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Merge branch 'develop' into features/cflags

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This commit is contained in:
Todd Gamblin
2016-05-05 10:49:15 -07:00
parent 4ba73dac34 407920e40a
commit 9fb1a9537d
78 changed files with 1592 additions and 471 deletions
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13
var/spack/repos/builtin/packages/adol-c/openmp_exam.patch Normal file
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@@ -0,0 +1,13 @@
diff --git a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
index fc6fc28..14103d2 100644
--- a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
+++ b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
@@ -27,7 +27,7 @@ using namespace std;
#include <ctime>
#include <cmath>
-#include "adolc.h"
+#include <adolc/adolc.h>
#ifdef _OPENMP
#include <omp.h>

80
var/spack/repos/builtin/packages/adol-c/package.py Normal file
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@@ -0,0 +1,80 @@
from spack import *
import sys
class AdolC(Package):
"""A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading."""
homepage = "https://projects.coin-or.org/ADOL-C"
url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/')
version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
variant('doc', default=True, description='Install documentation')
variant('openmp', default=False, description='Enable OpenMP support')
variant('sparse', default=False, description='Enable sparse drivers')
variant('tests', default=True, description='Build all included examples as a test case')
patch('openmp_exam.patch')
def install(self, spec, prefix):
make_args = ['--prefix=%s' % prefix]
# --with-cflags=FLAGS use CFLAGS=FLAGS (default: -O3 -Wall -ansi)
# --with-cxxflags=FLAGS use CXXFLAGS=FLAGS (default: -O3 -Wall)
if '+openmp' in spec:
if spec.satisfies('%gcc'):
make_args.extend([
'--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path>
])
else:
raise InstallError("OpenMP flags for compilers other than GCC are not implemented.")
if '+sparse' in spec:
make_args.extend([
'--enable-sparse'
])
# We can simply use the bundled examples to check
# whether Adol-C works as expected
if '+tests' in spec:
make_args.extend([
'--enable-docexa', # Documeted examples
'--enable-addexa' # Additional examples
])
if '+openmp' in spec:
make_args.extend([
'--enable-parexa' # Parallel examples
])
configure(*make_args)
make()
make("install")
# Copy the config.h file, as some packages might require it
source_directory = self.stage.source_path
config_h = join_path(source_directory,'ADOL-C','src','config.h')
install(config_h, join_path(prefix.include,'adolc'))
# Install documentation to {prefix}/share
if '+doc' in spec:
install_tree(join_path('ADOL-C','doc'),
join_path(prefix.share,'doc'))
# Install examples to {prefix}/share
if '+tests' in spec:
install_tree(join_path('ADOL-C','examples'),
join_path(prefix.share,'examples'))
# Run some examples that don't require user input
# TODO: Check that bundled examples produce the correct results
with working_dir(join_path(source_directory,'ADOL-C','examples')):
Executable('./tapeless_scalar')()
Executable('./tapeless_vector')()
with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
Executable('./checkpointing/checkpointing')()
if '+openmp' in spec:
with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
Executable('./checkpointing/checkpointing')()

1
var/spack/repos/builtin/packages/astyle/package.py
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@@ -14,4 +14,5 @@ def install(self, spec, prefix):
make('-f',
join_path(self.stage.source_path,'build','clang','Makefile'),
parallel=False)
mkdirp(self.prefix.bin)
install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin)

2
var/spack/repos/builtin/packages/autoconf/package.py
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@@ -8,6 +8,8 @@ class Autoconf(Package):
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
depends_on("m4")
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

17
var/spack/repos/builtin/packages/bbcp/package.py Normal file
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@@ -0,0 +1,17 @@
from spack import *
class Bbcp(Package):
"""Securely and quickly copy data from source to target"""
homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master")
def install(self, spec, prefix):
cd("src")
make()
# BBCP wants to build the executable in a directory whose name depends on the system type
makesname = Executable("../MakeSname")
bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n")
destination_path = "%s/bin/" % prefix
mkdirp(destination_path)
install(bbcp_executable_path, destination_path)

12
var/spack/repos/builtin/packages/cnmem/package.py Normal file
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@@ -0,0 +1,12 @@
from spack import *
class Cnmem(Package):
"""CNMem mempool for CUDA devices"""
homepage = "https://github.com/NVIDIA/cnmem"
version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
def install(self, spec, prefix):
cmake('.',*std_cmake_args)
make()
make('install')

13
var/spack/repos/builtin/packages/dealii/package.py
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@@ -12,6 +12,7 @@ class Dealii(Package):
variant('mpi', default=True, description='Compile with MPI')
variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)')
variant('doc', default=False, description='Compile with documentation')
variant('gsl' , default=True, description='Compile with GSL')
variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)')
variant('metis', default=True, description='Compile with Metis')
variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)')
@@ -39,6 +40,8 @@ class Dealii(Package):
depends_on ("mpi", when="+mpi")
depends_on ("arpack-ng+mpi", when='+arpack+mpi')
depends_on ("doxygen", when='+doc')
depends_on ("gsl", when='@8.5.0:+gsl')
depends_on ("gsl", when='@dev+gsl')
depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
depends_on ("metis@5:", when='+metis')
depends_on ("netcdf+mpi", when="+netcdf+mpi")
@@ -50,8 +53,8 @@ class Dealii(Package):
depends_on ("trilinos", when='+trilinos+mpi')
# developer dependnecies
#depends_on ("numdiff") #FIXME
#depends_on ("astyle") #FIXME
depends_on ("numdiff", when='@dev')
depends_on ("astyle@2.04", when='@dev')
def install(self, spec, prefix):
options = []
@@ -80,7 +83,6 @@ def install(self, spec, prefix):
(join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)), # FIXME don't hardcode names
'-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
'-DP4EST_DIR=%s' % spec['p4est'].prefix,
'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
'-DTBB_DIR=%s' % spec['tbb'].prefix,
'-DZLIB_DIR=%s' % spec['zlib'].prefix
@@ -100,7 +102,7 @@ def install(self, spec, prefix):
])
# Optional dependencies for which librariy names are the same as CMake variables
for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'):
if library in spec:
options.extend([
'-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
@@ -251,3 +253,6 @@ def install(self, spec, prefix):
cmake('.')
make('release')
make('run',parallel=False)
def setup_environment(self, spack_env, env):
env.set('DEAL_II_DIR', self.prefix)

1
var/spack/repos/builtin/packages/eigen/package.py
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@@ -45,6 +45,7 @@ class Eigen(Package):
# TODO : dependency on googlehash, superlu, adolc missing
depends_on('cmake')
depends_on('metis@5:', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')

1
var/spack/repos/builtin/packages/flex/package.py
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@@ -6,6 +6,7 @@ class Flex(Package):
homepage = "http://flex.sourceforge.net/"
url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz"
version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec')
version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
def install(self, spec, prefix):

1
var/spack/repos/builtin/packages/gcc/package.py
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@@ -38,6 +38,7 @@ class Gcc(Package):
list_url = 'http://open-source-box.org/gcc/'
list_depth = 2
version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1')
version('5.3.0', 'c9616fd448f980259c31de613e575719')
version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
version('4.9.3', '6f831b4d251872736e8e9cc09746f327')

32
var/spack/repos/builtin/packages/git/package.py
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@@ -7,7 +7,8 @@ class Git(Package):
homepage = "http://git-scm.com"
url = "https://github.com/git/git/tarball/v2.7.1"
version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c')
version('2.8.1', '1308448d95afa41a4135903f22262fc8')
version('2.8.0', 'eca687e46e9750121638f258cff8317b')
version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6')
version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060')
@@ -23,18 +24,10 @@ class Git(Package):
#version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
# Git compiles with curl support by default on but if your system
# does not have it you will not be able to clone https repos
variant("curl", default=False, description="Add the internal support of curl for https clone")
# Git compiles with expat support by default on but if your system
# does not have it you will not be able to push https repos
variant("expat", default=False, description="Add the internal support of expat for https push")
depends_on("openssl")
depends_on("autoconf")
depends_on("curl", when="+curl")
depends_on("expat", when="+expat")
depends_on("curl")
depends_on("expat")
# Also depends_on gettext: apt-get install gettext (Ubuntu)
@@ -49,23 +42,12 @@ def install(self, spec, prefix):
"--prefix=%s" % prefix,
"--without-pcre",
"--with-openssl=%s" % spec['openssl'].prefix,
"--with-zlib=%s" % spec['zlib'].prefix
"--with-zlib=%s" % spec['zlib'].prefix,
"--with-curl=%s" % spec['curl'].prefix,
"--with-expat=%s" % spec['expat'].prefix,
]
if '+curl' in spec:
configure_args.append("--with-curl=%s" % spec['curl'].prefix)
if '+expat' in spec:
configure_args.append("--with-expat=%s" % spec['expat'].prefix)
which('autoreconf')('-i')
configure(*configure_args)
make()
make("install")

2
var/spack/repos/builtin/packages/glm/package.py
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@@ -11,6 +11,8 @@ class Glm(Package):
url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz"
version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8')
depends_on ("cmake")
def install(self, spec, prefix):
with working_dir('spack-build', create=True):

2
var/spack/repos/builtin/packages/gmp/package.py
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@@ -35,6 +35,8 @@ class Gmp(Package):
version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
version('6.0.0' , '6ef5869ae735db9995619135bd856b84')
depends_on("m4")
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()

2
var/spack/repos/builtin/packages/hdf5/package.py
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@@ -38,7 +38,7 @@ class Hdf5(Package):
list_depth = 3
version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True)
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
version('1.8.13', 'c03426e9e77d7766944654280b467289')

21
var/spack/repos/builtin/packages/hydra/package.py Normal file
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@@ -0,0 +1,21 @@
from spack import *
class Hydra(Package):
"""Hydra is a process management system for starting parallel jobs.
Hydra is designed to natively work with existing launcher daemons
(such as ssh, rsh, fork), as well as natively integrate with resource
management systems (such as slurm, pbs, sge)."""
homepage = "http://www.mpich.org"
url = "http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz"
list_url = "http://www.mpich.org/static/downloads/"
list_depth = 2
version('3.2', '4d670916695bf7e3a869cc336a881b39')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

42
var/spack/repos/builtin/packages/ior/package.py Normal file
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@@ -0,0 +1,42 @@
from spack import *
import os
class Ior(Package):
"""The IOR software is used for benchmarking parallel file systems
using POSIX, MPI-IO, or HDF5 interfaces."""
homepage = "https://github.com/LLNL/ior"
url = "https://github.com/LLNL/ior/archive/3.0.1.tar.gz"
version('3.0.1', '71150025e0bb6ea1761150f48b553065')
variant('hdf5', default=False, description='support IO with HDF5 backend')
variant('ncmpi', default=False, description='support IO with NCMPI backend')
depends_on('mpi')
depends_on('hdf5+mpi', when='+hdf5')
depends_on('netcdf+mpi', when='+ncmpi')
def install(self, spec, prefix):
os.system('./bootstrap')
config_args = [
'MPICC=%s' % spec['mpi'].prefix.bin + '/mpicc',
'--prefix=%s' % prefix,
]
if '+hdf5' in spec:
config_args.append('--with-hdf5')
else:
config_args.append('--without-hdf5')
if '+ncmpi' in spec:
config_args.append('--with-ncmpi')
else:
config_args.append('--without-ncmpi')
configure(*config_args)
make()
make('install')

2
var/spack/repos/builtin/packages/libtool/package.py
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@@ -8,6 +8,8 @@ class Libtool(Package):
version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e')
version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50')
depends_on('m4')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

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var/spack/repos/builtin/packages/mfem/package.py Normal file
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@@ -0,0 +1,125 @@
from spack import *
import glob, string
class Mfem(Package):
"""Free, lightweight, scalable C++ library for finite element methods."""
homepage = 'http://www.mfem.org'
url = 'https://github.com/mfem/mfem'
# version('3.1', git='https://github.com/mfem/mfem.git',
# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
url='http://goo.gl/xrScXn', expand=False)
variant('metis', default=False, description='Activate support for metis')
variant('hypre', default=False, description='Activate support for hypre')
variant('suite-sparse', default=False,
description='Activate support for SuiteSparse')
variant('mpi', default=False, description='Activate support for MPI')
variant('lapack', default=False, description='Activate support for LAPACK')
variant('debug', default=False, description='Build debug version')
depends_on('blas', when='+lapack')
depends_on('lapack', when='+lapack')
depends_on('mpi', when='+mpi')
depends_on('metis', when='+mpi')
depends_on('hypre', when='+mpi')
depends_on('hypre', when='+hypre')
depends_on('metis@4:', when='+metis')
depends_on('suite-sparse', when='+suite-sparse')
depends_on('blas', when='+suite-sparse')
depends_on('lapack', when='+suite-sparse')
depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:')
depends_on('cmake', when='^metis@5:')
def check_variants(self, spec):
if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec):
raise InstallError('mfem+mpi must be built with +hypre ' +
'and +metis!')
if '+suite-sparse' in spec and ('+metis' not in spec or
'+lapack' not in spec):
raise InstallError('mfem+suite-sparse must be built with ' +
'+metis and +lapack!')
if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec):
raise InstallError('To work around CMake bug with clang, must ' +
'build mfem with mfem[+variants] %clang ' +
'^cmake %gcc to force CMake to build with gcc')
return
def install(self, spec, prefix):
self.check_variants(spec)
options = ['PREFIX=%s' % prefix]
if '+lapack' in spec:
lapack_lib = '-L{0} -llapack -L{1} -lblas'.format(
spec['lapack'].prefix.lib, spec['blas'].prefix.lib)
options.extend(['MFEM_USE_LAPACK=YES',
'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
'LAPACK_LIB=%s' % lapack_lib])
if '+hypre' in spec:
options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix,
'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib +
' -lHYPRE'])
if '+metis' in spec:
metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib
if spec['metis'].satisfies('@5:'):
metis_str = 'MFEM_USE_METIS_5=YES'
else:
metis_str = 'MFEM_USE_METIS_5=NO'
options.extend([metis_str,
'METIS_DIR=%s' % spec['metis'].prefix,
'METIS_OPT=-I%s' % spec['metis'].prefix.include,
'METIS_LIB=%s' % metis_lib])
if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES'])
if '+suite-sparse' in spec:
ssp = spec['suite-sparse'].prefix
ss_lib = '-L%s' % ssp.lib
ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' +
' -lccolamd -lsuitesparseconfig')
no_librt_archs = ['darwin-i686', 'darwin-x86_64']
no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs))
if not no_rt: ss_lib += ' -lrt'
ss_lib += (' ' + metis_lib + ' ' + lapack_lib)
options.extend(['MFEM_USE_SUITESPARSE=YES',
'SUITESPARSE_DIR=%s' % ssp,
'SUITESPARSE_OPT=-I%s' % ssp.include,
'SUITESPARSE_LIB=%s' % ss_lib])
if '+debug' in spec: options.extend(['MFEM_DEBUG=YES'])
# Dirty hack to cope with URL redirect
tgz_file = string.split(self.url,'/')[-1]
tar = which('tar')
tar('xzvf', tgz_file)
cd(glob.glob('mfem*')[0])
# End dirty hack to cope with URL redirect
make('config', *options)
make('all')
# Run a small test before installation
args = ['-m', join_path('data','star.mesh'), '--no-visualization']
if '+mpi' in spec:
Executable(join_path(spec['mpi'].prefix.bin,
'mpirun'))('-np',
'4',
join_path('examples','ex1p'),
*args)
else:
Executable(join_path('examples', 'ex1'))(*args)
make('install')

7
var/spack/repos/builtin/packages/mpich/package.py
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@@ -55,9 +55,10 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('MPICH_FC', spack_fc)
def setup_dependent_package(self, module, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
# FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
module.mpicc = join_path(self.prefix.bin, 'mpicc')
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.mpif77 = join_path(self.prefix.bin, 'mpif77')
def install(self, spec, prefix):
config_args = ["--prefix=" + prefix,

1
var/spack/repos/builtin/packages/mrnet/package.py
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@@ -6,6 +6,7 @@ class Mrnet(Package):
url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
version('4.1.0', '5a248298b395b329e2371bf25366115c')
version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')

6
var/spack/repos/builtin/packages/mvapich2/package.py
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@@ -147,6 +147,12 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
spack_env.set('MPICH_F90', spack_fc)
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.mpicxx = join_path(self.prefix.bin, 'mpicxx')
self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
def install(self, spec, prefix):
# we'll set different configure flags depending on our environment
configure_args = [

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var/spack/repos/builtin/packages/ncview/package.py Normal file
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@@ -0,0 +1,20 @@
from spack import *
class Ncview(Package):
"""Simple viewer for NetCDF files."""
homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html"
url = "ftp://cirrus.ucsd.edu/pub/ncview/ncview-2.1.7.tar.gz"
version('2.1.7', 'debd6ca61410aac3514e53122ab2ba07')
depends_on("netcdf")
depends_on("udunits2")
# OS Dependencies
# Ubuntu: apt-get install libxaw7-dev
# CentOS 7: yum install libXaw-devel
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

20
var/spack/repos/builtin/packages/netcdf/package.py
View File

@@ -12,15 +12,19 @@ class Netcdf(Package):
version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
variant('mpi', default=True, description='Enables MPI parallelism')
variant('hdf4', default=False, description="Enable HDF4 support")
variant('mpi', default=True, description='Enables MPI parallelism')
variant('hdf4', default=False, description='Enable HDF4 support')
# Dependencies:
depends_on("curl") # required for DAP support
depends_on("m4")
depends_on("hdf", when='+hdf4')
depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support
depends_on("hdf5~mpi", when='~mpi') # required for NetCDF-4 support
depends_on("zlib") # required for NetCDF-4 support
# Required for DAP support
depends_on("curl")
# Required for NetCDF-4 support
depends_on("zlib")
depends_on("hdf5+mpi", when='+mpi')
depends_on("hdf5~mpi", when='~mpi')
def install(self, spec, prefix):
# Environment variables
@@ -48,7 +52,7 @@ def install(self, spec, prefix):
# /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
LIBS.append("-lcurl")
CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib)
if '+mpi' in spec:
config_args.append('--enable-parallel4')

35
var/spack/repos/builtin/packages/openblas/make.patch Normal file
View File

@@ -0,0 +1,35 @@
diff --git a/Makefile.system b/Makefile.system
index b89f60e..2dbdad0 100644
--- a/Makefile.system
+++ b/Makefile.system
@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
endif
GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
+ifdef MAKE_NO_J
+GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
+endif
+
ifdef MAKE_NB_JOBS
GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
endif
diff --git a/getarch.c b/getarch.c
index f9c49e6..dffad70 100644
--- a/getarch.c
+++ b/getarch.c
@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
#endif
#endif
+#ifndef MAKE_NO_J
#ifdef MAKE_NB_JOBS
printf("MAKE += -j %d\n", MAKE_NB_JOBS);
#elif NO_PARALLEL_MAKE==1
@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
printf("MAKE += -j %d\n", get_num_cores());
#endif
#endif
+#endif
break;

69
var/spack/repos/builtin/packages/openblas/package.py
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@@ -1,6 +1,7 @@
from spack import *
import sys
import os
import shutil
class Openblas(Package):
"""OpenBLAS: An optimized BLAS library"""
@@ -13,18 +14,21 @@ class Openblas(Package):
variant('shared', default=True, description="Build shared libraries as well as static libs.")
variant('openmp', default=True, description="Enable OpenMP support.")
variant('fpic', default=True, description="Build position independent code")
# virtual dependency
provides('blas')
provides('lapack')
patch('make.patch')
def install(self, spec, prefix):
# Openblas is picky about compilers. Configure fails with
# FC=/abs/path/to/f77, whereas FC=f77 works fine.
# To circumvent this, provide basename only:
make_defs = ['CC=%s' % os.path.basename(spack_cc),
'FC=%s' % os.path.basename(spack_f77)]
'FC=%s' % os.path.basename(spack_f77),
'MAKE_NO_J=1']
make_targets = ['libs', 'netlib']
@@ -32,6 +36,8 @@ def install(self, spec, prefix):
if '+shared' in spec:
make_targets += ['shared']
else:
if '+fpic' in spec:
make_defs.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC'])
make_defs += ['NO_SHARED=1']
# fix missing _dggsvd_ and _sggsvd_
@@ -64,6 +70,10 @@ def install(self, spec, prefix):
if '+shared' in spec:
symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix)
# Openblas may pass its own test but still fail to compile Lapack
# symbols. To make sure we get working Blas and Lapack, do a small test.
self.check_install(spec)
def setup_dependent_package(self, module, dspec):
# This is WIP for a prototype interface for virtual packages.
@@ -76,3 +86,60 @@ def setup_dependent_package(self, module, dspec):
if '+shared' in self.spec:
self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
def check_install(self, spec):
"Build and run a small program to test that we have Lapack symbols"
print "Checking Openblas installation..."
checkdir = "spack-check"
with working_dir(checkdir, create=True):
source = r"""
#include <cblas.h>
#include <stdio.h>
int main(void) {
int i=0;
double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
for (i = 0; i < 9; i++)
printf("%f\n", C[i]);
return 0;
}
"""
expected = """\
11.000000
-9.000000
5.000000
-9.000000
21.000000
-1.000000
5.000000
-1.000000
3.000000
"""
with open("check.c", 'w') as f:
f.write(source)
cc = which('cc')
# TODO: Automate these path and library settings
cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c")
cc('-o', "check", "check.o",
"-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas", "-lpthread")
try:
check = Executable('./check')
output = check(return_output=True)
except:
output = ""
success = output == expected
if not success:
print "Produced output does not match expected output."
print "Expected output:"
print '-'*80
print expected
print '-'*80
print "Produced output:"
print '-'*80
print output
print '-'*80
raise RuntimeError("Openblas install check failed")
shutil.rmtree(checkdir)

13
var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c Normal file
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@@ -0,0 +1,13 @@
#include <cblas.h>
#include <stdio.h>
int main(void) {
int i=0;
double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
for (i = 0; i < 9; i++)
printf("%f\n", C[i]);
return 0;
}

9
var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output Normal file
View File

@@ -0,0 +1,9 @@
11.000000
-9.000000
5.000000
-9.000000
21.000000
-1.000000
5.000000
-1.000000
3.000000

11
var/spack/repos/builtin/packages/openmpi/package.py
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@@ -1,7 +1,5 @@
import os
from spack import *
import os
class Openmpi(Package):
"""Open MPI is a project combining technologies and resources from
@@ -38,6 +36,7 @@ class Openmpi(Package):
depends_on('hwloc')
def url_for_version(self, version):
return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
@@ -48,6 +47,12 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('OMPI_FC', spack_fc)
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.mpicxx = join_path(self.prefix.bin, 'mpic++')
self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
def install(self, spec, prefix):
config_args = ["--prefix=%s" % prefix,

47
var/spack/repos/builtin/packages/openssl/package.py
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@@ -3,6 +3,7 @@
from spack import *
class Openssl(Package):
"""The OpenSSL Project is a collaborative effort to develop a
robust, commercial-grade, full-featured, and Open Source
@@ -14,10 +15,12 @@ class Openssl(Package):
version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
version('1.0.1r', '1abd905e079542ccae948af37e393d28')
version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
depends_on("zlib")
parallel = False
@@ -30,26 +33,14 @@ def url_for_version(self, version):
# Same idea, but just to avoid issuing the same message multiple times
warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
if openssl_url is None:
latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz'
older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
# Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
# return the url for older format
version_number = '.'.join([str(x) for x in version[:-1]])
older_url = older.format(version_number=version_number, version_full=version)
latest_url = latest.format(version=version)
response = urllib.urlopen(latest.format(version=version))
if response.getcode() == 404:
openssl_url = older_url
# Checks if we already warned the user for this particular version of OpenSSL.
# If not we display a warning message and mark this version
if self.spec.satisfies('@external'):
# The version @external is reserved to system openssl. In that case return a fake url and exit
openssl_url = '@external (reserved version for system openssl)'
if not warnings_given_to_user.get(version, False):
tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
tty.warn('Consider updating to the latest version of this package.')
tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
tty.msg('Using openssl@external : the version @external is reserved for system openssl')
warnings_given_to_user[version] = True
else:
openssl_url = latest_url
# Store the computed URL
openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL
openssl_urls[version] = openssl_url
# Store the updated dictionary of URLS
Openssl._openssl_url = openssl_urls
@@ -58,6 +49,28 @@ def url_for_version(self, version):
return openssl_url
def check_for_outdated_release(self, version, warnings_given_to_user):
latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz'
older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
# Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
# return the url for older format
version_number = '.'.join([str(x) for x in version[:-1]])
try:
openssl_url = latest.format(version=version)
urllib.urlopen(openssl_url)
except IOError:
openssl_url = older.format(version_number=version_number, version_full=version)
# Checks if we already warned the user for this particular version of OpenSSL.
# If not we display a warning message and mark this version
if not warnings_given_to_user.get(version, False):
tty.warn(
'This installation depends on an old version of OpenSSL, which may have known security issues. ')
tty.warn('Consider updating to the latest version of this package.')
tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
warnings_given_to_user[version] = True
return openssl_url
def install(self, spec, prefix):
# OpenSSL uses a variable APPS in its Makefile. If it happens to be set
# in the environment, then this will override what is set in the

38
var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py Normal file
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@@ -0,0 +1,38 @@
from spack import *
class OsuMicroBenchmarks(Package):
"""The Ohio MicroBenchmark suite is a collection of independent MPI
message passing performance microbenchmarks developed and written at
The Ohio State University. It includes traditional benchmarks and
performance measures such as latency, bandwidth and host overhead
and can be used for both traditional and GPU-enhanced nodes."""
homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/"
url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz"
version('5.3', '42e22b931d451e8bec31a7424e4adfc2')
variant('cuda', default=False, description="Enable CUDA support")
depends_on('mpi')
depends_on('cuda', when='+cuda')
def install(self, spec, prefix):
config_args = [
'CC=%s' % spec['mpi'].prefix.bin + '/mpicc',
'CXX=%s' % spec['mpi'].prefix.bin + '/mpicxx',
'LDFLAGS=-lrt',
'--prefix=%s' % prefix
]
if '+cuda' in spec:
config_args.extend([
'--enable-cuda',
'--with-cuda=%s' % spec['cuda'].prefix,
])
configure(*config_args)
make()
make('install')

27
var/spack/repos/builtin/packages/p4est/package.py
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@@ -7,10 +7,17 @@ class P4est(Package):
version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
# disable by default to make it work on frontend of clusters
variant('tests', default=False, description='Run small tests')
variant('tests', default=True, description='Run small tests')
# build dependencies
depends_on('automake')
depends_on('autoconf')
depends_on('libtool@2.4.2:')
# other dependencies
depends_on('lua') # Needed for the submodule sc
depends_on('mpi')
depends_on('zlib')
def install(self, spec, prefix):
options = ['--enable-mpi',
@@ -19,16 +26,20 @@ def install(self, spec, prefix):
'--without-blas',
'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
'CFLAGS=-O2',
'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
'CC=%s' % self.spec['mpi'].mpicc,
'CXX=%s' % self.spec['mpi'].mpicxx,
'FC=%s' % self.spec['mpi'].mpifc,
'F77=%s' % self.spec['mpi'].mpif77
]
configure('--prefix=%s' % prefix, *options)
make()
# Make tests optional as sometimes mpiexec can't be run with an error:
# mpiexec has detected an attempt to run as root.
# Running at root is *strongly* discouraged as any mistake (e.g., in
# defining TMPDIR) or bug can result in catastrophic damage to the OS
# file system, leaving your system in an unusable state.
if '+tests' in self.spec:
make("check")
make("check")
make("install")

14
var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch Normal file
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@@ -0,0 +1,14 @@
diff --git a/eo/src/CMakeLists.txt b/eo/src/CMakeLists.txt
index b2b445a..d45ddc7 100644
--- a/eo/src/CMakeLists.txt
+++ b/eo/src/CMakeLists.txt
@@ -47,7 +47,7 @@ install(DIRECTORY do es ga gp other utils
add_subdirectory(es)
add_subdirectory(ga)
add_subdirectory(utils)
-#add_subdirectory(serial)
+add_subdirectory(serial) # Required when including <paradiseo/eo/utils/eoTimer.h> , which is need by <paradiseo/eo/mpi/eoMpi.h>
if(ENABLE_PYEO)
add_subdirectory(pyeo)

13
var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch Normal file
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@@ -0,0 +1,13 @@
diff --git a/cmake/Config.cmake b/cmake/Config.cmake
index 02593ba..d198ca9 100644
--- a/cmake/Config.cmake
+++ b/cmake/Config.cmake
@@ -6,7 +6,7 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
# detect OS X version. (use '/usr/bin/sw_vers -productVersion' to extract V from '10.V.x'.)
execute_process (COMMAND /usr/bin/sw_vers -productVersion OUTPUT_VARIABLE MACOSX_VERSION_RAW)
- string(REGEX REPLACE "10\\.([0-9]).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}")
+ string(REGEX REPLACE "10\\.([0-9]+).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}")
if(${MACOSX_VERSION} LESS 5)
message(FATAL_ERROR "Unsupported version of OS X : ${MACOSX_VERSION_RAW}")
return()

13
var/spack/repos/builtin/packages/paradiseo/fix_tests.patch Normal file
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@@ -0,0 +1,13 @@
diff --git a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
index 994a9a4..c4ba77b 100644
--- a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
+++ b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
@@ -41,7 +41,7 @@
#include <moeo>
#include <cassert>
-#include<archive/moeo2DMinHyperVolumeArchive.h>
+#include<archive/moeo2DMinHypervolumeArchive.h>
//-----------------------------------------------------------------------------

13
var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch Normal file
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@@ -0,0 +1,13 @@
diff --git a/eo/tutorial/Lesson3/exercise3.1.cpp b/eo/tutorial/Lesson3/exercise3.1.cpp
index dc37479..d178941 100644
--- a/eo/tutorial/Lesson3/exercise3.1.cpp
+++ b/eo/tutorial/Lesson3/exercise3.1.cpp
@@ -289,7 +289,7 @@ void main_function(int argc, char **argv)
checkpoint.add(fdcStat);
// The Stdout monitor will print parameters to the screen ...
- eoStdoutMonitor monitor(false);
+ eoStdoutMonitor monitor;
// when called by the checkpoint (i.e. at every generation)
checkpoint.add(monitor);

66
var/spack/repos/builtin/packages/paradiseo/package.py Normal file
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@@ -0,0 +1,66 @@
from spack import *
import sys
class Paradiseo(Package):
"""A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics."""
homepage = "http://paradiseo.gforge.inria.fr/"
# Installing from the development version is a better option at this
# point than using the very old supplied packages
version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git')
# This is a version that the package formula author has tested successfully.
# However, the clone is very large (~1Gb git history). The history in the
# head version has been trimmed significantly.
version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
variant('mpi', default=True, description='Compile with parallel and distributed metaheuristics module')
variant('smp', default=True, description='Compile with symmetric multi-processing module ')
variant('edo', default=True, description='Compile with (Experimental) EDO module')
#variant('tests', default=False, description='Compile with build tests')
#variant('doc', default=False, description='Compile with documentation')
variant('debug', default=False, description='Builds a debug version of the libraries')
variant('openmp', default=False, description='Enable OpenMP support')
variant('gnuplot', default=False, description='Enable GnuPlot support')
# Required dependencies
depends_on ("cmake")
# Optional dependencies
depends_on ("mpi", when="+mpi")
depends_on ("doxygen", when='+doc')
depends_on ("gnuplot", when='+gnuplot')
depends_on ("eigen", when='+edo')
depends_on ("boost~mpi", when='+edo~mpi')
depends_on ("boost+mpi", when='+edo+mpi')
# Patches
patch('enable_eoserial.patch')
patch('fix_osx_detection.patch')
patch('fix_tests.patch')
patch('fix_tutorials.patch')
def install(self, spec, prefix):
options = []
options.extend(std_cmake_args)
options.extend([
'-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
'-DINSTALL_TYPE:STRING=MIN',
'-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'),
'-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler
'-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'),
'-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'),
'-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'),
'-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE')
])
with working_dir('spack-build', create=True):
# Configure
cmake('..', *options)
# Build, test and install
make("VERBOSE=1")
if '+tests' in spec:
make("test")
make("install")

14
var/spack/repos/builtin/packages/py-SQLAlchemy/package.py Normal file
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@@ -0,0 +1,14 @@
from spack import *
class PySqlalchemy(Package):
"""The Python SQL Toolkit and Object Relational Mapper"""
homepage = 'http://www.sqlalchemy.org/'
url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz"
version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

2
var/spack/repos/builtin/packages/py-bottleneck/package.py
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@@ -7,7 +7,7 @@ class PyBottleneck(Package):
version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
extends('python', ignore=r'bin/f2py$')
extends('python')
depends_on('py-numpy')
def install(self, spec, prefix):

22
var/spack/repos/builtin/packages/py-csvkit/package.py Normal file
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@@ -0,0 +1,22 @@
from spack import *
class PyCsvkit(Package):
"""A library of utilities for working with CSV, the king of tabular file
formats"""
homepage = 'http://csvkit.rtfd.org/'
url = "https://pypi.python.org/packages/source/c/csvkit/csvkit-0.9.1.tar.gz"
version('0.9.1', '48d78920019d18846933ee969502fff6')
extends('python')
depends_on('py-dateutil')
depends_on('py-dbf')
depends_on('py-xlrd')
depends_on('py-SQLAlchemy')
depends_on('py-six')
depends_on('py-openpyxl')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

15
var/spack/repos/builtin/packages/py-dbf/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class PyDbf(Package):
"""Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro
.dbf files (including memos)"""
homepage = 'https://pypi.python.org/pypi/dbf'
url = "https://pypi.python.org/packages/source/d/dbf/dbf-0.96.005.tar.gz"
version('0.96.005', 'bce1a1ed8b454a30606e7e18dd2f8277')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

14
var/spack/repos/builtin/packages/py-jdcal/package.py Normal file
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@@ -0,0 +1,14 @@
from spack import *
class PyJdcal(Package):
"""Julian dates from proleptic Gregorian and Julian calendars"""
homepage = 'http://github.com/phn/jdcal'
url = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz"
version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

2
var/spack/repos/builtin/packages/py-matplotlib/package.py
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@@ -12,7 +12,7 @@ class PyMatplotlib(Package):
variant('gui', default=False, description='Enable GUI')
variant('ipython', default=False, description='Enable ipython support')
extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$')
extends('python', ignore=r'bin/nosetests.*$|bin/pbr$')
depends_on('py-pyside', when='+gui')
depends_on('py-ipython', when='+ipython')

2
var/spack/repos/builtin/packages/py-numexpr/package.py
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@@ -9,7 +9,7 @@ class PyNumexpr(Package):
version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
version('2.5', '84f66cced45ba3e30dcf77a937763aaa')
extends('python', ignore=r'bin/f2py$')
extends('python')
depends_on('py-numpy')
def install(self, spec, prefix):

17
var/spack/repos/builtin/packages/py-openpyxl/package.py Normal file
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@@ -0,0 +1,17 @@
from spack import *
class PyOpenpyxl(Package):
"""A Python library to read/write Excel 2007 xlsx/xlsm files"""
homepage = 'http://openpyxl.readthedocs.org/'
url = "https://pypi.python.org/packages/source/o/openpyxl/openpyxl-2.4.0-a1.tar.gz"
version('2.4.0-a1', 'e5ca6d23ceccb15115d45cdf26e736fc')
extends('python')
depends_on('py-jdcal')
depends_on('py-setuptools')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

2
var/spack/repos/builtin/packages/py-pandas/package.py
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@@ -10,7 +10,7 @@ class PyPandas(Package):
version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
extends('python', ignore=r'bin/f2py$')
extends('python')
depends_on('py-dateutil')
depends_on('py-numpy')
depends_on('py-setuptools')

2
var/spack/repos/builtin/packages/py-scikit-image/package.py
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@@ -7,7 +7,7 @@ class PyScikitImage(Package):
version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1')
extends('python', ignore=r'bin/.*\.py$|bin/f2py$')
extends('python', ignore=r'bin/.*\.py$')
depends_on('py-dask')
depends_on('py-pillow')

15
var/spack/repos/builtin/packages/py-xlrd/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class PyXlrd(Package):
"""Library for developers to extract data from Microsoft Excel (tm)
spreadsheet files"""
homepage = 'http://www.python-excel.org/'
url = "https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.4.tar.gz"
version('0.9.4', '911839f534d29fe04525ef8cd88fe865')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

2
var/spack/repos/builtin/packages/python/package.py
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@@ -151,6 +151,8 @@ def python_ignore(self, ext_pkg, args):
patterns.append(r'setuptools\.pth')
patterns.append(r'bin/easy_install[^/]*$')
patterns.append(r'setuptools.*egg$')
if ext_pkg.name != 'py-numpy':
patterns.append(r'bin/f2py$')
return match_predicate(ignore_arg, patterns)

16
var/spack/repos/builtin/packages/qt/package.py
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@@ -101,7 +101,7 @@ def patch(self):
@property
def common_config_args(self):
return [
config_args = [
'-prefix', self.prefix,
'-v',
'-opensource',
@@ -115,7 +115,16 @@ def common_config_args(self):
'-no-openvg',
'-no-pch',
# NIS is deprecated in more recent glibc
'-no-nis']
'-no-nis'
]
if '+gtk' in self.spec:
config_args.append('-gtkstyle')
else:
config_args.append('-no-gtkstyle')
return config_args
# Don't disable all the database drivers, but should
# really get them into spack at some point.
@@ -128,8 +137,7 @@ def configure(self):
'-thread',
'-shared',
'-release',
'-fast'
)
'-fast')
@when('@4')
def configure(self):

11
var/spack/repos/builtin/packages/qthreads/ldflags.patch Normal file
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@@ -0,0 +1,11 @@
--- a/configure
+++ b/configure
@@ -40456,7 +40456,7 @@
hwloc_saved_LDFLAGS="$LDFLAGS"
if test "x$with_hwloc" != x; then
CPPFLAGS="-I$with_hwloc/include $CPPFLAGS"
- LDFLAGS="-L$with_hwloc/lib $CPPFLAGS"
+ LDFLAGS="-L$with_hwloc/lib $LDFLAGS"
fi

7
var/spack/repos/builtin/packages/qthreads/package.py
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@@ -16,7 +16,12 @@ class Qthreads(Package):
version('1.10', '5af8c8bbe88c2a6d45361643780d1671')
patch("ldflags.patch")
patch("restrict.patch")
patch("trap.patch")
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
configure("--prefix=%s" % prefix,
"--enable-guard-pages")
make()
make("install")

12
var/spack/repos/builtin/packages/qthreads/restrict.patch Normal file
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@@ -0,0 +1,12 @@
--- a/include/qthread/common.h.in
+++ b/include/qthread/common.h.in
@@ -84,7 +84,9 @@
/* Define to the equivalent of the C99 'restrict' keyword, or to
nothing if this is not supported. Do not define if restrict is
supported directly. */
+#ifndef restrict
#undef restrict
+#endif
/* Work around a bug in Sun C++: it does not support _Restrict or
__restrict__, even though the corresponding Sun C compiler ends up with
"#define restrict _Restrict" or "#define restrict __restrict__" in the

11
var/spack/repos/builtin/packages/qthreads/trap.patch Normal file
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@@ -0,0 +1,11 @@
--- a/include/qthread/qthread.hpp
+++ b/include/qthread/qthread.hpp
@@ -236,7 +236,7 @@
return qthread_incr64((uint64_t *)operand, incr);
default:
- *(int *)(0) = 0;
+ __builtin_trap();
}
return T(0); // never hit - keep compiler happy
}

12
var/spack/repos/builtin/packages/raja/package.py Normal file
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@@ -0,0 +1,12 @@
from spack import *
class Raja(Package):
"""RAJA Parallel Framework."""
homepage = "http://software.llnl.gov/RAJA/"
version('git', git='https://github.com/LLNL/RAJA.git', branch="master")
def install(self, spec, prefix):
cmake('.',*std_cmake_args)
make()
make('install')

13
var/spack/repos/builtin/packages/scons/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Scons(Package):
"""SCons is a software construction tool"""
homepage = "http://scons.org"
url = "http://downloads.sourceforge.net/project/scons/scons/2.5.0/scons-2.5.0.tar.gz"
version('2.5.0', '9e00fa0df8f5ca5c5f5975b40e0ed354')
extends('python')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix=%s' % prefix)

51
var/spack/repos/builtin/packages/serf/package.py Normal file
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@@ -0,0 +1,51 @@
##############################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License (as published by
# the Free Software Foundation) version 2.1 dated February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Serf(Package):
"""Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library"""
homepage = 'https://serf.apache.org/'
url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2'
version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
depends_on('apr')
depends_on('apr-util')
depends_on('scons')
depends_on('expat')
depends_on('openssl')
def install(self, spec, prefix):
scons = which("scons")
options = ['PREFIX=%s' % prefix]
options.append('APR=%s' % spec['apr'].prefix)
options.append('APU=%s' % spec['apr-util'].prefix)
options.append('OPENSSL=%s' % spec['openssl'].prefix)
options.append('LINKFLAGS=-L%s/lib' % spec['expat'].prefix)
options.append('CPPFLAGS=-I%s/include' % spec['expat'].prefix)
scons(*options)
scons('install')

2
var/spack/repos/builtin/packages/subversion/package.py
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@@ -37,6 +37,7 @@ class Subversion(Package):
depends_on('apr-util')
depends_on('zlib')
depends_on('sqlite')
depends_on('serf')
# Optional: We need swig if we want the Perl, Python or Ruby
# bindings.
@@ -54,6 +55,7 @@ def install(self, spec, prefix):
options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
options.append('--with-zlib=%s' % spec['zlib'].prefix)
options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
options.append('--with-serf=%s' % spec['serf'].prefix)
#options.append('--with-swig=%s' % spec['swig'].prefix)
configure(*options)

4
var/spack/repos/builtin/packages/superlu-dist/package.py
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@@ -6,7 +6,9 @@ class SuperluDist(Package):
homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
version('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('4.2', 'ae9fafae161f775fbac6eba11e530a65')
version('4.1', '4edee38cc29f687bd0c8eb361096a455')
version('4.0', 'c0b98b611df227ae050bc1635c6940e0')

14
var/spack/repos/builtin/packages/swig/package.py
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@@ -22,6 +22,7 @@
# 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 Swig(Package):
@@ -33,14 +34,19 @@ class Swig(Package):
code. In addition, SWIG provides a variety of customization
features that let you tailor the wrapping process to suit your
application."""
homepage = "http://www.swig.org"
url = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
homepage = "http://www.swig.org"
url = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz"
version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97')
version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
version('2.0.2', 'eaf619a4169886923e5f828349504a29')
version('1.3.40', '2df766c9e03e02811b1ab4bba1c7b9cc')
depends_on('pcre')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
configure('--prefix=%s' % prefix)
make()
make("install")
make('install')

124
var/spack/repos/builtin/packages/turbomole/package.py Normal file
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@@ -0,0 +1,124 @@
from spack import *
import os
import subprocess
class Turbomole(Package):
"""TURBOMOLE: Program Package for ab initio Electronic Structure
Calculations. NB: Requires a license to download."""
# NOTE: Turbomole requires purchase of a license to download. Go to the
# NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details.
# NOTE: Spack will search the current directory for this file. It is
# NOTE: probably best to add this file to a Spack mirror so that it can be
# NOTE: found from anywhere. For information on setting up a Spack mirror
# NOTE: see http://software.llnl.gov/spack/mirrors.html
homepage = "http://www.turbomole-gmbh.com/"
version('7.0.2', '92b97e1e52e8dcf02a4d9ac0147c09d6',
url="file://%s/turbolinux702.tar.gz" % os.getcwd())
variant('mpi', default=False, description='Set up MPI environment')
variant('smp', default=False, description='Set up SMP environment')
# Turbomole's install is odd. There are three variants
# - serial
# - parallel, MPI
# - parallel, SMP
#
# Only one of these can be active at a time. MPI and SMP are set as
# variants so there could be up to 3 installs per version. Switching
# between them would be accomplished with `module swap` commands.
def do_fetch(self, mirror_only=True):
if '+mpi' in self.spec and '+smp' in self.spec:
raise InstallError('Can not have both SMP and MPI enabled in the same build.')
super(Turbomole, self).do_fetch(mirror_only)
def get_tm_arch(self):
# For python-2.7 we could use `tm_arch = subprocess.check_output()`
# Use the following for compatibility with python 2.6
if 'TURBOMOLE' in os.getcwd():
tm_arch = subprocess.Popen(['sh', 'scripts/sysname'],
stdout=subprocess.PIPE).communicate()[0]
return tm_arch.rstrip('\n')
else:
return
def install(self, spec, prefix):
if spec.satisfies('@:7.0.2'):
calculate_version = 'calculate_2.4_linux64'
molecontrol_version = 'MoleControl_2.5'
tm_arch=self.get_tm_arch()
tar = which('tar')
dst = join_path(prefix, 'TURBOMOLE')
tar('-x', '-z', '-f', 'thermocalc.tar.gz')
with working_dir('thermocalc'):
cmd = 'sh install <<<y'
subprocess.call(cmd, shell=True)
install_tree('basen', join_path(dst, 'basen'))
install_tree('cabasen', join_path(dst, 'cabasen'))
install_tree(calculate_version, join_path(dst, calculate_version))
install_tree('cbasen', join_path(dst, 'cbasen'))
install_tree('DOC', join_path(dst, 'DOC'))
install_tree('jbasen', join_path(dst, 'jbasen'))
install_tree('jkbasen', join_path(dst, 'jkbasen'))
install_tree(molecontrol_version, join_path(dst, molecontrol_version))
install_tree('parameter', join_path(dst, 'parameter'))
install_tree('perlmodules', join_path(dst, 'perlmodules'))
install_tree('scripts', join_path(dst, 'scripts'))
install_tree('smprun_scripts', join_path(dst, 'smprun_scripts'))
install_tree('structures', join_path(dst, 'structures'))
install_tree('thermocalc', join_path(dst, 'thermocalc'))
install_tree('TURBOTEST', join_path(dst, 'TURBOTEST'))
install_tree('xbasen', join_path(dst, 'xbasen'))
install('Config_turbo_env', dst)
install('Config_turbo_env.tcsh', dst)
install('README', dst)
install('README_LICENSES', dst)
install('TURBOMOLE_702_LinuxPC', dst)
if '+mpi' in spec:
install_tree('bin/%s_mpi' % tm_arch, join_path(dst, 'bin', '%s_mpi' % tm_arch))
install_tree('libso/%s_mpi' % tm_arch, join_path(dst, 'libso', '%s_mpi' % tm_arch))
install_tree('mpirun_scripts/%s_mpi' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_mpi' % tm_arch))
elif '+smp' in spec:
install_tree('bin/%s_smp' % tm_arch, join_path(dst, 'bin', '%s_smp' % tm_arch))
install_tree('libso/%s_smp' % tm_arch, join_path(dst, 'libso', '%s_smp' % tm_arch))
install_tree('mpirun_scripts/%s_smp' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_smp' % tm_arch))
else:
install_tree('bin/%s' % tm_arch, join_path(dst, 'bin', tm_arch))
if '+mpi' in spec or '+smp' in spec:
install('mpirun_scripts/ccsdf12', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/dscf', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/grad', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/mpgrad', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/pnoccsd', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/rdgrad', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/ricc2', join_path(dst, 'mpirun_scripts'))
install('mpirun_scripts/ridft', join_path(dst, 'mpirun_scripts'))
def setup_environment(self, spack_env, run_env):
if self.spec.satisfies('@:7.0.2'):
molecontrol_version = 'MoleControl_2.5'
tm_arch=self.get_tm_arch()
run_env.set('TURBODIR', join_path(self.prefix, 'TURBOMOLE'))
run_env.set('MOLE_CONTROL', join_path(self.prefix, 'TURBOMOLE', molecontrol_version))
run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'thermocalc'))
run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'scripts'))
if '+mpi' in self.spec:
run_env.set('PARA_ARCH', 'MPI')
run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_mpi' % tm_arch))
elif '+smp' in self.spec:
run_env.set('PARA_ARCH', 'SMP')
run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_smp' % tm_arch))
else:
run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', tm_arch))

4
var/spack/repos/builtin/packages/wget/package.py
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@@ -17,6 +17,8 @@ class Wget(Package):
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
"--with-ssl=openssl")
"--with-ssl=openssl",
"OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include,
"OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec['openssl'].prefix.lib)
make()
make("install")

4
var/spack/repos/builtin/packages/xerces-c/package.py
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@@ -24,8 +24,8 @@ class XercesC(Package):
"""
homepage = "https://xerces.apache.org/xerces-c"
url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.2.tar.gz"
version('3.1.2', '9eb1048939e88d6a7232c67569b23985')
url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.3.tar.bz2"
version('3.1.3', '5e333b55cb43e6b025ddf0e5d0f0fb0d')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,

35
var/spack/repos/builtin/packages/zoltan/package.py
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@@ -1,3 +1,4 @@
import re, os, glob
from spack import *
class Zoltan(Package):
@@ -12,8 +13,13 @@ class Zoltan(Package):
base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions"
version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f')
version('3.8', '9d8fba8a990896881b85351d4327c4a9')
version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9')
version('3.3', '5eb8f00bda634b25ceefa0122bd18d65')
variant('debug', default=False, description='Builds a debug version of the library')
variant('shared', default=True, description='Builds a shared version of the library')
variant('fortran', default=True, description='Enable Fortran support')
variant('mpi', default=False, description='Enable MPI support')
@@ -24,28 +30,49 @@ def install(self, spec, prefix):
'--enable-f90interface' if '+fortan' in spec else '--disable-f90interface',
'--enable-mpi' if '+mpi' in spec else '--disable-mpi',
]
config_cflags = [
'-O0' if '+debug' in spec else '-O3',
'-g' if '+debug' in spec else '-g0',
]
if '+shared' in spec:
config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
config_args.append('RANLIB=echo')
config_cflags.append('-fPIC')
if '+mpi' in spec:
config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin)
config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin)
config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin)
config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin)
# NOTE: Early versions of Zoltan come packaged with a few embedded
# library packages (e.g. ParMETIS, Scotch), which messes with Spack's
# ability to descend directly into the package's source directory.
if spec.satisfies('@:3.3'):
if spec.satisfies('@:3.6'):
cd('Zoltan_v%s' % self.version)
mkdirp('build')
cd('build')
config_zoltan = Executable('../configure')
config_zoltan('--prefix=%s' % pwd(), *config_args)
config_zoltan(
'--prefix=%s' % pwd(),
'--with-cflags=%s' % ' '.join(config_cflags),
'--with-cxxflags=%s' % ' '.join(config_cflags),
*config_args)
make()
make('install')
# NOTE: Unfortunately, Zoltan doesn't provide any configuration options for
# the extension of the output library files, so this script must change these
# extensions as a post-processing step.
if '+shared' in spec:
for libpath in glob.glob('lib/*.a'):
libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath))
move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname)))
mkdirp(prefix)
move('include', prefix)
move('lib', prefix)