diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/cp2k/package.py | 51 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/gromacs/package.py | 33 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/plumed/package.py | 28 |
3 files changed, 83 insertions, 29 deletions
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py index 8fdd1e0ca3..5f59286323 100644 --- a/var/spack/repos/builtin/packages/cp2k/package.py +++ b/var/spack/repos/builtin/packages/cp2k/package.py @@ -40,6 +40,7 @@ class Cp2k(Package): version('3.0', 'c05bc47335f68597a310b1ed75601d35') variant('mpi', default=True, description='Enable MPI support') + variant('plumed', default=False, description='Enable PLUMED support') depends_on('python') # Build dependency @@ -49,6 +50,8 @@ class Cp2k(Package): depends_on('mpi', when='+mpi') depends_on('scalapack', when='+mpi') + depends_on('plumed+shared+mpi', when='+plumed+mpi') + depends_on('plumed+shared~mpi', when='+plumed~mpi') # TODO : add dependency on libint # TODO : add dependency on libsmm, libxsmm @@ -56,7 +59,6 @@ class Cp2k(Package): # TODO : add dependency on CUDA # TODO : add dependency on PEXSI # TODO : add dependency on QUIP - # TODO : add dependency on plumed # TODO : add dependency on libwannier90 parallel = False @@ -70,22 +72,6 @@ class Cp2k(Package): # Write the custom makefile with open(makefile, 'w') as mkf: - mkf.write('CC = {0.compiler.cc}\n'.format(self)) - if '%intel' in self.spec: - # CPP is a commented command in Intel arch of CP2K - # This is the hack through which cp2k developers avoid doing : - # - # ${CPP} <file>.F > <file>.f90 - # - # and use `-fpp` instead - mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self)) - mkf.write('AR = xiar -r\n') - else: - mkf.write('CPP = {0.compiler.cc} -E\n'.format(self)) - mkf.write('AR = ar -r\n') - fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc - mkf.write('FC = {0}\n'.format(fc)) - mkf.write('LD = {0}\n'.format(fc)) # Optimization flags optflags = { 'gcc': ['-O2', @@ -110,6 +96,37 @@ class Cp2k(Package): ]) ldflags = ['-L' + spec['fftw'].prefix.lib] libs = [] + if '+plumed' in self.spec: + # Include Plumed.inc in the Makefile + mkf.write('include {0}\n'.format( + join_path(self.spec['plumed'].prefix.lib, + 'plumed', + 'src', + 'lib', + 'Plumed.inc') + )) + # Add required macro + cppflags.extend(['-D__PLUMED2']) + libs.extend([ + join_path(self.spec['plumed'].prefix.lib, 'libplumed.so') + ]) + + mkf.write('CC = {0.compiler.cc}\n'.format(self)) + if '%intel' in self.spec: + # CPP is a commented command in Intel arch of CP2K + # This is the hack through which cp2k developers avoid doing : + # + # ${CPP} <file>.F > <file>.f90 + # + # and use `-fpp` instead + mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self)) + mkf.write('AR = xiar -r\n') + else: + mkf.write('CPP = {0.compiler.cc} -E\n'.format(self)) + mkf.write('AR = ar -r\n') + fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc + mkf.write('FC = {0}\n'.format(fc)) + mkf.write('LD = {0}\n'.format(fc)) # Intel if '%intel' in self.spec: cppflags.extend([ diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 55eacc8d38..607927fe8b 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -22,19 +22,21 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## + from spack import * class Gromacs(Package): - """ - GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for - simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry - department of University of Groningen, and is now maintained by contributors in universities and research centers - across the world. - - GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. - It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is - released under the GNU Lesser General Public License. + """GROMACS (GROningen MAchine for Chemical Simulations) is a molecular + dynamics package primarily designed for simulations of proteins, lipids + and nucleic acids. It was originally developed in the Biophysical + Chemistry department of University of Groningen, and is now maintained + by contributors in universities and research centers across the world. + + GROMACS is one of the fastest and most popular software packages + available and can run on CPUs as well as GPUs. It is free, open source + released under the GNU General Public License. Starting from version 4.6, + GROMACS is released under the GNU Lesser General Public License. """ homepage = 'http://www.gromacs.org' @@ -43,17 +45,24 @@ class Gromacs(Package): version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98') variant('mpi', default=True, description='Activate MPI support') - variant('shared', default=True, description='Enables the build of shared libraries') + variant('shared', default=True, + description='Enables the build of shared libraries') variant('debug', default=False, description='Enables debug mode') - variant('double', default=False, description='Produces a double precision version of the executables') + variant('double', default=False, description='Produces a double precision version of the executables') # NOQA: ignore=E501 + variant('plumed', default=False, description='Enable PLUMED support') depends_on('mpi', when='+mpi') - + depends_on('plumed+mpi', when='+plumed+mpi') + depends_on('plumed~mpi', when='+plumed~mpi') depends_on('fftw') depends_on('cmake', type='build') # TODO : add GPU support + def patch(self): + if '+plumed' in self.spec: + self.spec['plumed'].package.apply_patch(self) + def install(self, spec, prefix): options = [] diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 32571455eb..abb03e0770 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -22,6 +22,7 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## +import subprocess from spack import * @@ -55,6 +56,33 @@ class Plumed(Package): depends_on('mpi', when='+mpi') depends_on('gsl', when='+gsl') + # Dictionary mapping PLUMED versions to the patches it provides + # interactively + plumed_patches = { + '2.2.3': { + 'amber-14': '1', + 'gromacs-4.5.7': '2', + 'gromacs-4.6.7': '3', + 'gromacs-5.0.7': '4', + 'gromacs-5.1.2': '5', + 'lammps-6Apr13': '6', + 'namd-2.8': '7', + 'namd-2.9': '8', + 'espresso-5.0.2': '9' + } + } + + def apply_patch(self, other): + plumed = subprocess.Popen( + [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'], + stdin=subprocess.PIPE + ) + opts = Plumed.plumed_patches[str(self.version)] + search = '{0.name}-{0.version}'.format(other) + choice = opts[search] + '\n' + plumed.stdin.write(choice) + plumed.wait() + def setup_dependent_package(self, module, ext_spec): # Make plumed visible from dependent packages module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed')) |