218 lines
9.3 KiB
Python
218 lines
9.3 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import collections
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import os.path
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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/v2.5.3.tar.gz'
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git = 'https://github.com/plumed/plumed2.git'
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version('master', branch='master')
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version('2.7.0', sha256='14450ea566c25ac9bf71fd77bb9c0c95e9038462b5739c73a515be82e2011cd6')
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version('2.6.2', preferred=True, sha256='bbc2ef0cb08d404513b8b737c72333b6656389e15effd6a0f9ace2a5758c9a4a')
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version('2.6.1', sha256='c1b3c397b2d971140aa240dde50e48a04ce78e3dedb02b6dca80fa53f8026e4e')
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version('2.6.0', sha256='3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820')
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version('2.5.5', sha256='70faa9ff1938e286dc388cb793b39840953e5646855b684f48df1bc864b737e8')
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version('2.5.4', sha256='a1647e598191f261e75d06351e607475d395af481315052a4c28563ac9989a7f')
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version('2.5.3', sha256='543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc')
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version('2.5.2', sha256='85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4')
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version('2.5.1', sha256='de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba')
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version('2.5.0', sha256='53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7')
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version('2.4.6', sha256='c22ad19f5cd36ce9fe4ba0b53158fc2a3d985c48fc04606e3f3b3e835b994cb3')
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version('2.4.4', sha256='1e5c24109314481fad404da97d61c7339b219e27e120c9c80bacc79c9f6a51a8')
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version('2.4.2', sha256='528ce57f1f5330480bcd403140166a4580efd2acaea39c85dfeca5e2cd649321')
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version('2.4.1', sha256='f00410ebdd739c2ddf55fcd714ff4bd88a1029e02d2fc9cea0b5fca34e0fc4eb')
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version('2.3.5', sha256='a6a66ca4582c1aecc6138c96be015e13cd06a718e8446b2f13e610fe34602e4f')
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version('2.3.3', sha256='ac058ff529f207d5b4169fb5a87bdb3c77307dfef1ac543ad8b6c74c5de7fc91')
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version('2.3.0', sha256='b1c8a54a313a0569e27e36420770074f35406453f73de70e55c424652abeddf1')
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version('2.2.4', sha256='d7a1dba34a7fe03f23e8d39ab6e15b230c4851373fdceb3602e2de26ea53ce37')
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version('2.2.3', sha256='2db19c5f6a2918833941d0bf47b5431d0865529d786df797ccc966d763ed7b0c')
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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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variant('arrayfire', default='none',
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values=('none', 'cpu', 'cuda', 'opencl'),
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description='Activates FireArray 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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# For libmatheval support through the 'function' module
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# which is enabled by default (or when optional_modules=all)
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depends_on('libmatheval', when='@:2.4.99')
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depends_on('arrayfire', when='arrayfire=cpu')
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depends_on('arrayfire+cuda', when='arrayfire=cuda')
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depends_on('arrayfire+opencl', when='arrayfire=opencl')
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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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depends_on('py-cython', type='build', when='@2.5:')
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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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os.path.join(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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@property
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def plumed_inc(self):
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return os.path.join(
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self.prefix.lib, 'plumed', 'src', 'lib', 'Plumed.inc'
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)
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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 patch(self):
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# Ensure Spack's wrappers are used to compile the Python interface
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env = 'CXX={0} LDSHARED="{0} -pthread -shared" ' \
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'LDCXXSHARED="{0} -pthread -shared"'.format(spack_cxx)
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filter_file('plumed_program_name=plumed',
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'{0} plumed_program_name=plumed'.format(env),
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'src/lib/Makefile', 'python/Makefile')
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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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extra_libs = []
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# Set flags to help find gsl
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if '+gsl' in spec:
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gsl_libs = spec['gsl'].libs
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blas_libs = spec['blas'].libs
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extra_libs.append(
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(gsl_libs + blas_libs).ld_flags
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)
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# Set flags to help with ArrayFire
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if 'arrayfire=none' not in spec:
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libaf = 'arrayfire:{0}'.format(spec.variants['arrayfire'].value)
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extra_libs.append(spec[libaf].libs.search_flags)
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if extra_libs:
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configure_opts.append('LDFLAGS={0}'.format(
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' '.join(extra_libs)
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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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'--enable-af_cpu={0}'.format('yes' if 'arrayfire=cpu' in spec else 'no'),
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'--enable-af_cuda={0}'.format('yes' if 'arrayfire=cuda' in spec else 'no'),
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'--enable-af_ocl={0}'.format('yes' if 'arrayfire=ocl' 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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