Found upstream plumed package and modified this one to match
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Andrew Williams
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@ -22,17 +22,26 @@
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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(Package):
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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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molecular dynamics engines.
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# PLUMED homepage. The source is available on github.
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homepage = "http://www.plumed.org/home"
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url = "https://github.com/plumed/plumed2"
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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'
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version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3')
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@ -45,17 +54,80 @@ class Plumed(Package):
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description='Build support for optional imd module.')
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variant('manyrestraints', default=False,
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description='Build support for optional manyrestraints module.')
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variant('mpi', default=False,
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description='Enable MPI support.')
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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("mpi", when="+mpi")
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depends_on("netlib-lapack")
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depends_on("openblas")
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# Dependencies. LAPACK and BLAS are recommended but not essentia
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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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# Dictionary mapping PLUMED versions to the patches it provides
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# interactively
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plumed_patches = {
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'2.2.3': {
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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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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, ext_spec):
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# Make plumed visible from dependent packages
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module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
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def install(self, spec, prefix):
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# Prefix is the only compulsory argument.
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config_args = ["--prefix=" + prefix]
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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 = ["--prefix=" + prefix]
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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 intelmpi 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 spec.satisfies('^intelmpi'):
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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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module_opts=[]
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@ -70,28 +142,9 @@ def install(self, spec, prefix):
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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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if module_opts:
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config_args.extend(["--enable-modules=%s" % "".join(module_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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config_args.extend([
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"--enable-mpi",
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"CC=%s" % self.spec['mpi'].mpicc,
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"CXX=%s" % self.spec['mpi'].mpicxx,
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"FC=%s" % self.spec['mpi'].mpifc,
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"F77=%s" % self.spec['mpi'].mpif77
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])
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# If the MPI dependency is provided by the intelmpi 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 spec.satisfies('^intelmpi'):
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config_args.extend([
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"STATIC_LIBS=-mt_mpi"
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])
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# Configure
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configure(*config_args)
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configure_opts.extend([
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'--enable-modules={0}'.format("".join(module_opts))])
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configure(*configure_opts)
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make()
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make("install")
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make('install')
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