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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import platform
import sys
import os
from spack import *
class Namd(MakefilePackage):
"""NAMDis a parallel molecular dynamics code designed for
high-performance simulation of large biomolecular systems."""
homepage = "http://www.ks.uiuc.edu/Research/namd/"
url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd())
version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9')
variant('fftw', default='3', values=('none', '2', '3', 'mkl'),
description='Enable the use of FFTW/FFTW3/MKL FFT')
variant('interface', default='none', values=('none', 'tcl', 'python'),
description='Enables TCL and/or python interface')
depends_on('charmpp')
depends_on('fftw@:2.99', when="fftw=2")
depends_on('fftw@3:', when="fftw=3")
depends_on('intel-mkl', when="fftw=mkl")
depends_on('tcl', when='interface=tcl')
depends_on('tcl', when='interface=python')
depends_on('python', when='interface=python')
def _copy_arch_file(self, lib):
config_filename = 'arch/{0}.{1}'.format(self.arch, lib)
copy('arch/Linux-x86_64.{0}'.format(lib),
config_filename)
if lib == 'tcl':
filter_file(r'-ltcl8\.5',
'-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)),
config_filename)
def _append_option(self, opts, lib):
if lib != 'python':
self._copy_arch_file(lib)
spec = self.spec
opts.extend([
'--with-{0}'.format(lib),
'--{0}-prefix'.format(lib), spec[lib].prefix
])
@property
def arch(self):
plat = sys.platform
if plat.startswith("linux"):
plat = "linux"
march = platform.machine()
return '{0}-{1}'.format(plat, march)
@property
def build_directory(self):
return '{0}-spack'.format(self.arch)
def edit(self, spec, prefix):
with working_dir('arch'):
with open('{0}.arch'.format(self.build_directory), 'w') as fh:
# this options are take from the default provided
# configuration files
optims_opts = {
'gcc': '-m64 -O3 -fexpensive-optimizations -ffast-math',
'intel': '-O2 -ip'
}
optim_opts = optims_opts[self.compiler.name] \
if self.compiler.name in optims_opts else ''
fh.write('\n'.join([
'NAMD_ARCH = {0}'.format(self.arch),
'CHARMARCH = ',
'CXX = {0.cxx} {0.cxx11_flag}'.format(
self.compiler),
'CXXOPTS = {0}'.format(optim_opts),
'CC = {0}'.format(self.compiler.cc),
'COPTS = {0}'.format(optim_opts),
''
]))
self._copy_arch_file('base')
opts = ['--charm-base', spec['charm'].prefix]
fftw_version = spec.variants['fftw'].value
if fftw_version == 'none':
opts.append('--without-fftw')
elif fftw_version == 'mkl':
self._append_option(opts, 'mkl')
else:
_fftw = 'fftw{0}'.format('' if fftw_version == '2' else '3')
self._copy_arch_file(_fftw)
opts.extend(['--with-{0}'.format(_fftw),
'--fftw-prefix', spec['fftw'].prefix])
interface_type = spec.variants['interface'].value
if interface_type != 'none':
self._append_option(opts, 'tcl')
if interface_type == 'python':
self._append_option(opts, 'python')
else:
opts.extend([
'--without-tcl',
'--without-python'
])
config = Executable('./config')
config(self.build_directory, *opts)
def install(self, spec, prefix):
with working_dir(self.build_directory):
mkdirp(prefix.bin)
install('namd2', prefix.bin)
# I'm not sure this is a good idea or if an autoload of the charm
# module would not be better.
install('charmrun', prefix.bin)
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