added package : pexsi (#1550)
* pexsi : added package * cp2k : added pexsi (works for gcc+openmpi with and without plumed)
This commit is contained in:
Massimiliano Culpo
committed by
Todd Gamblin
Todd Gamblin
parent
fa310c825d
commit
497bbb3ae3
79
var/spack/repos/builtin/packages/pexsi/make.inc
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79
var/spack/repos/builtin/packages/pexsi/make.inc
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# Different compiling and linking options.
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SUFFIX = linux
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# Compiler and tools
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################################################################
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CC = @MPICC
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CXX = @MPICXX
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FC = @MPIFC
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LOADER = @MPICXX
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AR = ar
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ARFLAGS = rvcu
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# For System V based machine without ranlib, like Cray and SGI,
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# use touch instead.
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RANLIB = @RANLIB
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CP = cp
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RM = rm
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RMFLAGS = -f
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################################################################
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# PEXSI directory
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PEXSI_DIR = @PEXSI_STAGE
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# Required libraries directories
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DSUPERLU_DIR = @SUPERLU_PREFIX
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METIS_DIR = @METIS_PREFIX
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PARMETIS_DIR = @PARMETIS_PREFIX
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LAPACK_DIR = @LAPACK_PREFIX
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BLAS_DIR = @BLAS_PREFIX
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# Includes
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PEXSI_INCLUDE = -I${PEXSI_DIR}/include
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DSUPERLU_INCLUDE = -I${DSUPERLU_DIR}/include
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INCLUDES = ${PEXSI_INCLUDE} ${DSUPERLU_INCLUDE}
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# Libraries
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CPP_LIB = @STDCXX_LIB @MPICXX_LIB
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#GFORTRAN_LIB = /usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.a
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LAPACK_LIB = @LAPACK_LIBS
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BLAS_LIB = @BLAS_LIBS
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DSUPERLU_LIB = ${DSUPERLU_DIR}/lib/libsuperlu_dist.a
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PEXSI_LIB = ${PEXSI_DIR}/src/libpexsi_${SUFFIX}.a
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# Graph partitioning libraries
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METIS_LIB = -L${METIS_DIR}/lib -lmetis
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PARMETIS_LIB = -L${PARMETIS_DIR}/libparmetis -lparmetis
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# Different compiling and linking options.
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COMPILE_DEF = -DDEBUG=0 -DRELEASE
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COMPILE_FLAG = -O3 -w
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LIBS = ${PEXSI_LIB} ${DSUPERLU_LIB} ${PARMETIS_LIB} ${METIS_LIB} ${LAPACK_LIB} ${BLAS_LIB} ${GFORTRAN_LIB}
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COMPILE_DEF += -DAdd_
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CPPFLAG = -std=c++11
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CFLAGS = ${COMPILE_FLAG} ${PROFILE_FLAG} ${INCLUDES}
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FFLAGS = ${COMPILE_FLAG} ${PROFILE_FLAG} ${INCLUDES}
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CXXFLAGS = ${COMPILE_FLAG} ${CPPFLAG} ${PROFILE_FLAG} ${INCLUDES}
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CCDEFS = ${COMPILE_DEF}
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CPPDEFS = ${COMPILE_DEF}
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LOADOPTS = ${PROFILE_FLAG} ${LIBS}
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FLOADOPTS = ${PROFILE_FLAG} ${LIBS} ${CPP_LIB}
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# Generate auto-dependencies
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%.d: %.c
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@set -e; rm -f $@; \
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$(CC) -M $(CCDEFS) $(CFLAGS) $< > $@.$$$$; \
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sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@;\
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rm -f $@.$$$$
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%.d: %.cpp
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@set -e; rm -f $@; \
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$(CXX) -M $(CPPDEFS) $(CXXFLAGS) $< > $@.$$$$; \
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sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@;\
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rm -f $@.$$$$
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103
var/spack/repos/builtin/packages/pexsi/package.py
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103
var/spack/repos/builtin/packages/pexsi/package.py
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@@ -0,0 +1,103 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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import inspect
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import os.path
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import shutil
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from spack import *
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class Pexsi(Package):
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"""The PEXSI library is written in C++, and uses message passing interface
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(MPI) to parallelize the computation on distributed memory computing
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systems and achieve scalability on more than 10,000 processors.
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The Pole EXpansion and Selected Inversion (PEXSI) method is a fast
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method for electronic structure calculation based on Kohn-Sham density
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functional theory. It efficiently evaluates certain selected elements
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of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian,
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which yields a density matrix. It can be used as an alternative to
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diagonalization methods for obtaining the density, energy and forces
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in electronic structure calculations.
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"""
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homepage = 'https://math.berkeley.edu/~linlin/pexsi/index.html'
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url = 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'
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version('0.9.0', '0c1a2de891ba1445dfc184b2fa270ed8')
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depends_on('parmetis')
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depends_on('superlu-dist@3.3', when='@0.9.0')
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parallel = False
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def install(self, spec, prefix):
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substitutions = {
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'@MPICC': self.spec['mpi'].mpicc,
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'@MPICXX': self.spec['mpi'].mpicxx,
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'@MPIFC': self.spec['mpi'].mpifc,
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'@MPICXX_LIB': ' '.join(self.spec['mpi'].mpicxx_shared_libs),
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'@RANLIB': 'ranlib',
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'@PEXSI_STAGE': self.stage.source_path,
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'@SUPERLU_PREFIX': self.spec['superlu-dist'].prefix,
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'@METIS_PREFIX': self.spec['metis'].prefix,
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'@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
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'@LAPACK_PREFIX': self.spec['lapack'].prefix,
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'@BLAS_PREFIX': self.spec['blas'].prefix,
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'@LAPACK_LIBS': self.spec['lapack'].lapack_shared_lib,
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'@BLAS_LIBS': self.spec['lapack'].blas_shared_lib,
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'@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs)
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}
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template = join_path(
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os.path.dirname(inspect.getmodule(self).__file__),
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'make.inc'
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)
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makefile = join_path(
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self.stage.source_path,
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'make.inc'
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)
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shutil.copy(template, makefile)
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for key, value in substitutions.items():
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filter_file(key, value, makefile)
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make()
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# 'make install' does not exist, despite what documentation says
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mkdirp(self.prefix.lib)
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install(
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join_path(self.stage.source_path, 'src', 'libpexsi_linux.a'),
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join_path(self.prefix.lib, 'libpexsi.a')
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)
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install_tree(
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join_path(self.stage.source_path, 'include'),
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self.prefix.include
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)
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# fortran "interface"
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make('-C', 'fortran')
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install_tree(
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join_path(self.stage.source_path, 'fortran'),
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join_path(self.prefix, 'fortran')
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)
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