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added package : pexsi (#1550)

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* pexsi : added package
* cp2k : added pexsi (works for gcc+openmpi with and without plumed)
This commit is contained in:
Massimiliano Culpo 2016-09-03 17:13:47 +02:00 committed by Todd Gamblin
parent fa310c825d
commit 497bbb3ae3
9 changed files with 229 additions and 9 deletions
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4
lib/spack/spack/compilers/gcc.py
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@ -83,3 +83,7 @@ def fc_version(cls, fc):
@classmethod
def f77_version(cls, f77):
return cls.fc_version(f77)
@property
def stdcxx_libs(self):
return ('-lstdc++', )

4
lib/spack/spack/compilers/intel.py
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@ -80,3 +80,7 @@ def default_version(cls, comp):
"""
return get_compiler_version(
comp, '--version', r'\((?:IFORT|ICC)\) ([^ ]+)')
@property
def stdcxx_libs(self):
return ('-cxxlib', )

22
var/spack/repos/builtin/packages/cp2k/package.py
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@ -52,12 +52,12 @@ class Cp2k(Package):
depends_on('scalapack', when='+mpi')
depends_on('plumed+shared+mpi', when='+plumed+mpi')
depends_on('plumed+shared~mpi', when='+plumed~mpi')
depends_on('pexsi', when='+mpi')
# TODO : add dependency on libint
# TODO : add dependency on libsmm, libxsmm
# TODO : add dependency on elpa
# TODO : add dependency on CUDA
# TODO : add dependency on PEXSI
# TODO : add dependency on QUIP
# TODO : add dependency on libwannier90
@ -88,6 +88,7 @@ def install(self, spec, prefix):
}
cppflags = [
'-D__FFTW3',
'-D__LIBPEXSI',
'-I' + spec['fftw'].prefix.include
]
fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
@ -144,11 +145,28 @@ def install(self, spec, prefix):
'-D__parallel',
'-D__SCALAPACK'
])
fcflags.extend([
'-I' + join_path(spec['pexsi'].prefix, 'fortran')
])
ldflags.extend([
'-L' + spec['scalapack'].prefix.lib
])
libs.extend([
join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
join_path(spec['superlu-dist'].prefix.lib,
'libsuperlu_dist.a'),
join_path(
spec['parmetis'].prefix.lib,
'libparmetis.{0}'.format(dso_suffix)
),
join_path(
spec['metis'].prefix.lib,
'libmetis.{0}'.format(dso_suffix)
),
])
libs.extend(spec['scalapack'].scalapack_shared_libs)
libs.extend(self.spec['mpi'].mpicxx_shared_libs)
libs.extend(self.compiler.stdcxx_libs)
# LAPACK / BLAS
ldflags.extend([
'-L' + spec['lapack'].prefix.lib,

4
var/spack/repos/builtin/packages/mpich/package.py
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@ -66,6 +66,10 @@ def setup_dependent_package(self, module, dep_spec):
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')
self.spec.mpicxx_shared_libs = [
join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
def install(self, spec, prefix):
config_args = ["--prefix=" + prefix,

4
var/spack/repos/builtin/packages/mvapich2/package.py
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@ -227,6 +227,10 @@ def setup_dependent_package(self, module, dep_spec):
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')
self.spec.mpicxx_shared_libs = [
join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
def install(self, spec, prefix):
# we'll set different configure flags depending on our

4
var/spack/repos/builtin/packages/openmpi/package.py
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@ -129,6 +129,10 @@ def setup_dependent_package(self, module, dep_spec):
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')
self.spec.mpicxx_shared_libs = [
join_path(self.prefix.lib, 'libmpi_cxx.{0}'.format(dso_suffix)),
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
def setup_environment(self, spack_env, run_env):
# As of 06/2016 there is no mechanism to specify that packages which

79
var/spack/repos/builtin/packages/pexsi/make.inc Normal file
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@ -0,0 +1,79 @@
# Different compiling and linking options.
SUFFIX = linux
# Compiler and tools
################################################################
CC = @MPICC
CXX = @MPICXX
FC = @MPIFC
LOADER = @MPICXX
AR = ar
ARFLAGS = rvcu
# For System V based machine without ranlib, like Cray and SGI,
# use touch instead.
RANLIB = @RANLIB
CP = cp
RM = rm
RMFLAGS = -f
################################################################
# PEXSI directory
PEXSI_DIR = @PEXSI_STAGE
# Required libraries directories
DSUPERLU_DIR = @SUPERLU_PREFIX
METIS_DIR = @METIS_PREFIX
PARMETIS_DIR = @PARMETIS_PREFIX
LAPACK_DIR = @LAPACK_PREFIX
BLAS_DIR = @BLAS_PREFIX
# Includes
PEXSI_INCLUDE = -I${PEXSI_DIR}/include
DSUPERLU_INCLUDE = -I${DSUPERLU_DIR}/include
INCLUDES = ${PEXSI_INCLUDE} ${DSUPERLU_INCLUDE}
# Libraries
CPP_LIB = @STDCXX_LIB @MPICXX_LIB
#GFORTRAN_LIB = /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a
LAPACK_LIB = @LAPACK_LIBS
BLAS_LIB = @BLAS_LIBS
DSUPERLU_LIB = ${DSUPERLU_DIR}/lib/libsuperlu_dist.a
PEXSI_LIB = ${PEXSI_DIR}/src/libpexsi_${SUFFIX}.a
# Graph partitioning libraries
METIS_LIB = -L${METIS_DIR}/lib -lmetis
PARMETIS_LIB = -L${PARMETIS_DIR}/libparmetis -lparmetis
# Different compiling and linking options.
COMPILE_DEF = -DDEBUG=0 -DRELEASE
COMPILE_FLAG = -O3 -w
LIBS = ${PEXSI_LIB} ${DSUPERLU_LIB} ${PARMETIS_LIB} ${METIS_LIB} ${LAPACK_LIB} ${BLAS_LIB} ${GFORTRAN_LIB}
COMPILE_DEF += -DAdd_
CPPFLAG = -std=c++11
CFLAGS = ${COMPILE_FLAG} ${PROFILE_FLAG} ${INCLUDES}
FFLAGS = ${COMPILE_FLAG} ${PROFILE_FLAG} ${INCLUDES}
CXXFLAGS = ${COMPILE_FLAG} ${CPPFLAG} ${PROFILE_FLAG} ${INCLUDES}
CCDEFS = ${COMPILE_DEF}
CPPDEFS = ${COMPILE_DEF}
LOADOPTS = ${PROFILE_FLAG} ${LIBS}
FLOADOPTS = ${PROFILE_FLAG} ${LIBS} ${CPP_LIB}
# Generate auto-dependencies
%.d: %.c
@set -e; rm -f $@; \
$(CC) -M $(CCDEFS) $(CFLAGS) $< > $@.$$$$; \
sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@;\
rm -f $@.$$$$
%.d: %.cpp
@set -e; rm -f $@; \
$(CXX) -M $(CPPDEFS) $(CXXFLAGS) $< > $@.$$$$; \
sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@;\
rm -f $@.$$$$

103
var/spack/repos/builtin/packages/pexsi/package.py Normal file
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@ -0,0 +1,103 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import inspect
import os.path
import shutil
from spack import *
class Pexsi(Package):
"""The PEXSI library is written in C++, and uses message passing interface
(MPI) to parallelize the computation on distributed memory computing
systems and achieve scalability on more than 10,000 processors.
The Pole EXpansion and Selected Inversion (PEXSI) method is a fast
method for electronic structure calculation based on Kohn-Sham density
functional theory. It efficiently evaluates certain selected elements
of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian,
which yields a density matrix. It can be used as an alternative to
diagonalization methods for obtaining the density, energy and forces
in electronic structure calculations.
"""
homepage = 'https://math.berkeley.edu/~linlin/pexsi/index.html'
url = 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'
version('0.9.0', '0c1a2de891ba1445dfc184b2fa270ed8')
depends_on('parmetis')
depends_on('superlu-dist@3.3', when='@0.9.0')
parallel = False
def install(self, spec, prefix):
substitutions = {
'@MPICC': self.spec['mpi'].mpicc,
'@MPICXX': self.spec['mpi'].mpicxx,
'@MPIFC': self.spec['mpi'].mpifc,
'@MPICXX_LIB': ' '.join(self.spec['mpi'].mpicxx_shared_libs),
'@RANLIB': 'ranlib',
'@PEXSI_STAGE': self.stage.source_path,
'@SUPERLU_PREFIX': self.spec['superlu-dist'].prefix,
'@METIS_PREFIX': self.spec['metis'].prefix,
'@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
'@LAPACK_PREFIX': self.spec['lapack'].prefix,
'@BLAS_PREFIX': self.spec['blas'].prefix,
'@LAPACK_LIBS': self.spec['lapack'].lapack_shared_lib,
'@BLAS_LIBS': self.spec['lapack'].blas_shared_lib,
'@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs)
}
template = join_path(
os.path.dirname(inspect.getmodule(self).__file__),
'make.inc'
)
makefile = join_path(
self.stage.source_path,
'make.inc'
)
shutil.copy(template, makefile)
for key, value in substitutions.items():
filter_file(key, value, makefile)
make()
# 'make install' does not exist, despite what documentation says
mkdirp(self.prefix.lib)
install(
join_path(self.stage.source_path, 'src', 'libpexsi_linux.a'),
join_path(self.prefix.lib, 'libpexsi.a')
)
install_tree(
join_path(self.stage.source_path, 'include'),
self.prefix.include
)
# fortran "interface"
make('-C', 'fortran')
install_tree(
join_path(self.stage.source_path, 'fortran'),
join_path(self.prefix, 'fortran')
)

14
var/spack/repos/builtin/packages/superlu-dist/package.py
View File

@ -30,13 +30,14 @@ class SuperluDist(Package):
"""A general purpose library for the direct solution of large, sparse,
nonsymmetric systems of linear equations on high performance machines."""
homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
version('4.1', '4edee38cc29f687bd0c8eb361096a455')
version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
version('3.3', 'f4805659157d93a962500902c219046b')
depends_on('mpi')
depends_on('blas')
@ -61,14 +62,13 @@ def install(self, spec, prefix):
'ARCH = ar',
'ARCHFLAGS = cr',
'RANLIB = true',
'CC = %s' % spec['mpi'].mpicc,
'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %
(spec['parmetis'].prefix.include,
spec['metis'].prefix.include),
'CC = {0}'.format(self.spec['mpi'].mpicc),
'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' % (
spec['parmetis'].prefix.include, spec['metis'].prefix.include),
'NOOPTS = -fPIC -std=c99',
'FORTRAN = %s' % spec['mpi'].mpif77,
'FORTRAN = {0}'.format(self.spec['mpi'].mpif77),
'F90FLAGS = -O2',
'LOADER = %s' % spec['mpi'].mpif77,
'LOADER = {0}'.format(self.spec['mpi'].mpif77),
'LOADOPTS =',
'CDEFS = -DAdd_'
])