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lammps: version bump, switch to cmake (#5313)
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@junghans @tgamblin
junghans authored and tgamblin committed Sep 10, 2017
1 parent b60e7e1 commit effba3c
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13 changes: 13 additions & 0 deletions var/spack/repos/builtin/packages/lammps/lib.patch
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@@ -0,0 +1,13 @@
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 6d35db75a..5987869b8 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -530,7 +530,7 @@ target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
if(INSTALL_LIB)
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+ install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
elseif(BUILD_SHARED_LIBS)
message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
endif()
197 changes: 39 additions & 158 deletions var/spack/repos/builtin/packages/lammps/package.py
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Expand Up @@ -23,184 +23,65 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
import datetime as dt


class Lammps(MakefilePackage):
class Lammps(CMakePackage):
"""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"
url = "https://github.com/lammps/lammps/archive/stable_01Sep2017.tar.gz"

version('2016.11.17', '8aecc58a39f9775203517c62a592d13b')
version('20170901', 'c498680052f80c6ddb880052ad369af0')

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"))
vdate = dt.datetime.strptime(str(version), "%Y%m%d")
return "https://github.com/lammps/lammps/archive/patch_{0}.tar.gz".format(
vdate.strftime("%d%b%Y").lstrip('0'))

supported_packages = ['voronoi', 'rigid', 'user-nc-dump',
supported_packages = ['voronoi', 'rigid', 'user-nc-dump', 'kspace',
'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')
variant('mpi', default=True,
description='Build with mpi')

depends_on('mpi')
depends_on('fftw')
depends_on('mpi', when='+mpi')
depends_on('fftw', when='+ksapce')
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 = {0}'.format(self.compiler.pic_flag))
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'].libs +
self.spec['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:
if '+{0}'.format(pkg) in spec:
_build_pkg_name = 'build_{0}'.format(pkg.replace('-', '_'))
if hasattr(self, _build_pkg_name):
_build_pkg = getattr(self, _build_pkg_name)
_build_pkg()

with working_dir('src'):
make('yes-{0}'.format(pkg))

with working_dir('src'):
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)

mkdirp(prefix.include.lammps)
install('library.h', prefix.include.lammps)
patch("lib.patch", when="@20170901")

root_cmakelists_dir = 'cmake'

def cmake_args(self):
spec = self.spec

return [
'-DBUILD_SHARED_LIBS={0}'.format(
'ON' if '+lib' in spec else 'OFF'),
'-DENABLE_MPI={0}'.format(
'ON' if '+mpi' in spec else 'OFF'),
'-DENABLE_RIGID={0}'.format(
'ON' if '+rigid' in spec else 'OFF'),
'-DENABLE_MEAM={0}'.format(
'ON' if '+meam' in spec else 'OFF'),
'-DENABLE_KSAPCE={0}'.format(
'ON' if '+kspace' in spec else 'OFF'),
'-DFFT=FFTW3', # doesn't do harm withiout KSPACE
'-DENABLE_MANYBODY={0}'.format(
'ON' if '+manybody' in spec else 'OFF'),
'-DENABLE_USER-NETCDF={0}'.format(
'ON' if '+user-nc-dump' in spec else 'OFF'),
'-DENABLE_VORONOI={0}'.format(
'ON' if '+voronoi' in spec else 'OFF'),
'-DENABLE_USER-ATC={0}'.format(
'ON' if '+user-atc' in spec else 'OFF'),
]

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