187 lines
7.2 KiB
Python
187 lines
7.2 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, 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/spack/spack
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# Please also see the NOTICE and LICENSE files 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 collections
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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('2.4.2', '0f66f24b4c763ae8b2f39574113e9935')
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version('2.4.1', '6558e1fd02fc46e847ab6a3fb5ed5411')
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version('2.3.5', '3cc5f025cb6f5d963f3c778f15c77d44')
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version('2.3.3', '9f5729e406e79a06a16976fcb020e024')
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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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force_autoreconf = True
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parallel = False
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def apply_patch(self, other):
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# The name of MD engines differ slightly from the ones used in Spack
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format_strings = collections.defaultdict(
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lambda: '{0.name}-{0.version}'
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)
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format_strings['espresso'] = 'q{0.name}-{0.version}'
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format_strings['amber'] = '{0.name}{0.version}'
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get_md = lambda x: format_strings[x.name].format(x)
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# Get available patches
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plumed_patch = Executable(
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join_path(self.spec.prefix.bin, 'plumed-patch')
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)
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out = plumed_patch('-q', '-l', output=str)
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available = out.split(':')[-1].split()
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# Check that `other` is among the patchable applications
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if get_md(other) not in available:
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msg = '{0.name}@{0.version} is not among the MD engine'
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msg += ' that can be patched by {1.name}@{1.version}.\n'
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msg += 'Supported engines are:\n'
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for x in available:
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msg += x + '\n'
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raise RuntimeError(msg.format(other, self.spec))
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# Call plumed-patch to patch executables
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target = format_strings[other.name].format(other)
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plumed_patch('-p', '-e', target)
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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 = dependent_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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# The configure.ac script may detect the wrong linker for
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# LD_RO which causes issues at link time. Here we work around
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# the issue saying we have no LD_RO executable.
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configure_opts = ['--disable-ld-r']
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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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# Set flags to help find gsl
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if '+gsl' in self.spec:
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gsl_libs = self.spec['gsl'].libs
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blas_libs = self.spec['blas'].libs
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configure_opts.append('LDFLAGS={0}'.format(
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(gsl_libs + blas_libs).ld_flags
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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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