lammps: version bump, switch to cmake (#5313)
This commit is contained in:
Christoph Junghans
committed by
Todd Gamblin
Todd Gamblin
parent
b60e7e14b9
commit
effba3c95e
13
var/spack/repos/builtin/packages/lammps/lib.patch
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13
var/spack/repos/builtin/packages/lammps/lib.patch
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@@ -0,0 +1,13 @@
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diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
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index 6d35db75a..5987869b8 100644
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--- a/cmake/CMakeLists.txt
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+++ b/cmake/CMakeLists.txt
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@@ -530,7 +530,7 @@ target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
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set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
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if(INSTALL_LIB)
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install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
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- install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
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+ install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
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elseif(BUILD_SHARED_LIBS)
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message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
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endif()
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@@ -23,24 +23,23 @@
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import os
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import datetime as dt
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class Lammps(MakefilePackage):
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class Lammps(CMakePackage):
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"""LAMMPS stands for Large-scale Atomic/Molecular Massively
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Parallel Simulator."""
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homepage = "http://lammps.sandia.gov/"
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url = "https://github.com/lammps/lammps/archive/stable_17Nov2016.tar.gz"
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url = "https://github.com/lammps/lammps/archive/stable_01Sep2017.tar.gz"
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version('2016.11.17', '8aecc58a39f9775203517c62a592d13b')
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version('20170901', 'c498680052f80c6ddb880052ad369af0')
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def url_for_version(self, version):
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vdate = dt.datetime.strptime(str(version), "%Y.%m.%d")
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return "https://github.com/lammps/lammps/archive/stable_{0}.tar.gz".format(
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vdate.strftime("%d%b%Y"))
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vdate = dt.datetime.strptime(str(version), "%Y%m%d")
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return "https://github.com/lammps/lammps/archive/patch_{0}.tar.gz".format(
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vdate.strftime("%d%b%Y").lstrip('0'))
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supported_packages = ['voronoi', 'rigid', 'user-nc-dump',
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supported_packages = ['voronoi', 'rigid', 'user-nc-dump', 'kspace',
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'user-atc', 'meam', 'manybody']
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for pkg in supported_packages:
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@@ -48,159 +47,41 @@ def url_for_version(self, version):
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description='Activate the {0} package'.format(pkg))
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variant('lib', default=True,
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description='Build the liblammps in addition to the executable')
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variant('mpi', default=True,
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description='Build with mpi')
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depends_on('mpi')
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depends_on('fftw')
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depends_on('mpi', when='+mpi')
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depends_on('fftw', when='+ksapce')
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depends_on('voropp', when='+voronoi')
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depends_on('netcdf+mpi', when='+user-nc-dump')
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depends_on('blas', when='+user-atc')
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depends_on('lapack', when='+user-atc')
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def setup_environment(self, spack_env, run_env):
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self.target_name = self.compiler.name
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patch("lib.patch", when="@20170901")
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def edit(self, spec, prefix):
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config = []
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root_cmakelists_dir = 'cmake'
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config.append('CC = c++')
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if self.compiler.name == 'intel':
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# This is taken from MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
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config.append('OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits') # noqa: E501
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config.append('CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)') # noqa: E501
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config.append('LINKFLAGS = -qopenmp $(OPTFLAGS)')
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else:
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# This is taken from MAKE/OPTIONS/Makefile.g++
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config.append('OPTFLAGS = -O3')
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config.append('CCFLAGS = -fopenmp')
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config.append('LINKFLAGS = -fopenmp $(OPTFLAGS)')
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def cmake_args(self):
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spec = self.spec
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config.append('SHFLAGS = {0}'.format(self.compiler.pic_flag))
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config.append('DEPFLAGS = -M')
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config.append('LINK = c++')
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config.append('LIB = ')
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config.append('SIZE = size')
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config.append('ARCHIVE = ar')
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config.append('ARFLAGS = -rc')
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config.append('SHLIBFLAGS = -shared')
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config.append('LMP_INC = -DLAMMPS_GZIP')
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mpi_path = self.spec['mpi'].prefix.lib
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mpi_inc = self.spec['mpi'].prefix.include
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config.append(
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'MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I{0}'.format(
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mpi_inc))
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config.append('MPI_PATH = -L{0}'.format(mpi_path))
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config.append('MPI_LIB = {0}'.format(
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' '.join(self.spec['mpi'].mpicxx_shared_libs)))
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config.append('FFT_INC = -DFFT_FFTW3 -L{0}'.format(
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self.spec['fftw'].prefix.include))
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config.append('FFT_PATH = -L{0}'.format(self.spec['fftw'].prefix.lib))
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config.append('FFT_LIB = -lfftw3')
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config.append('JPG_INC = ')
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config.append('JPG_PATH = ')
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config.append('JPG_LIB = ')
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makefile_inc_template = \
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join_path(os.path.dirname(self.module.__file__),
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'Makefile.inc')
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with open(makefile_inc_template, "r") as fhr:
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config.extend(fhr.read().split('\n'))
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with working_dir('src/MAKE/'):
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with open('Makefile.{0}'.format(self.target_name), 'w') as fh:
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fh.write('\n'.join(config))
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def build_meam(self):
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with working_dir('lib/meam'):
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filter_file(r'EXTRAMAKE = Makefile.lammps.ifort',
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'EXTRAMAKE = Makefile.lammps.spack',
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'Makefile.ifort')
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filter_file('F90 = *ifort',
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'F90 = {0}'.format(self.compiler.fc),
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'Makefile.ifort')
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with open('Makefile.lammps.spack', 'w') as fh:
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syslib = ''
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syspath = ''
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if self.compiler.name == 'gcc':
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syslib = '-lgfortran'
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elif self.compiler.name == 'intel':
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syslib = '-lifcore'
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makefile = ['meam_SYSINC =',
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'meam_SYSLIB = {0}'.format(syslib),
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'meam_SYSPATH = {0}'.format(syspath)]
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fh.write('\n'.join(makefile))
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make('lib', '-f', 'Makefile.ifort')
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def build_user_atc(self):
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with working_dir('lib/atc'):
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filter_file(r'CC =.*',
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'CC = {0}'.format(self.compiler.cxx),
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'Makefile.icc')
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mpi_include = self.spec['mpi'].prefix.include
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filter_file(r'CCFLAGS = *',
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'CCFLAGS = -I{0} '.format(mpi_include),
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'Makefile.icc')
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filter_file('LINK =.*',
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'LINK = {0}'.format(self.compiler.cxx),
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'Makefile.icc')
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make('lib', '-f', 'Makefile.icc')
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with open('Makefile.lammps', 'w') as fh:
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lapack_blas = (self.spec['lapack'].libs +
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self.spec['blas'].libs)
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makefile = [
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'user-atc_SYSINC =',
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'user-atc_SYSLIB = {0}'.format(lapack_blas.ld_flags),
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'user-atc_SYSPATH = ']
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fh.write('\n'.join(makefile))
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def build_voronoi(self):
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# no need to set the voronoi_SYS variable in Makefile.lammps
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# since the spack wrapper takes care of the path
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with working_dir('src/VORONOI'):
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filter_file(r'#include "voro\+\+\.hh"',
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'#include <voro++/voro++.hh>',
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'compute_voronoi_atom.h')
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def build(self, spec, prefix):
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for pkg in self.supported_packages:
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if '+{0}'.format(pkg) in spec:
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_build_pkg_name = 'build_{0}'.format(pkg.replace('-', '_'))
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if hasattr(self, _build_pkg_name):
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_build_pkg = getattr(self, _build_pkg_name)
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_build_pkg()
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with working_dir('src'):
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make('yes-{0}'.format(pkg))
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with working_dir('src'):
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make(self.target_name)
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if '+lib' in spec:
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make('mode=shlib', self.target_name)
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def install(self, spec, prefix):
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with working_dir('src'):
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mkdirp(prefix.bin)
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install('lmp_{0}'.format(self.target_name), prefix.bin)
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if '+lib' in spec:
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mkdirp(prefix.lib)
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install('liblammps_{0}.{1}'.format(self.target_name,
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dso_suffix), prefix.lib)
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mkdirp(prefix.include.lammps)
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install('library.h', prefix.include.lammps)
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return [
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'-DBUILD_SHARED_LIBS={0}'.format(
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'ON' if '+lib' in spec else 'OFF'),
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'-DENABLE_MPI={0}'.format(
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'ON' if '+mpi' in spec else 'OFF'),
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'-DENABLE_RIGID={0}'.format(
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'ON' if '+rigid' in spec else 'OFF'),
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'-DENABLE_MEAM={0}'.format(
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'ON' if '+meam' in spec else 'OFF'),
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'-DENABLE_KSAPCE={0}'.format(
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'ON' if '+kspace' in spec else 'OFF'),
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'-DFFT=FFTW3', # doesn't do harm withiout KSPACE
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'-DENABLE_MANYBODY={0}'.format(
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'ON' if '+manybody' in spec else 'OFF'),
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'-DENABLE_USER-NETCDF={0}'.format(
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'ON' if '+user-nc-dump' in spec else 'OFF'),
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'-DENABLE_VORONOI={0}'.format(
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'ON' if '+voronoi' in spec else 'OFF'),
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'-DENABLE_USER-ATC={0}'.format(
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'ON' if '+user-atc' in spec else 'OFF'),
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]
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