185 lines
6.7 KiB
Python
185 lines
6.7 KiB
Python
##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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import subprocess
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from spack import *
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class Plumed(AutotoolsPackage):
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"""PLUMED is an open source library for free energy calculations in
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molecular systems which works together with some of the most popular
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molecular dynamics engines.
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Free energy calculations can be performed as a function of many order
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parameters with a particular focus on biological problems, using state
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of the art methods such as metadynamics, umbrella sampling and
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Jarzynski-equation based steered MD.
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The software, written in C++, can be easily interfaced with both fortran
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and C/C++ codes.
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"""
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homepage = 'http://www.plumed.org/'
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url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
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version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5')
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version('2.2.4', 'afb00da25a3fbd47acf377e53342059d')
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version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
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# Variants. PLUMED by default builds a number of optional modules.
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# The ones listed here are not built by default for various reasons,
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# such as stability, lack of testing, or lack of demand.
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# FIXME: This needs to be an optional
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variant(
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'optional_modules',
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default='all',
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values=lambda x: True,
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description='String that is used to build optional modules'
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)
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variant('shared', default=True, description='Builds shared libraries')
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variant('mpi', default=True, description='Activates MPI support')
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variant('gsl', default=True, description='Activates GSL support')
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# Dependencies. LAPACK and BLAS are recommended but not essential.
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depends_on('zlib')
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depends_on('blas')
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depends_on('lapack')
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depends_on('mpi', when='+mpi')
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depends_on('gsl', when='+gsl')
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depends_on('autoconf', type='build')
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depends_on('automake', type='build')
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depends_on('libtool', type='build')
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# Dictionary mapping PLUMED versions to the patches it provides
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# interactively
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plumed_patches = {
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'2.3.0': {
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'amber-14': '1',
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'gromacs-2016.1': '2',
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'gromacs-4.5.7': '3',
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'gromacs-5.0.7': '4',
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'gromacs-5.1.4': '5',
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'lammps-6Apr13': '6',
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'namd-2.8': '7',
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'namd-2.9': '8',
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'espresso-5.0.2': '9'
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},
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'2.2.4': {
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'amber-14': '1',
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'gromacs-4.5.7': '2',
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'gromacs-4.6.7': '3',
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'gromacs-5.0.7': '4',
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'gromacs-5.1.2': '5',
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'lammps-6Apr13': '6',
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'namd-2.8': '7',
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'namd-2.9': '8',
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'espresso-5.0.2': '9'
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},
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'2.2.3': {
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'amber-14': '1',
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'gromacs-4.5.7': '2',
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'gromacs-4.6.7': '3',
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'gromacs-5.0.7': '4',
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'gromacs-5.1.2': '5',
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'lammps-6Apr13': '6',
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'namd-2.8': '7',
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'namd-2.9': '8',
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'espresso-5.0.2': '9'
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}
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}
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force_autoreconf = True
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def apply_patch(self, other):
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plumed = subprocess.Popen(
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[join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'],
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stdin=subprocess.PIPE
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)
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opts = Plumed.plumed_patches[str(self.version)]
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search = '{0.name}-{0.version}'.format(other)
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choice = opts[search] + '\n'
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plumed.stdin.write(choice)
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plumed.wait()
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def setup_dependent_package(self, module, dependent_spec):
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# Make plumed visible from dependent packages
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module.plumed = self.spec['plumed'].command
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@run_before('autoreconf')
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def filter_gslcblas(self):
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# This part is needed to avoid linking with gsl cblas
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# interface which will mask the cblas interface
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# provided by optimized libraries due to linking order
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filter_file('-lgslcblas', '', 'configure.ac')
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def configure_args(self):
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spec = self.spec
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# From plumed docs :
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# Also consider that this is different with respect to what some other
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# configure script does in that variables such as MPICXX are
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# completely ignored here. In case you work on a machine where CXX is
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# set to a serial compiler and MPICXX to a MPI compiler, to compile
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# with MPI you should use:
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#
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# > ./configure CXX="$MPICXX"
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configure_opts = []
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# If using MPI then ensure the correct compiler wrapper is used.
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if '+mpi' in spec:
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configure_opts.extend([
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'--enable-mpi',
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'CXX={0}'.format(spec['mpi'].mpicxx)
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])
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# If the MPI dependency is provided by the intel-mpi package then
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# the following additional argument is required to allow it to
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# build.
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if 'intel-mpi' in spec:
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configure_opts.extend([
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'STATIC_LIBS=-mt_mpi'
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])
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# Additional arguments
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configure_opts.extend([
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'--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'),
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'--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no')
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])
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# Construct list of optional modules
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# If we have specified any optional modules then add the argument to
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# enable or disable them.
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optional_modules = self.spec.variants['optional_modules'].value
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if optional_modules:
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# From 'configure --help' @2.3:
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# all/none/reset or : separated list such as
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# +crystallization:-bias default: reset
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configure_opts.append(
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'--enable-modules={0}'.format(optional_modules)
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)
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return configure_opts
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