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Boostrapping the lammps package (#3032)

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* First commit for the lammps package
* reviewed by adamjstewart and davydden
This commit is contained in:
Nicolas Richart 2017-02-06 04:34:53 +01:00 committed by Todd Gamblin
parent dfff1f5cf4
commit 7c09ad5305
3 changed files with 309 additions and 0 deletions
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49
var/spack/repos/builtin/packages/lammps/Makefile.inc Normal file
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SHELL = /bin/sh
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
# Individual dependencies
depend : fastdep.exe $(SRC)
@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
fastdep.exe: ../DEPEND/fastdep.c
cc -O -o $@ $<
sinclude .depend

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var/spack/repos/builtin/packages/lammps/package.py Normal file
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##############################################################################
# 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 *
import os
import string
import datetime as dt
class Lammps(MakefilePackage):
"""LAMMPS stands for Large-scale Atomic/Molecular Massively
Parallel Simulator."""
homepage = "http://lammps.sandia.gov/"
url = "https://github.com/lammps/lammps/archive/stable_17Nov2016.tar.gz"
version('2016.11.17', '8aecc58a39f9775203517c62a592d13b')
def url_for_version(self, version):
vdate = dt.datetime.strptime(str(version), "%Y.%m.%d")
return "https://github.com/lammps/lammps/archive/stable_{0}.tar.gz".format(
vdate.strftime("%d%b%Y"))
supported_packages = ['voronoi', 'rigid', 'user-nc-dump',
'user-atc', 'meam', 'manybody']
for pkg in supported_packages:
variant(pkg, default=False,
description='Activate the {0} package'.format(pkg))
variant('lib', default=True,
description='Build the liblammps in addition to the executable')
depends_on('mpi')
depends_on('fftw')
depends_on('voropp', when='+voronoi')
depends_on('netcdf+mpi', when='+user-nc-dump')
depends_on('blas', when='+user-atc')
depends_on('lapack', when='+user-atc')
def setup_environment(self, spack_env, run_env):
self.target_name = self.compiler.name
def edit(self, spec, prefix):
config = []
config.append('CC = c++')
if self.compiler.name == 'intel':
# This is taken from MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
config.append('OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits') # noqa: E501
config.append('CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)') # noqa: E501
config.append('LINKFLAGS = -qopenmp $(OPTFLAGS)')
else:
# This is taken from MAKE/OPTIONS/Makefile.g++
config.append('OPTFLAGS = -O3')
config.append('CCFLAGS = -fopenmp')
config.append('LINKFLAGS = -fopenmp $(OPTFLAGS)')
config.append('SHFLAGS = -fPIC')
config.append('DEPFLAGS = -M')
config.append('LINK = c++')
config.append('LIB = ')
config.append('SIZE = size')
config.append('ARCHIVE = ar')
config.append('ARFLAGS = -rc')
config.append('SHLIBFLAGS = -shared')
config.append('LMP_INC = -DLAMMPS_GZIP')
mpi_path = self.spec['mpi'].prefix.lib
mpi_inc = self.spec['mpi'].prefix.include
config.append(
'MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I{0}'.format(
mpi_inc))
config.append('MPI_PATH = -L{0}'.format(mpi_path))
config.append('MPI_LIB = {0}'.format(
' '.join(self.spec['mpi'].mpicxx_shared_libs)))
config.append('FFT_INC = -DFFT_FFTW3 -L{0}'.format(
self.spec['fftw'].prefix.include))
config.append('FFT_PATH = -L{0}'.format(self.spec['fftw'].prefix.lib))
config.append('FFT_LIB = -lfftw3')
config.append('JPG_INC = ')
config.append('JPG_PATH = ')
config.append('JPG_LIB = ')
makefile_inc_template = \
join_path(os.path.dirname(self.module.__file__),
'Makefile.inc')
with open(makefile_inc_template, "r") as fhr:
config.extend(fhr.read().split('\n'))
with working_dir('src/MAKE/'):
with open('Makefile.{0}'.format(self.target_name), 'w') as fh:
fh.write('\n'.join(config))
def build_meam(self):
with working_dir('lib/meam'):
filter_file(r'EXTRAMAKE = Makefile.lammps.ifort',
'EXTRAMAKE = Makefile.lammps.spack',
'Makefile.ifort')
filter_file('F90 = *ifort',
'F90 = {0}'.format(self.compiler.fc),
'Makefile.ifort')
with open('Makefile.lammps.spack', 'w') as fh:
syslib = ''
syspath = ''
if self.compiler.name == 'gcc':
syslib = '-lgfortran'
elif self.compiler.name == 'intel':
syslib = '-lifcore'
makefile = ['meam_SYSINC =',
'meam_SYSLIB = {0}'.format(syslib),
'meam_SYSPATH = {0}'.format(syspath)]
fh.write('\n'.join(makefile))
make('lib', '-f', 'Makefile.ifort')
def build_user_atc(self):
with working_dir('lib/atc'):
filter_file(r'CC =.*',
'CC = {0}'.format(self.compiler.cxx),
'Makefile.icc')
mpi_include = self.spec['mpi'].prefix.include
filter_file(r'CCFLAGS = *',
'CCFLAGS = -I{0} '.format(mpi_include),
'Makefile.icc')
filter_file('LINK =.*',
'LINK = {0}'.format(self.compiler.cxx),
'Makefile.icc')
make('lib', '-f', 'Makefile.icc')
with open('Makefile.lammps', 'w') as fh:
lapack_blas = (self.spec['lapack'].lapack_libs +
self.spec['blas'].blas_libs)
makefile = [
'user-atc_SYSINC =',
'user-atc_SYSLIB = {0}'.format(lapack_blas.ld_flags),
'user-atc_SYSPATH = ']
fh.write('\n'.join(makefile))
def build_voronoi(self):
# no need to set the voronoi_SYS variable in Makefile.lammps
# since the spack wrapper takes care of the path
with working_dir('src/VORONOI'):
filter_file(r'#include "voro\+\+\.hh"',
'#include <voro++/voro++.hh>',
'compute_voronoi_atom.h')
def build(self, spec, prefix):
for pkg in self.supported_packages:
_build_pkg_name = string.replace('build_{0}'.format(pkg), '-', '_')
if hasattr(self, _build_pkg_name):
_build_pkg = getattr(self, _build_pkg_name)
_build_pkg()
with working_dir('src'):
for pkg in self.supported_packages:
if '+{0}'.format(pkg) in spec:
make('yes-{0}'.format(pkg))
make(self.target_name)
if '+lib' in spec:
make('mode=shlib', self.target_name)
def install(self, spec, prefix):
with working_dir('src'):
mkdirp(prefix.bin)
install('lmp_{0}'.format(self.target_name), prefix.bin)
if '+lib' in spec:
mkdirp(prefix.lib)
install('liblammps_{0}.{1}'.format(self.target_name,
dso_suffix), prefix.lib)
# TODO: install the necessary headers
mkdirp(prefix.include)

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var/spack/repos/builtin/packages/voropp/package.py Normal file
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##############################################################################
# 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 Voropp(MakefilePackage):
"""Voro++ is a open source software library for the computation of the
Voronoi diagram, a widely-used tessellation that has applications in many
scientific fields."""
homepage = "http://math.lbl.gov/voro++/about.html"
# This url is wrong but it passes the test the ++ make the url parser fail,
# the correct url is constructed by url_for_version that has to be used in
# any case due to the difference between the package name and the url
url = "http://math.lbl.gov/voropp/download/dir/voropp-0.4.6.tar.gz"
version('0.4.6', '2338b824c3b7b25590e18e8df5d68af9')
def url_for_version(self, version):
url = "http://math.lbl.gov/voro++/download/dir/voro++-{0}.tar.gz".format( # noqa: E501
str(version))
return url
def edit(self, spec, prefix):
filter_file(r'CC=g\+\+',
'CC={0}'.format(self.compiler.cxx),
'config.mk')
filter_file(r'PREFIX=/usr/local',
'PREFIX={0}'.format(self.prefix),
'config.mk')