Merge pull request #1473 from epfl-scitas/packages/plumed_dependents
plumed : added dependents (gromacs, cp2k)
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becker33
GitHub
commit
fb9f6fe9b5
3 changed files with 82 additions and 28 deletions
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@ -40,6 +40,7 @@ class Cp2k(Package):
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version('3.0', 'c05bc47335f68597a310b1ed75601d35')
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variant('mpi', default=True, description='Enable MPI support')
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variant('plumed', default=False, description='Enable PLUMED support')
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depends_on('python') # Build dependency
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@ -49,6 +50,8 @@ class Cp2k(Package):
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depends_on('mpi', when='+mpi')
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depends_on('scalapack', when='+mpi')
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depends_on('plumed+shared+mpi', when='+plumed+mpi')
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depends_on('plumed+shared~mpi', when='+plumed~mpi')
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# TODO : add dependency on libint
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# TODO : add dependency on libsmm, libxsmm
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@ -56,7 +59,6 @@ class Cp2k(Package):
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# TODO : add dependency on CUDA
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# TODO : add dependency on PEXSI
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# TODO : add dependency on QUIP
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# TODO : add dependency on plumed
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# TODO : add dependency on libwannier90
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parallel = False
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@ -70,22 +72,6 @@ def install(self, spec, prefix):
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# Write the custom makefile
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with open(makefile, 'w') as mkf:
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mkf.write('CC = {0.compiler.cc}\n'.format(self))
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if '%intel' in self.spec:
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# CPP is a commented command in Intel arch of CP2K
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# This is the hack through which cp2k developers avoid doing :
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#
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# ${CPP} <file>.F > <file>.f90
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#
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# and use `-fpp` instead
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mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self))
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mkf.write('AR = xiar -r\n')
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else:
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mkf.write('CPP = {0.compiler.cc} -E\n'.format(self))
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mkf.write('AR = ar -r\n')
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fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
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mkf.write('FC = {0}\n'.format(fc))
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mkf.write('LD = {0}\n'.format(fc))
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# Optimization flags
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optflags = {
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'gcc': ['-O2',
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@ -110,6 +96,37 @@ def install(self, spec, prefix):
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])
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ldflags = ['-L' + spec['fftw'].prefix.lib]
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libs = []
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if '+plumed' in self.spec:
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# Include Plumed.inc in the Makefile
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mkf.write('include {0}\n'.format(
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join_path(self.spec['plumed'].prefix.lib,
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'plumed',
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'src',
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'lib',
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'Plumed.inc')
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))
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# Add required macro
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cppflags.extend(['-D__PLUMED2'])
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libs.extend([
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join_path(self.spec['plumed'].prefix.lib, 'libplumed.so')
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])
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mkf.write('CC = {0.compiler.cc}\n'.format(self))
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if '%intel' in self.spec:
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# CPP is a commented command in Intel arch of CP2K
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# This is the hack through which cp2k developers avoid doing :
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#
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# ${CPP} <file>.F > <file>.f90
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#
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# and use `-fpp` instead
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mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self))
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mkf.write('AR = xiar -r\n')
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else:
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mkf.write('CPP = {0.compiler.cc} -E\n'.format(self))
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mkf.write('AR = ar -r\n')
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fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
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mkf.write('FC = {0}\n'.format(fc))
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mkf.write('LD = {0}\n'.format(fc))
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# Intel
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if '%intel' in self.spec:
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cppflags.extend([
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@ -22,19 +22,21 @@
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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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from spack import *
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class Gromacs(Package):
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"""
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GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
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simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
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department of University of Groningen, and is now maintained by contributors in universities and research centers
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across the world.
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"""GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
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dynamics package primarily designed for simulations of proteins, lipids
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and nucleic acids. It was originally developed in the Biophysical
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Chemistry department of University of Groningen, and is now maintained
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by contributors in universities and research centers across the world.
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GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs.
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It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
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released under the GNU Lesser General Public License.
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GROMACS is one of the fastest and most popular software packages
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available and can run on CPUs as well as GPUs. It is free, open source
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released under the GNU General Public License. Starting from version 4.6,
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GROMACS is released under the GNU Lesser General Public License.
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"""
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homepage = 'http://www.gromacs.org'
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@ -43,17 +45,24 @@ class Gromacs(Package):
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version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
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variant('mpi', default=True, description='Activate MPI support')
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variant('shared', default=True, description='Enables the build of shared libraries')
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variant('shared', default=True,
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description='Enables the build of shared libraries')
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variant('debug', default=False, description='Enables debug mode')
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variant('double', default=False, description='Produces a double precision version of the executables')
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variant('double', default=False, description='Produces a double precision version of the executables') # NOQA: ignore=E501
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variant('plumed', default=False, description='Enable PLUMED support')
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depends_on('mpi', when='+mpi')
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depends_on('plumed+mpi', when='+plumed+mpi')
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depends_on('plumed~mpi', when='+plumed~mpi')
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depends_on('fftw')
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depends_on('cmake', type='build')
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# TODO : add GPU support
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def patch(self):
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if '+plumed' in self.spec:
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self.spec['plumed'].package.apply_patch(self)
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def install(self, spec, prefix):
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options = []
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@ -22,6 +22,7 @@
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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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@ -55,6 +56,33 @@ class Plumed(Package):
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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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