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Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases

Browse Source 
Conflicts:
	lib/spack/spack/package.py
This commit is contained in:
alalazo
2016-07-20 21:02:19 +02:00
parent 6c00a13ed5 79e066d53c
commit 40cb314638
58 changed files with 1566 additions and 737 deletions
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4
var/spack/repos/builtin/packages/adios/package.py
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@@ -12,9 +12,9 @@ class Adios(Package):
"""
homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
# Lots of setting up here for this package
# module swap PrgEnv-intel PrgEnv-$COMP

42
var/spack/repos/builtin/packages/cdo/package.py Normal file
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@@ -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 Cdo(Package):
"""CDO is a collection of command line Operators to manipulate and analyse
Climate and NWP model Data. """
homepage = "https://code.zmaw.de/projects/cdo"
url = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz"
version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2')
depends_on('netcdf')
def install(self, spec, prefix):
configure('--prefix={0}'.format(prefix))
make()
make('install')

1
var/spack/repos/builtin/packages/cmake/package.py
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@@ -30,6 +30,7 @@ class Cmake(Package):
homepage = 'https://www.cmake.org'
url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
version('3.6.0', 'aa40fbecf49d99c083415c2411d12db9')
version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02')
version('3.5.1', 'ca051f4a66375c89d1a524e726da0296')
version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e')

1
var/spack/repos/builtin/packages/flex/package.py
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@@ -35,6 +35,7 @@ class Flex(Package):
version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
depends_on("bison", type='build')
depends_on("m4", type='build')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

45
var/spack/repos/builtin/packages/hypre/package.py
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@@ -23,7 +23,9 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os, sys
import os
import sys
class Hypre(Package):
"""Hypre is a library of high performance preconditioners that
@@ -37,7 +39,7 @@ class Hypre(Package):
version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
# hypre does not know how to build shared libraries on Darwin
variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
# SuperluDist have conflicting headers with those in Hypre
variant('internal-superlu', default=True, description="Use internal Superlu routines")
@@ -46,21 +48,26 @@ class Hypre(Package):
depends_on("lapack")
def install(self, spec, prefix):
blas_dir = spec['blas'].prefix
lapack_dir = spec['lapack'].prefix
mpi_dir = spec['mpi'].prefix
os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
os.environ['CC'] = spec['mpi'].mpicc
os.environ['CXX'] = spec['mpi'].mpicxx
os.environ['F77'] = spec['mpi'].mpif77
# Since +shared does not build on macOS and also Atlas does not have
# a single static lib to build against, link against shared libs with
# a hope that --whole-archive linker option (or alike) was used
# to command the linker to include whole static libs' content into the
# shared lib
# Note: --with-(lapack|blas)_libs= needs space separated list of names
configure_args = [
"--prefix=%s" % prefix,
"--with-lapack-libs=lapack",
"--with-lapack-lib-dirs=%s/lib" % lapack_dir,
"--with-blas-libs=blas",
"--with-blas-lib-dirs=%s/lib" % blas_dir]
'--prefix=%s' % prefix,
'--with-lapack-libs=%s' % to_lib_name(
spec['lapack'].lapack_shared_lib),
'--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
'--with-blas-libs=%s' % to_lib_name(
spec['blas'].blas_shared_lib),
'--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
]
if '+shared' in self.spec:
configure_args.append("--enable-shared")
@@ -76,4 +83,12 @@ def install(self, spec, prefix):
configure(*configure_args)
make()
if self.run_tests:
make("check")
make("test")
Executable(join_path('test', 'ij'))()
sstruct = Executable(join_path('test', 'struct'))
sstruct()
sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
'-rhsone')
make("install")

25
var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch Normal file
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@@ -0,0 +1,25 @@
diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c
index fa72a0e..1f4845f 100644
--- a/src/libjasper/jpc/jpc_dec.c
+++ b/src/libjasper/jpc/jpc_dec.c
@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile)
/* Apply an inverse intercomponent transform if necessary. */
switch (tile->cp->mctid) {
case JPC_MCT_RCT:
- assert(dec->numcomps == 3);
+ if (dec->numcomps != 3 && dec->numcomps != 4) {
+ jas_eprintf("bad number of components (%d)\n", dec->numcomps);
+ return -1;
+ }
jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data,
tile->tcomps[2].data);
break;
case JPC_MCT_ICT:
- assert(dec->numcomps == 3);
+ if (dec->numcomps != 3 && dec->numcomps != 4) {
+ jas_eprintf("bad number of components (%d)\n", dec->numcomps);
+ return -1;
+ }
jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data,
tile->tcomps[2].data);
break;

63
var/spack/repos/builtin/packages/jasper/package.py Normal file
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@@ -0,0 +1,63 @@
##############################################################################
# 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 Jasper(Package):
"""Library for manipulating JPEG-2000 images"""
homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
variant('shared', default=True,
description='Builds shared versions of the libraries')
variant('debug', default=False,
description='Builds debug versions of the libraries')
depends_on('libjpeg-turbo')
# Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
# when certain JPEG-2000 files with an alpha channel are processed
# see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
patch('fix_alpha_channel_assert_fail.patch')
def install(self, spec, prefix):
configure_options = [
'--prefix={0}'.format(prefix),
'--mandir={0}'.format(spec.prefix.man),
]
if '+shared' in spec:
configure_options.append('--enable-shared')
if '+debug' not in spec:
configure_options.append('--disable-debug')
configure(*configure_options)
make()
make('install')

38
var/spack/repos/builtin/packages/mkl/package.py
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@@ -9,7 +9,13 @@ class Mkl(IntelInstaller):
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"""
mirror, see http://software.llnl.gov/spack/mirrors.html.
To set the threading layer at run time set MKL_THREADING_LAYER
variable to one of the following values: INTEL, SEQUENTIAL, PGI.
To set interface layer at run time, use set the MKL_INTERFACE_LAYER
variable to LP64 or ILP64.
"""
homepage = "https://software.intel.com/en-us/intel-mkl"
@@ -18,6 +24,11 @@ class Mkl(IntelInstaller):
version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
# virtual dependency
provides('blas')
provides('lapack')
# TODO: MKL also provides implementation of Scalapack.
def install(self, spec, prefix):
self.intel_prefix = os.path.join(prefix, "pkg")
@@ -26,3 +37,28 @@ def 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))
def setup_dependent_package(self, module, dspec):
# For now use Single Dynamic Library:
# To set the threading layer at run time, use the
# mkl_set_threading_layer function or set MKL_THREADING_LAYER
# variable to one of the following values: INTEL, SEQUENTIAL, PGI.
# To set interface layer at run time, use the mkl_set_interface_layer
# function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
# Otherwise one would need to specify several libraries
# (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
# different interface and threading layers.
name = 'libmkl_rt.%s' % dso_suffix
libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
self.spec.blas_shared_lib = join_path(libdir, name)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# set up MKLROOT for everyone using MKL package
spack_env.set('MKLROOT', self.prefix)
def setup_environment(self, spack_env, env):
env.set('MKLROOT', self.prefix)

74
var/spack/repos/builtin/packages/mumps/package.py
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@@ -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 glob
class Mumps(Package):
"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -44,13 +47,11 @@ 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')
depends_on('parmetis', when="+parmetis")
depends_on('blas')
depends_on('lapack')
depends_on('scalapack', when='+mpi')
depends_on('mpi', when='+mpi')
@@ -60,42 +61,52 @@ class Mumps(Package):
# 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: # NOQA: ignore=E501
raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: ignore=E501
makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
makefile_conf = ["LIBBLAS = %s" % to_link_flags(
self.spec['blas'].blas_shared_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
# /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
@@ -104,7 +115,7 @@ def write_makefile_inc(self):
# 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: ignore=E501
'OPTL = %s -O ' % fpic,
'OPTC = %s -O -DINTSIZE64' % fpic])
else:
@@ -113,7 +124,6 @@ def write_makefile_inc(self):
'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'),
@@ -134,16 +144,17 @@ def write_makefile_inc(self):
if '+shared' in self.spec:
if sys.platform == 'darwin':
# Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
# 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 $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib), # NOQA: ignore=E501
'RANLIB=echo'
])
else:
makefile_conf.extend([
'LIBEXT=.so',
'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, # NOQA: ignore=E501
'RANLIB=echo'
])
else:
@@ -153,9 +164,8 @@ def write_makefile_inc(self):
'RANLIB = ranlib'
])
makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
'Makefile.inc')
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'))
@@ -164,8 +174,6 @@ def write_makefile_inc(self):
makefile_inc = '\n'.join(makefile_conf)
fh.write(makefile_inc)
def install(self, spec, prefix):
make_libs = []
@@ -189,15 +197,15 @@ def install(self, spec, prefix):
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
if '~mpi' in spec:
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')):
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
# FIXME: extend the tests to mpirun -np 2 when build with MPI
# FIXME: use something like numdiff to compare output files
with working_dir('examples'):
if '+float' in spec:
os.system('./ssimpletest < input_simpletest_real')

7
var/spack/repos/builtin/packages/netcdf/package.py
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@@ -33,6 +33,7 @@ class Netcdf(Package):
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
version('4.4.1', '7843e35b661c99e1d49e60791d5072d8')
version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
@@ -47,8 +48,10 @@ class Netcdf(Package):
# Required for NetCDF-4 support
depends_on("zlib")
depends_on("hdf5+mpi", when='+mpi')
depends_on("hdf5~mpi", when='~mpi')
depends_on('hdf5@:1.8+mpi', when='@:4.4.0+mpi')
depends_on('hdf5+mpi', when='@4.4.1:+mpi')
depends_on('hdf5@:1.8~mpi', when='@:4.4.0~mpi')
depends_on('hdf5~mpi', when='@4.4.1:~mpi')
def install(self, spec, prefix):
# Environment variables

33
var/spack/repos/builtin/packages/netlib-scalapack/package.py
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@@ -25,8 +25,10 @@
from spack import *
import sys
class NetlibScalapack(Package):
"""ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
"""ScaLAPACK is a library of high-performance linear algebra routines for
parallel distributed memory machines"""
homepage = "http://www.netlib.org/scalapack/"
url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
@@ -48,10 +50,22 @@ class NetlibScalapack(Package):
def install(self, spec, prefix):
options = [
"-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
"-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
"-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON", # forces scalapack to use find_package(LAPACK)
]
"-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else
'OFF'),
"-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else
'ON'),
# forces scalapack to use find_package(LAPACK):
"-DUSE_OPTIMIZED_LAPACK_BLAS:BOOL=ON",
]
# Make sure we use Spack's Lapack:
options.extend([
'-DLAPACK_FOUND=true',
'-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
'-DLAPACK_LIBRARIES=%s' % (
spec['lapack'].lapack_shared_lib if '+shared' in spec else
spec['lapack'].lapack_static_lib),
])
if '+fpic' in spec:
options.extend([
@@ -66,16 +80,15 @@ def install(self, spec, prefix):
make()
make("install")
# The shared libraries are not installed correctly on Darwin; correct this
# The shared libraries are not installed correctly on Darwin:
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)
def setup_dependent_package(self, module, dependent_spec):
spec = self.spec
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
lib_suffix = dso_suffix if '+shared' in spec else 'a'
spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
spec.cc_link = spec.fc_link
spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]
spec.libraries = [join_path(spec.prefix.lib,
'libscalapack.%s' % lib_suffix)]

1
var/spack/repos/builtin/packages/py-h5py/package.py
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@@ -46,6 +46,7 @@ class PyH5py(Package):
depends_on('hdf5@1.8.4:')
depends_on('hdf5+mpi', when='+mpi')
depends_on('mpi', when='+mpi')
depends_on('py-mpi4py', when='+mpi')
# Build and runtime dependencies
depends_on('py-numpy@1.6.1:', type=nolink)

1
var/spack/repos/builtin/packages/py-numpy/package.py
View File

@@ -44,6 +44,7 @@ class PyNumpy(Package):
extends('python')
depends_on('py-nose', type='build')
depends_on('py-setuptools', type='build')
depends_on('blas', when='+blas')
depends_on('lapack', when='+lapack')

42
var/spack/repos/builtin/packages/python/package.py
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@@ -53,6 +53,7 @@ class Python(Package):
extendable = True
variant('tk', default=False, description='Provide support for Tkinter')
variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
# From https://docs.python.org/2/c-api/unicode.html: Python's default
# builds use a 16-bit type for Py_UNICODE and store Unicode values
@@ -68,6 +69,8 @@ class Python(Package):
depends_on("ncurses")
depends_on("sqlite")
depends_on("zlib")
depends_on("tk", when="+tk")
depends_on("tcl", when="+tk")
def install(self, spec, prefix):
# Need this to allow python build to find the Python installation.
@@ -77,24 +80,32 @@ def install(self, spec, prefix):
# 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
cppflags = ' -I'.join([
include_dirs = [
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([
library_dirs = [
spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib,
spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib
])
]
if '+tk' in spec:
include_dirs.extend([
spec['tk'].prefix.include, spec['tcl'].prefix.include
])
library_dirs.extend([
spec['tk'].prefix.lib, spec['tcl'].prefix.lib
])
config_args = [
"--prefix={0}".format(prefix),
"--with-threads",
"--enable-shared",
"CPPFLAGS=-I{0}".format(cppflags),
"LDFLAGS=-L{0}".format(ldflags)
"CPPFLAGS=-I{0}".format(" -I".join(include_dirs)),
"LDFLAGS=-L{0}".format(" -L".join(library_dirs))
]
if '+ucs4' in spec:
@@ -116,6 +127,25 @@ def install(self, spec, prefix):
self.filter_compilers(spec, prefix)
# TODO: Once better testing support is integrated, add the following tests
# https://wiki.python.org/moin/TkInter
#
# if '+tk' in spec:
# env['TK_LIBRARY'] = join_path(spec['tk'].prefix.lib,
# 'tk{0}'.format(spec['tk'].version.up_to(2)))
# env['TCL_LIBRARY'] = join_path(spec['tcl'].prefix.lib,
# 'tcl{0}'.format(spec['tcl'].version.up_to(2)))
#
# $ python
# >>> import _tkinter
#
# if spec.satisfies('@3:')
# >>> import tkinter
# >>> tkinter._test()
# else:
# >>> import Tkinter
# >>> Tkinter._test()
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.

29
var/spack/repos/builtin/packages/suite-sparse/package.py
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@@ -32,21 +32,20 @@ class SuiteSparse(Package):
homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
# FIXME: (see below)
# variant('tbb', default=True, description='Build with Intel TBB')
variant('tbb', default=True, description='Build with Intel TBB')
depends_on('blas')
depends_on('lapack')
depends_on('metis@5.1.0', when='@4.5.1:')
# FIXME:
# in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
# flags does not seem to be used, which leads to linking errors on Linux.
# Try re-enabling in future versions.
# depends_on('tbb', when='+tbb')
depends_on('tbb', when='@4.5.3:+tbb')
patch('tbb_453.patch', when='@4.5.3')
def install(self, spec, prefix):
# The build system of SuiteSparse is quite old-fashioned.
@@ -73,20 +72,24 @@ def install(self, spec, prefix):
])
# Intel TBB in SuiteSparseQR
if '+tbb' in spec:
if 'tbb' in spec:
make_args.extend([
'SPQR_CONFIG=-DHAVE_TBB',
'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
])
# BLAS arguments require path to libraries
# FIXME: (blas/lapack always provide libblas and liblapack as aliases)
# Make sure Spack's Blas/Lapack is used. Otherwise System's
# Blas/Lapack might be picked up.
blas = to_link_flags(spec['blas'].blas_shared_lib)
lapack = to_link_flags(spec['lapack'].lapack_shared_lib)
if '@4.5.1' in spec:
# adding -lstdc++ is clearly an ugly way to do this, but it follows
# with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
make_args.extend([
'BLAS=-lblas -lstdc++',
'LAPACK=-llapack'
])
blas += ' -lstdc++'
make_args.extend([
'BLAS=%s' % blas,
'LAPACK=%s' % lapack
])
make('install', *make_args)

13
var/spack/repos/builtin/packages/suite-sparse/tbb_453.patch Normal file
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@@ -0,0 +1,13 @@
diff --git a/SPQR/Lib/Makefile b/SPQR/Lib/Makefile
index eaade58..d0de852 100644
--- a/SPQR/Lib/Makefile
+++ b/SPQR/Lib/Makefile
@@ -13,7 +13,7 @@ ccode: all
include ../../SuiteSparse_config/SuiteSparse_config.mk
# SPQR depends on CHOLMOD, AMD, COLAMD, LAPACK, the BLAS and SuiteSparse_config
-LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(LAPACK) $(BLAS)
+LDLIBS += -lamd -lcolamd -lcholmod -lsuitesparseconfig $(TBB) $(LAPACK) $(BLAS)
# compile and install in SuiteSparse/lib
library:

16
var/spack/repos/builtin/packages/tcl/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Tcl(Package):
"""Tcl (Tool Command Language) is a very powerful but easy to
learn dynamic programming language, suitable for a very wide
@@ -34,9 +35,6 @@ class Tcl(Package):
extensible."""
homepage = "http://www.tcl.tk"
def url_for_version(self, version):
return 'http://prdownloads.sourceforge.net/tcl/tcl%s-src.tar.gz' % version
version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304')
version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f')
@@ -44,8 +42,18 @@ def url_for_version(self, version):
depends_on('zlib')
def url_for_version(self, version):
base_url = 'http://prdownloads.sourceforge.net/tcl'
return '{0}/tcl{1}-src.tar.gz'.format(base_url, version)
def setup_environment(self, spack_env, env):
# When using Tkinter from within spack provided python+tk, python
# will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
self.spec.version.up_to(2))))
def install(self, spec, prefix):
with working_dir('unix'):
configure("--prefix=%s" % prefix)
configure("--prefix={0}".format(prefix))
make()
make("install")

4
var/spack/repos/builtin/packages/the_silver_searcher/package.py
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@@ -24,11 +24,13 @@
##############################################################################
from spack import *
class TheSilverSearcher(Package):
"""Fast recursive grep alternative"""
homepage = "http://geoff.greer.fm/ag/"
url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.30.0.tar.gz"
url = "http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz"
version('0.32.0', '3fdfd5836924246073d5344257a06823')
version('0.30.0', '95e2e7859fab1156c835aff7413481db')
depends_on('pcre')

19
var/spack/repos/builtin/packages/tk/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Tk(Package):
"""Tk is a graphical user interface toolkit that takes developing
desktop applications to a higher level than conventional
@@ -33,16 +34,24 @@ class Tk(Package):
and more."""
homepage = "http://www.tcl.tk"
def url_for_version(self, version):
return "http://prdownloads.sourceforge.net/tcl/tk%s-src.tar.gz" % version
version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221')
depends_on("tcl")
def url_for_version(self, version):
base_url = "http://prdownloads.sourceforge.net/tcl"
return "{0}/tk{1}-src.tar.gz".format(base_url, version)
def setup_environment(self, spack_env, env):
# When using Tkinter from within spack provided python+tk, python
# will not be able to find Tcl/Tk unless TK_LIBRARY is set.
env.set('TK_LIBRARY', join_path(self.prefix.lib, 'tk{0}'.format(
self.spec.version.up_to(2))))
def install(self, spec, prefix):
with working_dir('unix'):
configure("--prefix=%s" % prefix,
"--with-tcl=%s" % spec['tcl'].prefix.lib)
configure("--prefix={0}".format(prefix),
"--with-tcl={0}".format(spec['tcl'].prefix.lib))
make()
make("install")

7
var/spack/repos/builtin/packages/trilinos/package.py
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@@ -118,6 +118,7 @@ def install(self, spec, prefix):
options.extend(std_cmake_args)
mpi_bin = spec['mpi'].prefix.bin
# Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
options.extend([
'-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
'-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@@ -131,10 +132,12 @@ def install(self, spec, prefix):
'-DTPL_ENABLE_MPI:BOOL=ON',
'-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
'-DTPL_ENABLE_BLAS=ON',
'-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
'-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
spec['blas'].blas_shared_lib),
'-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
'-DTPL_ENABLE_LAPACK=ON',
'-DLAPACK_LIBRARY_NAMES=lapack',
'-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
spec['lapack'].lapack_shared_lib),
'-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
'-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
'-DTrilinos_ENABLE_CXX11:BOOL=ON',