC="%s"' % spack_cc , 'CC="%s"' % self.compiler.cc, mpicc, **kwargs) - filter_file('CXX="%s"'% spack_cxx, 'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs) - filter_file('F77="%s"'% spack_f77, 'F77="%s"' % self.compiler.f77, mpif77, **kwargs) - filter_file('FC="%s"' % spack_fc , 'FC="%s"' % self.compiler.fc, mpif90, **kwargs) + mpicc = join_path(bin, 'mpicc') + mpicxx = join_path(bin, 'mpicxx') + mpif77 = join_path(bin, 'mpif77') + mpif90 = join_path(bin, 'mpif90') + + # Substitute Spack compile wrappers for the real + # underlying compiler + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs) + filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs) + filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs) + filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs) + + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + for wrapper in (mpicc, mpicxx, mpif77, mpif90): + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch new file mode 100644 index 0000000000..592f48037c --- /dev/null +++ b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch @@ -0,0 +1,119 @@ +diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile +--- MUMPS_5.0.1/libseq/Makefile 2015-07-23 19:08:32.000000000 +0200 ++++ MUMPS_5.0.1.new/libseq/Makefile 2016-06-07 10:41:16.585179151 +0200 +@@ -8,11 +8,15 @@ + + include ../Makefile.inc + +-libmpiseq: libmpiseq$(PLAT)$(LIBEXT) ++libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT) + + libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o + $(AR)$@ mpi.o mpic.o elapse.o + $(RANLIB) $@ ++ ++libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o ++ $(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT) ++ + .f.o: + $(FC) $(OPTF) -c $*.f $(OUTF)$*.o + .c.o: +diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile +--- MUMPS_5.0.1/Makefile 2015-07-23 19:08:29.000000000 +0200 ++++ MUMPS_5.0.1.new/Makefile 2016-06-07 10:50:21.863281217 +0200 +@@ -51,7 +51,7 @@ + dexamples: d + (cd examples ; $(MAKE) d) + +-requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT) + + # dummy MPI library (sequential version) + +@@ -62,16 +62,25 @@ + $(libdir)/libpord$(PLAT)$(LIBEXT): + if [ "$(LPORDDIR)" != "" ] ; then \ + cd $(LPORDDIR); \ +- $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \ ++ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \ + fi; + if [ "$(LPORDDIR)" != "" ] ; then \ + cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ + fi; + ++$(libdir)/libpord$(PLAT)$(SHLIBEXT): ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); \ ++ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \ ++ fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \ ++ fi; ++ + clean: + (cd src; $(MAKE) clean) + (cd examples; $(MAKE) clean) +- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT)) ++ (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT)) + (cd libseq; $(MAKE) clean) + if [ "$(LPORDDIR)" != "" ] ; then \ + cd $(LPORDDIR); $(MAKE) realclean; \ +diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile +--- MUMPS_5.0.1/PORD/lib/Makefile 2015-07-23 19:08:29.000000000 +0200 ++++ MUMPS_5.0.1.new/PORD/lib/Makefile 2016-06-07 10:49:48.889000958 +0200 +@@ -13,7 +13,7 @@ + + OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ + multisector.o gelim.o bucket.o tree.o \ +- symbfac.o interface.o sort.o minpriority.o ++ symbfac.o interface.o sort.o minpriority.o + + # Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c + # were not direcly used by MUMPS and have been removed from the +@@ -24,12 +24,15 @@ + .c.o: + $(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o + +-libpord$(LIBEXT):$(OBJS) ++libpord$(PLAT)$(LIBEXT):$(OBJS) + $(AR)$@ $(OBJS) + $(RANLIB) $@ + ++libpord$(PLAT)$(SHLIBEXT): $(OBJS) ++ $(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT) ++ + clean: + rm -f *.o + + realclean: +- rm -f *.o libpord.a ++ rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT) +diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile +--- MUMPS_5.0.1/src/Makefile 2015-07-23 19:08:29.000000000 +0200 ++++ MUMPS_5.0.1.new/src/Makefile 2016-06-07 10:40:52.534703722 +0200 +@@ -24,7 +24,10 @@ + include $(topdir)/Makefile.inc + + mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \ +- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) ++ $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \ ++ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \ ++ $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) ++ + + OBJS_COMMON_MOD = \ + ana_omp_m.o\ +@@ -162,6 +165,13 @@ + $(AR)$@ $? + $(RANLIB) $@ + ++$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) ++ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT): $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) ++ + # Dependencies between modules: + $(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \ + $(ARITH)mumps_struc_def.o \ diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 92c45c9b95..8a90ef72d0 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -23,7 +23,10 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, sys, glob +import os +import sys +import subprocess + class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -44,7 +47,6 @@ class Mumps(Package): variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') variant('shared', default=True, description='Build shared libraries') - depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') depends_on('metis@5:', when='+metis') @@ -54,49 +56,64 @@ class Mumps(Package): depends_on('scalapack', when='+mpi') depends_on('mpi', when='+mpi') + patch('mumps-shared.patch', when='+shared') + # this function is not a patch function because in case scalapack # is needed it uses self.spec['scalapack'].fc_link set by the # setup_dependent_environment in scalapck. This happen after patch # end before install # def patch(self): def write_makefile_inc(self): - if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: - raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') + if (('+parmetis' in self.spec or + '+ptscotch' in self.spec)) and '+mpi' not in self.spec: + raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: E501 - makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] + makefile_conf = [ + "LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib + ] orderings = ['-Dpord'] if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') - makefile_conf.extend( - ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, - "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, - join_lib, - join_lib.join(['esmumps', 'scotch', 'scotcherr']))]) + makefile_conf.extend([ + "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, + "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, + join_lib, + join_lib.join(['esmumps', + 'scotch', + 'scotcherr'])) + ]) orderings.append('-Dscotch') if '+ptscotch' in self.spec: orderings.append('-Dptscotch') if '+parmetis' in self.spec and '+metis' in self.spec: - libname = 'parmetis' if '+parmetis' in self.spec else 'metis' - makefile_conf.extend( - ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, - "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) + makefile_conf.extend([ + "IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % ( + self.spec['parmetis'].prefix.lib, 'parmetis', + self.spec['metis'].prefix.lib, 'metis') + ]) orderings.append('-Dparmetis') elif '+metis' in self.spec: - makefile_conf.extend( - ["IMETIS = -I%s" % self.spec['metis'].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) + makefile_conf.extend([ + "IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, + 'metis') + ]) orderings.append('-Dmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) - # when building shared libs need -fPIC, otherwise - # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC + # when building shared libs need -fPIC, otherwise /usr/bin/ld: + # graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can + # not be used when making a shared object; recompile with + # -fPIC fpic = '-fPIC' if '+shared' in self.spec else '' + # TODO: test this part, it needs a full blas, scalapack and # partitionning environment with 64bit integers if '+idx64' in self.spec: @@ -104,7 +121,7 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501 'OPTL = %s -O ' % fpic, 'OPTC = %s -O -DINTSIZE64' % fpic]) else: @@ -113,49 +130,47 @@ class Mumps(Package): 'OPTL = %s -O ' % fpic, 'OPTC = %s -O ' % fpic]) - if '+mpi' in self.spec: makefile_conf.extend( - ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), - "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), - "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + ["CC = %s" % self.spec['mpi'].mpicc, + "FC = %s" % self.spec['mpi'].mpifc, "SCALAP = %s" % self.spec['scalapack'].fc_link, "MUMPS_TYPE = par"]) else: makefile_conf.extend( ["CC = cc", "FC = fc", - "FL = fc", "MUMPS_TYPE = seq"]) # TODO: change the value to the correct one according to the # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER - makefile_conf.append("CDEFS = -DAdd_") + makefile_conf.extend([ + 'CDEFS = -DAdd_', + 'FL = $(FC)', + ]) if '+shared' in self.spec: + makefile_conf.append('SHLIBEXT = .%s' % dso_suffix) if sys.platform == 'darwin': - # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) - makefile_conf.extend([ - 'LIBEXT=.dylib', - 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), - 'RANLIB=echo' - ]) + makefile_conf.append( + 'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501 + ) else: - makefile_conf.extend([ - 'LIBEXT=.so', - 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, - 'RANLIB=echo' - ]) - else: - makefile_conf.extend([ - 'LIBEXT = .a', - 'AR = ar vr', - 'RANLIB = ranlib' - ]) - - - makefile_inc_template = join_path(os.path.dirname(self.module.__file__), - 'Makefile.inc') + makefile_conf.append( + 'LDFLAGS = -shared {0}{1}'.format( + self.compiler.fc_rpath_arg, + prefix.lib) + ) + + makefile_conf.extend([ + 'LIBEXT = .a', + 'AR = ar vr ', + 'RANLIB = ranlib' + ]) + + makefile_inc_template = \ + join_path(os.path.dirname(self.module.__file__), + 'Makefile.inc') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) @@ -164,46 +179,53 @@ class Mumps(Package): makefile_inc = '\n'.join(makefile_conf) fh.write(makefile_inc) - - def install(self, spec, prefix): make_libs = [] # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: - make_libs.append('sexamples') + make_libs.append('s') if '+complex' in spec: - make_libs.append('cexamples') + make_libs.append('c') if '+double' in spec: - make_libs.append('dexamples') + make_libs.append('d') if '+complex' in spec: - make_libs.append('zexamples') + make_libs.append('z') self.write_makefile_inc() - # Build fails in parallel - make(*make_libs, parallel=False) + make('mumps_lib', parallel=False) + make(*make_libs) install_tree('lib', prefix.lib) install_tree('include', prefix.include) - if '~mpi' in spec: - lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' - lib_suffix = lib_dsuffix if '+shared' in spec else '.a' - install('libseq/libmpiseq%s' % lib_suffix, prefix.lib) - for f in glob.glob(join_path('libseq','*.h')): - install(f, prefix.include) - - # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI - # FIXME: use something like numdiff to compare blessed output with the current - with working_dir('examples'): - if '+float' in spec: - os.system('./ssimpletest < input_simpletest_real') - if '+complex' in spec: - os.system('./csimpletest < input_simpletest_real') - if '+double' in spec: - os.system('./dsimpletest < input_simpletest_real') - if '+complex' in spec: - os.system('./zsimpletest < input_simpletest_cmplx') + if '~mpi' in spec: + install('libseq/libmpiseq.a', prefix.lib) + if '+shared' in spec: + install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib) + install('libseq/mpi.h', prefix.include) + install('libseq/mpif.h', prefix.include) + + # FIXME: extend the tests to mpirun -np 2 (or alike) when + # build with MPI + # FIXME: use something like numdiff to compare blessed output + # with the current + # TODO: test the installed mumps and not the one in stage + if '~mpi' in spec: + for t in make_libs: + make('{0}examples'.format(t)) + + with working_dir('examples'): + for t in make_libs: + input_file = 'input_simpletest_{0}'.format( + 'real' if t in ['s', 'd'] else 'cmplx') + with open(input_file) as input: + test = './{0}simpletest'.format(t) + ret = subprocess.call(test, + stdin=input) + if ret is not 0: + raise RuntimeError( + 'The test {0} did not pass'.format(test)) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index d1944023d1..34bace10d6 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os class Mvapich2(Package): @@ -245,27 +244,20 @@ class Mvapich2(Package): be bound to whatever compiler they were built with. """ bin = self.prefix.bin - mpicc = os.path.join(bin, 'mpicc') - mpicxx = os.path.join(bin, 'mpicxx') - mpif77 = os.path.join(bin, 'mpif77') - mpif90 = os.path.join(bin, 'mpif90') - - spack_cc = os.environ['CC'] - spack_cxx = os.environ['CXX'] - spack_f77 = os.environ['F77'] - spack_fc = os.environ['FC'] - - kwargs = { - 'ignore_absent': True, - 'backup': False, - 'string': True - } - - filter_file('CC="%s"' % spack_cc, - 'CC="%s"' % self.compiler.cc, mpicc, **kwargs) - filter_file('CXX="%s"' % spack_cxx, - 'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs) - filter_file('F77="%s"' % spack_f77, - 'F77="%s"' % self.compiler.f77, mpif77, **kwargs) - filter_file('FC="%s"' % spack_fc, - 'FC="%s"' % self.compiler.fc, mpif90, **kwargs) + mpicc = join_path(bin, 'mpicc') + mpicxx = join_path(bin, 'mpicxx') + mpif77 = join_path(bin, 'mpif77') + mpif90 = join_path(bin, 'mpif90') + + # Substitute Spack compile wrappers for the real + # underlying compiler + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs) + filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs) + filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs) + filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs) + + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + for wrapper in (mpicc, mpicxx, mpif77, mpif90): + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) 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..695fb82f62 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -61,6 +61,7 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') version('1.10.0', '280cf952de68369cebaca886c5ce0304') @@ -72,20 +73,27 @@ class Openmpi(Package): patch('configure.patch', when="@1.10.0:1.10.1") variant('psm', default=False, description='Build support for the PSM library.') - variant('psm2', default=False, description='Build support for the Intel PSM2 library.') - variant('pmi', default=False, description='Build support for PMI-based launchers') - variant('verbs', default=_verbs_dir() is not None, description='Build support for OpenFabrics verbs.') + variant('psm2', default=False, + description='Build support for the Intel PSM2 library.') + variant('pmi', default=False, + description='Build support for PMI-based launchers') + variant('verbs', default=_verbs_dir() is not None, + description='Build support for OpenFabrics verbs.') variant('mxm', default=False, description='Build Mellanox Messaging support') - variant('thread_multiple', default=False, description='Enable MPI_THREAD_MULTIPLE support') + variant('thread_multiple', default=False, + description='Enable MPI_THREAD_MULTIPLE support') # TODO : variant support for alps, loadleveler is missing - variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support') - variant('slurm', default=False, description='Build SLURM scheduler component') + variant('tm', default=False, + description='Build TM (Torque, PBSPro, and compatible) support') + variant('slurm', default=False, + description='Build SLURM scheduler component') variant('sqlite3', default=False, description='Build sqlite3 support') - variant('vt', default=True, description='Build support for contributed package vt') + variant('vt', default=True, + description='Build support for contributed package vt') # TODO : support for CUDA is missing @@ -96,8 +104,7 @@ class Openmpi(Package): depends_on('sqlite', when='+sqlite3') def url_for_version(self, version): - return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - + return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) # NOQA: ignore=E501 def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('OMPI_CC', spack_cc) @@ -106,14 +113,15 @@ class Openmpi(Package): spack_env.set('OMPI_F77', spack_f77) def setup_dependent_package(self, module, dep_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') @property def verbs(self): - # Up through version 1.6, this option was previously named --with-openib + # Up through version 1.6, this option was previously named + # --with-openib if self.spec.satisfies('@:1.6'): return 'openib' # In version 1.7, it was renamed to be --with-verbs @@ -121,6 +129,13 @@ 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", @@ -135,7 +150,7 @@ class Openmpi(Package): '--with-psm2' if '+psm2' in spec else '--without-psm2', '--with-mxm' if '+mxm' in spec else '--without-mxm', # Other options - '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', + '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', # NOQA: ignore=E501 '--with-pmi' if '+pmi' in spec else '--without-pmi', '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3', '--enable-vt' if '+vt' in spec else '--disable-vt' @@ -153,7 +168,7 @@ class Openmpi(Package): # use this for LANL builds, but for LLNL builds, we need: # "--with-platform=contrib/platform/llnl/optimized" if self.version == ver("1.6.5") and '+lanl' in spec: - config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas") + config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas") # NOQA: ignore=E501 if not self.compiler.f77 and not self.compiler.fc: config_args.append("--enable-mpi-fortran=no") @@ -173,40 +188,33 @@ class Openmpi(Package): be bound to whatever compiler they were built with. """ kwargs = {'ignore_absent': True, 'backup': False, 'string': False} - dir = os.path.join(self.prefix, 'share/openmpi/') - - cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt', - 'ortecc-wrapper-data.txt', 'shmemcc-wrapper-data.txt'] - - cxx_wrappers = ['mpic++-vt-wrapper-data.txt', 'mpic++-wrapper-data.txt', - 'ortec++-wrapper-data.txt'] - - fc_wrappers = ['mpifort-vt-wrapper-data.txt', - 'mpifort-wrapper-data.txt', 'shmemfort-wrapper-data.txt'] - - for wrapper in cc_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.cc, - os.path.join(dir, wrapper), **kwargs) - - for wrapper in cxx_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.cxx, - os.path.join(dir, wrapper), **kwargs) - - for wrapper in fc_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc, - os.path.join(dir, wrapper), **kwargs) - - # These are symlinks in newer versions, so check that here - f77_wrappers = ['mpif77-vt-wrapper-data.txt', 'mpif77-wrapper-data.txt'] - f90_wrappers = ['mpif90-vt-wrapper-data.txt', 'mpif90-wrapper-data.txt'] - - for wrapper in f77_wrappers: - path = os.path.join(dir, wrapper) - if not os.path.islink(path): - filter_file('compiler=.*', 'compiler=%s' % self.compiler.f77, - path, **kwargs) - for wrapper in f90_wrappers: - path = os.path.join(dir, wrapper) - if not os.path.islink(path): - filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc, - path, **kwargs) + wrapper_basepath = join_path(self.prefix, 'share', 'openmpi') + + wrappers = [ + ('mpicc-vt-wrapper-data.txt', self.compiler.cc), + ('mpicc-wrapper-data.txt', self.compiler.cc), + ('ortecc-wrapper-data.txt', self.compiler.cc), + ('shmemcc-wrapper-data.txt', self.compiler.cc), + ('mpic++-vt-wrapper-data.txt', self.compiler.cxx), + ('mpic++-wrapper-data.txt', self.compiler.cxx), + ('ortec++-wrapper-data.txt', self.compiler.cxx), + ('mpifort-vt-wrapper-data.txt', self.compiler.fc), + ('mpifort-wrapper-data.txt', self.compiler.fc), + ('shmemfort-wrapper-data.txt', self.compiler.fc), + ('mpif90-vt-wrapper-data.txt', self.compiler.fc), + ('mpif90-wrapper-data.txt', self.compiler.fc), + ('mpif77-vt-wrapper-data.txt', self.compiler.f77), + ('mpif77-wrapper-data.txt', self.compiler.f77) + ] + + for wrapper_name, compiler in wrappers: + wrapper = join_path(wrapper_basepath, wrapper_name) + if not os.path.islink(wrapper): + # Substitute Spack compile wrappers for the real + # underlying compiler + match = 'compiler=.*' + substitute = 'compiler={compiler}'.format(compiler=compiler) + filter_file(match, substitute, wrapper, **kwargs) + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 34ab0703ad..377bffe723 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -100,7 +100,7 @@ class Openssl(Package): # in the environment, then this will override what is set in the # Makefile, leading to build errors. env.pop('APPS', None) - if spec.satisfies("arch=darwin-x86_64") or spec.satisfies("arch=ppc64"): + if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"): # This needs to be done for all 64-bit architectures (except Linux, # where it happens automatically?) env['KERNEL_BITS'] = '64' diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py index 8e0f83110e..a43729a1ac 100644 --- a/var/spack/repos/builtin/packages/pcre/package.py +++ b/var/spack/repos/builtin/packages/pcre/package.py @@ -29,6 +29,7 @@ class Pcre(Package): """The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.""" + homepage = "http://www.pcre.org""" url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2" @@ -37,7 +38,15 @@ class Pcre(Package): patch("intel.patch") + variant('utf', default=True, + description='Enable support for UTF-8/16/32, ' + 'incompatible with EBCDIC.') + def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure_args = ['--prefix=%s' % prefix] + if '+utf' in spec: + configure_args.append('--enable-utf') + + configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 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 de72bac44e..0180b658f5 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -23,21 +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') 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/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py index 0d3b6a3e57..5a6ce72a4b 100644 --- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py +++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py @@ -24,15 +24,33 @@ ############################################################################## from spack import * + class RBiocgenerics(Package): """S4 generic functions needed by many Bioconductor packages.""" - homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html' - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz" - - version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False) + homepage = 'https://bioconductor.org/packages/BiocGenerics/' + version('bioc-3.3', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.3') + version('bioc-3.2', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.2') extends('R') + def validate(self, spec): + """ + Checks that the version of R is appropriate for the Bioconductor + version. + """ + if spec.satisfies('@bioc-3.3'): + if not spec.satisfies('^R@3.3.0:3.3.9'): + raise InstallError('Must use R-3.3 for Bioconductor-3.3') + elif spec.satisfies('@bioc-3.2'): + if not spec.satisfies('^R@3.2.0:3.2.9'): + raise InstallError('Must use R-3.2 for Bioconductor-3.2') + def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.validate(spec) + R('CMD', 'INSTALL', '--library=%s' % + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-R6/package.py b/var/spack/repos/builtin/packages/r-R6/package.py new file mode 100644 index 0000000000..0b75888e79 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-R6/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 RR6(Package): + """The R6 package allows the creation of classes with reference semantics, + similar to R's built-in reference classes. Compared to reference classes, + R6 classes are simpler and lighter-weight, and they are not built on S4 + classes so they do not require the methods package. These classes allow + public and private members, and they support inheritance, even when the + classes are defined in different packages.""" + + homepage = "https://github.com/wch/R6/" + url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + + version('2.1.2', 'b6afb9430e48707be87638675390e457') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 34a1eee79f..96f623a096 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RAbind(Package): """Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and @@ -32,11 +33,12 @@ class RAbind(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/abind" - version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False) + version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') extends('R') def install(self, spec, prefix): - - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py new file mode 100644 index 0000000000..c6e8f22a94 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-curl/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 RCurl(Package): + """The curl() and curl_download() functions provide highly configurable + drop-in replacements for base url() and download.file() with better + performance, support for encryption (https, ftps), gzip compression, + authentication, and other libcurl goodies. The core of the package + implements a framework for performing fully customized requests where data + can be processed either in memory, on disk, or streaming via the callback + or connection interfaces. Some knowledge of libcurl is recommended; for a + more-user-friendly web client see the 'httr' package which builds on this + package with http specific tools and logic.""" + + homepage = "https://github.com/jeroenooms/curl" + url = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + + version('0.9.7', 'a101f7de948cb828fef571c730f39217') + + extends('R') + + depends_on('curl') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py new file mode 100644 index 0000000000..5f0b7b8779 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RDevtools(Package): + """Collection of package development tools.""" + + homepage = "https://github.com/hadley/devtools" + url = "https://cran.r-project.org/src/contrib/devtools_1.11.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/devtools" + + version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') + + extends('R') + + depends_on('r-httr') + depends_on('r-memoise') + depends_on('r-whisker') + depends_on('r-digest') + depends_on('r-rstudioapi') + depends_on('r-jsonlite') + depends_on('r-git2r') + depends_on('r-withr') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py new file mode 100644 index 0000000000..1d11afb139 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -0,0 +1,56 @@ +############################################################################## +# 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 RDigest(Package): + """Implementation of a function 'digest()' for the creation of hash digests + of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and + murmurhash algorithms) permitting easy comparison of R language objects, as + well as a function 'hmac()' to create hash-based message authentication + code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 + and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the + crc32 algorithm is described in + ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, + sha-256 and aes, this package uses small standalone implementations that + were provided by Christophe Devine. For crc32, code from the zlib library + is used. For sha-512, an implementation by Aaron D. Gifford is used. For + xxhash, the implementation by Yann Collet is used. For murmurhash, an + implementation by Shane Day is used. Please note that this package is not + meant to be deployed for cryptographic purposes for which more + comprehensive (and widely tested) libraries such as OpenSSL should be + used.""" + + homepage = "http://dirk.eddelbuettel.com/code/digest.html" + url = "https://cran.r-project.org/src/contrib/digest_0.6.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/digest" + + version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index fffae68019..a09b458eaf 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RFilehash(Package): """Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple @@ -37,10 +38,12 @@ class RFilehash(Package): homepage = 'https://cran.r-project.org/' url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/filehash" - version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False) + version('2.3', '01fffafe09b148ccadc9814c103bdc2f') extends('R') def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py new file mode 100644 index 0000000000..1f08379d6e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-git2r/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 RGit2r(Package): + """Interface to the 'libgit2' library, which is a pure C implementation of + the 'Git' core methods. Provides access to 'Git' repositories to extract + data and running some basic 'Git' commands.""" + + homepage = "https://github.com/ropensci/git2r" + url = "https://cran.r-project.org/src/contrib/git2r_0.15.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/git2r" + + version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') + + extends('R') + + depends_on('zlib') + depends_on('openssl') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py new file mode 100644 index 0000000000..77ec34ab03 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 RHttr(Package): + """Useful tools for working with HTTP organised by HTTP verbs (GET(), + POST(), etc). Configuration functions make it easy to control additional + request components (authenticate(), add_headers() and so on).""" + + homepage = "https://github.com/hadley/httr" + url = "https://cran.r-project.org/src/contrib/httr_1.1.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/httr" + + version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') + + extends('R') + + depends_on('r-jsonlite') + depends_on('r-mime') + depends_on('r-curl') + depends_on('r-openssl') + depends_on('r-R6') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py new file mode 100644 index 0000000000..6e231ed345 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RJsonlite(Package): + """A fast JSON parser and generator optimized for statistical data and the + web. Started out as a fork of 'RJSONIO', but has been completely rewritten + in recent versions. The package offers flexible, robust, high performance + tools for working with JSON in R and is particularly powerful for building + pipelines and interacting with a web API. The implementation is based on + the mapping described in the vignette (Ooms, 2014). In addition to + converting JSON data from/to R objects, 'jsonlite' contains functions to + stream, validate, and prettify JSON data. The unit tests included with the + package verify that all edge cases are encoded and decoded consistently for + use with dynamic data in systems and applications.""" + + homepage = "https://github.com/jeroenooms/jsonlite" + url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + + version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index f86917ec0c..f6ba97740b 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RMagic(Package): """A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of @@ -32,12 +33,14 @@ class RMagic(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/magic" - version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False) + version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') extends('R') depends_on('r-abind') def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py new file mode 100644 index 0000000000..6a0fb78650 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-memoise/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 RMemoise(Package): + """Cache the results of a function so that when you call it again with the + same arguments it returns the pre-computed value.""" + + homepage = "https://github.com/hadley/memoise" + url = "https://cran.r-project.org/src/contrib/memoise_1.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/memoise" + + version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') + + extends('R') + + depends_on('r-digest') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py new file mode 100644 index 0000000000..fb079f44c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RMime(Package): + """Guesses the MIME type from a filename extension using the data derived + from /etc/mime.types in UNIX-type systems.""" + + homepage = "https://github.com/yihui/mime" + url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + + version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py new file mode 100644 index 0000000000..3e77923d76 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 ROpenssl(Package): + """Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey + parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. + Cryptographic signatures can either be created and verified manually or via + x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric + encryption; RSA for asymmetric (public key) encryption or EC for Diffie + Hellman. High-level envelope functions combine RSA and AES for encrypting + arbitrary sized data. Other utilities include key generators, hash + functions (md5, sha1, sha256, etc), base64 encoder, a secure random number + generator, and 'bignum' math methods for manually performing crypto + calculations on large multibyte integers.""" + + homepage = "https://github.com/jeroenooms/openssl#readme" + url = "https://cran.r-project.org/src/contrib/openssl_0.9.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/openssl" + + version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') + + extends('R') + + depends_on('openssl') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py new file mode 100644 index 0000000000..9520952bd7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RPackrat(Package): + """Manage the R packages your project depends on in an isolated, portable, + and reproducible way.""" + + homepage = "https://github.com/rstudio/packrat/" + url = "https://cran.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/packrat" + + version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py new file mode 100644 index 0000000000..0ef2d9b987 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RRstudioapi(Package): + """Access the RStudio API (if available) and provide informative error + messages when it's not.""" + + homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html" + url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + + version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py new file mode 100644 index 0000000000..f338d150f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -0,0 +1,42 @@ +############################################################################## +# 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 RWhisker(Package): + """logicless templating, reuse templates in many programming languages + including R""" + + homepage = "http://github.com/edwindj/whisker" + url = "https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/whisker" + + version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py new file mode 100644 index 0000000000..5ce7437c84 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-withr/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 RWithr(Package): + """A set of functions to run code 'with' safely and temporarily modified + global state. Many of these functions were originally a part of the + 'devtools' package, this provides a simple package with limited + dependencies to provide access to these functions.""" + + homepage = "http://github.com/jimhester/withr" + url = "https://cran.r-project.org/src/contrib/withr_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/withr" + + version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) 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') diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py new file mode 100644 index 0000000000..963d93442f --- /dev/null +++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py @@ -0,0 +1,38 @@ +############################################################################## +# 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 XorgUtilMacros(Package): + """The util-macros package contains the m4 macros used by all of the Xorg packages.""" + + homepage = "http://www.example.com" + url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2" + + version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py new file mode 100644 index 0000000000..7be6defb83 --- /dev/null +++ b/var/spack/repos/builtin/packages/xproto/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 Xproto(Package): + """The Xorg protocol headers provide the header files required to + build the system, and to allow other applications to build against + the installed X Window system.""" + homepage = "http://www.x.org/" + url = "https://www.x.org/archive//individual/proto/xproto-7.0.29.tar.gz" + + version('7.0.29', '16a78dd2c5ad73011105c96235f6a0af') + + depends_on("xorg-util-macros") + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") |