Merge pull request #1473 from epfl-scitas/packages/plumed_dependents

plumed : added dependents (gromacs, cp2k)

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 @@ def install(self, spec, prefix):
 
         # 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 @@ def install(self, spec, prefix):
             ])
             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([

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
-    GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
+    dynamics package primarily designed for simulations of proteins, lipids
-    simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
+    and nucleic acids. It was originally developed in the Biophysical
-    department of University of Groningen, and is now maintained by contributors in universities and research centers
+    Chemistry department of University of Groningen, and is now maintained
-    across the world.
+    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.
+    GROMACS is one of the fastest and most popular software packages
-    It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
+    available and can run on CPUs as well as GPUs. It is free, open source
-    released under the GNU Lesser General Public License.
+    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 = []

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'))