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Merge branch 'develop' into packages/elpa

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This commit is contained in:
alalazo
2016-01-21 08:33:59 +01:00
parent ab27fdc692 1c2a2dde8e
commit a8132470e4
8 changed files with 119 additions and 34 deletions
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4
lib/spack/env/cc vendored
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@@ -94,11 +94,11 @@ case "$command" in
command="$SPACK_CXX"
language="C++"
;;
f90|fc|f95|gfortran|ifort|pgf90|xlf90)
f90|fc|f95|gfortran|ifort|pgf90|xlf90|nagfor)
command="$SPACK_FC"
language="Fortran 90"
;;
f77|gfortran|ifort|pgf77|xlf)
f77|gfortran|ifort|pgf77|xlf|nagfor)
command="$SPACK_F77"
language="Fortran 77"
;;

1
lib/spack/env/nag/nagfor vendored Symbolic link
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@@ -0,0 +1 @@
../cc

2
lib/spack/spack/cmd/location.py
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@@ -32,7 +32,7 @@
import spack
import spack.cmd
description="Print out locations of various diectories used by Spack"
description="Print out locations of various directories used by Spack"
def setup_parser(subparser):
global directories

3
lib/spack/spack/compiler.py
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@@ -24,6 +24,7 @@
##############################################################################
import os
import re
import subprocess
import itertools
from datetime import datetime
@@ -51,7 +52,7 @@ def _verify_executables(*paths):
def get_compiler_version(compiler_path, version_arg, regex='(.*)'):
if not compiler_path in _version_cache:
compiler = Executable(compiler_path)
output = compiler(version_arg, return_output=True, error=os.devnull)
output = compiler(version_arg, return_output=True, error=subprocess.STDOUT)
match = re.search(regex, output)
_version_cache[compiler_path] = match.group(1) if match else 'unknown'

2
lib/spack/spack/compilers/__init__.py
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@@ -51,7 +51,7 @@
if platform.system() == 'Darwin':
_default_order = ['clang', 'gcc', 'intel']
else:
_default_order = ['gcc', 'intel', 'pgi', 'clang', 'xlc']
_default_order = ['gcc', 'intel', 'pgi', 'clang', 'xlc', 'nag']
def _auto_compiler_spec(function):

33
lib/spack/spack/compilers/nag.py Normal file
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@@ -0,0 +1,33 @@
from spack.compiler import *
class Nag(Compiler):
# Subclasses use possible names of C compiler
cc_names = []
# Subclasses use possible names of C++ compiler
cxx_names = []
# Subclasses use possible names of Fortran 77 compiler
f77_names = ['nagfor']
# Subclasses use possible names of Fortran 90 compiler
fc_names = ['nagfor']
# Named wrapper links within spack.build_env_path
link_paths = { # Use default wrappers for C and C++, in case provided in compilers.yaml
'cc' : 'cc',
'cxx' : 'cxx',
'f77' : 'nag/nagfor',
'fc' : 'nag/nagfor' }
@classmethod
def default_version(self, comp):
"""The '-V' option works for nag compilers.
Output looks like this::
NAG Fortran Compiler Release 6.0(Hibiya) Build 1037
Product NPL6A60NA for x86-64 Linux
Copyright 1990-2015 The Numerical Algorithms Group Ltd., Oxford, U.K.
"""
return get_compiler_version(
comp, '-V', r'NAG Fortran Compiler Release ([0-9.]+)')

84
var/spack/repos/builtin/packages/hdf5/package.py
View File

@@ -1,5 +1,31 @@
##############################################################################
# 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 Hdf5(Package):
"""HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
@@ -7,7 +33,7 @@ class Hdf5(Package):
"""
homepage = "http://www.hdfgroup.org/HDF5/"
url = "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz"
url = "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz"
list_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3
@@ -15,26 +41,53 @@ class Hdf5(Package):
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
version('1.8.13', 'c03426e9e77d7766944654280b467289')
variant('debug', default=False, description='Builds a debug version of the library')
variant('cxx', default=True, description='Enable C++ support')
variant('fortran', default=True, description='Enable Fortran support')
variant('unsupported', default=False, description='Enables unsupported configuration options')
variant('mpi', default=False, description='Enable MPI support')
variant('threadsafe', default=False, description='Enable multithreading')
variant('threadsafe', default=False, description='Enable thread-safe capabilities')
depends_on("mpi", when='+mpi')
depends_on("zlib")
# TODO: currently hard-coded to use OpenMPI
def validate(self, spec):
"""
Checks if incompatible variants have been activated at the same time
:param spec: spec of the package
:raises RuntimeError: in case of inconsistencies
"""
if '+fortran' in spec and not self.compiler.fc:
msg = 'cannot build a fortran variant without a fortran compiler'
raise RuntimeError(msg)
if '+threadsafe' in spec and ('+cxx' in spec or '+fortran' in spec):
raise RuntimeError("cannot use variant +threadsafe with either +cxx or +fortran")
def install(self, spec, prefix):
self.validate(spec)
# Handle compilation after spec validation
extra_args = []
if '+debug' in spec:
extra_args.append('--enable-debug=all')
else:
extra_args.append('--enable-production')
if '+unsupported' in spec:
extra_args.append("--enable-unsupported")
if '+cxx' in spec:
extra_args.extend([
'--enable-cxx'
])
extra_args.append('--enable-cxx')
if '+fortran' in spec:
extra_args.extend([
'--enable-fortran',
'--enable-fortran2003'
])
if '+mpi' in spec:
# The HDF5 configure script warns if cxx and mpi are enabled
# together. There doesn't seem to be a real reason for this, except
@@ -43,27 +96,26 @@ def install(self, spec, prefix):
# this is not actually a problem.
extra_args.extend([
"--enable-parallel",
"--enable-unsupported",
"CC=%s" % spec['mpi'].prefix.bin + "/mpicc",
"CXX=%s" % spec['mpi'].prefix.bin + "/mpic++",
"FC=%s" % spec['mpi'].prefix.bin + "/mpifort",
])
if '+threads' in spec:
if '+cxx' in spec or '+fortran' in spec:
die("Cannot use variant +threads with either +cxx or +fortran")
if '+cxx' in spec:
extra_args.append("CXX=%s" % spec['mpi'].prefix.bin + "/mpic++")
if '+fortran' in spec:
extra_args.append("FC=%s" % spec['mpi'].prefix.bin + "/mpifort")
if '+threadsafe' in spec:
extra_args.extend([
'--enable-threadsafe',
'--disable-hl',
'CPPFLAGS=-DHDatexit=""',
'CFLAGS=-DHDatexit=""'
])
configure(
"--prefix=%s" % prefix,
"--with-zlib=%s" % spec['zlib'].prefix,
"--enable-shared",
"--enable-shared", # TODO : this should be enabled by default, remove it?
*extra_args)
make()
make("install")

24
var/spack/repos/builtin/packages/openmpi/package.py
View File

@@ -19,43 +19,44 @@ class Openmpi(Package):
version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
version('1.10.0', '280cf952de68369cebaca886c5ce0304')
version('1.8.8', '0dab8e602372da1425e9242ae37faf8c')
version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')
version('1.8.8', '0dab8e602372da1425e9242ae37faf8c')
version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')
patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5")
patch('llnl-platforms.patch', when="@1.6.5")
patch('configure.patch', when="@1.10.0:")
variant('psm', default=False, description='Build support for the PSM library.')
variant('psm', default=False, description='Build support for the PSM library.')
variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
# TODO : variant support for other schedulers is missing
variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support')
provides('mpi@:2.2', when='@1.6.5')
provides('mpi@:3.0', when='@1.7.5:')
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)
def setup_dependent_environment(self, module, spec, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
os.environ['OMPI_CC'] = 'cc'
os.environ['OMPI_CC'] = 'cc'
os.environ['OMPI_CXX'] = 'c++'
os.environ['OMPI_FC'] = 'f90'
os.environ['OMPI_F77'] = 'f77'
def install(self, spec, prefix):
config_args = ["--prefix=%s" % prefix,
"--with-hwloc=%s" % spec['hwloc'].prefix,
"--with-tm", # necessary for Torque support
"--enable-shared",
"--enable-static"]
# Variants
if '+tm' in spec:
config_args.append("--with-tm") # necessary for Torque support
if '+psm' in spec:
config_args.append("--with-psm")
@@ -85,7 +86,6 @@ def install(self, spec, prefix):
self.filter_compilers()
def filter_compilers(self):
"""Run after install to make the MPI compilers use the
compilers that Spack built the package with.
@@ -94,7 +94,7 @@ def filter_compilers(self):
to Spack's generic cc, c++ and f90. We want them to
be bound to whatever compiler they were built with.
"""
kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : False }
kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
dir = os.path.join(self.prefix, 'share/openmpi/')
cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt',
@@ -132,5 +132,3 @@ def filter_compilers(self):
if not os.path.islink(path):
filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc,
path, **kwargs)