############################################################################## # Copyright (c) 2013-2017, 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/spack/spack # Please also see the NOTICE and LICENSE files 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 ############################################################################## import platform import shutil 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('charm') 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) shutil.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)