Merge pull request #1 from ARCCA/plumed

Plumed

etc/spack/packages.yaml

+packages:
+  intelmpi:
+    paths:
+      intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024/intel64
+    buildable: False
+#  all:
+#    providers:
+#      mpi: [intelmpi]

var/spack/repos/builtin/packages/intelmpi/package.py

+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# 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 Intelmpi(Package):
+    """Intel MPI"""
+
+    homepage = "http://www.example.com"
+    url      = "https://software.intel.com/en-us/intel-mpi-library"
+
+    version('4.1.0')
+
+    # Provides a virtual dependency 'mpi'
+    provides('mpi')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+        # NOTE: Need to find a better way of setting this compiler argument
+        # which is only required when building packages with intelmpi.
+        spack_env.set('CXXFLAGS', '-DMPICH_IGNORE_CXX_SEEK')
+
+    def setup_dependent_package(self, module, dep_spec):
+        self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
+        self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')

var/spack/repos/builtin/packages/plumed/package.py

@@ -41,14 +41,24 @@ class Plumed(Package):
     and C/C++ codes.
     """
     homepage = 'http://www.plumed.org/'
-    url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
+    url = 'https://github.com/plumed/plumed2'
 
-    version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
+    version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3')
 
+    # Variants. PLUMED by default builds a number of optional modules.
+    # The ones listed here are not built by default for various reasons,
+    # such as stability, lack of testing, or lack of demand.
+    variant('crystallization', default=False,
+            description='Build support for optional crystallization module.')
+    variant('imd', default=False,
+            description='Build support for optional imd module.')
+    variant('manyrestraints', default=False,
+            description='Build support for optional manyrestraints module.')
     variant('shared', default=True, description='Builds shared libraries')
     variant('mpi', default=True, description='Activates MPI support')
     variant('gsl', default=True, description='Activates GSL support')
 
+    # Dependencies. LAPACK and BLAS are recommended but not essential.
     depends_on('zlib')
     depends_on('blas')
     depends_on('lapack')
@@ -96,17 +106,45 @@ def install(self, spec, prefix):
         # with MPI you should use:
         #
         # > ./configure CXX="$MPICXX"
-        configure_opts = [
-            'CXX={0}'.format(spec['mpi'].mpicxx)
-        ] if '+mpi' in self.spec else []
+        configure_opts = ['--prefix=' + prefix]
 
+        # If using MPI then ensure the correct compiler wrapper is used.
+        if '+mpi' in spec:
+            configure_opts.extend([
+                '--enable-mpi',
+                'CXX={0}'.format(spec['mpi'].mpicxx)
+            ])
+
+            # If the MPI dependency is provided by the intelmpi package then
+            # the following additional argument is required to allow it to
+            # build.
+            if spec.satisfies('^intelmpi'):
+                configure_opts.extend([
+                    'STATIC_LIBS=-mt_mpi'
+                ])
+
+        # Additional arguments
         configure_opts.extend([
-            '--prefix={0}'.format(prefix),
             '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'),
-            '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'),
             '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no')
         ])
 
+        # Construct list of optional modules
+        module_opts = []
+        module_opts.extend([
+            '+crystallization' if (
+                '+crystallization' in spec) else '-crystallization',
+            '+imd' if '+imd' in spec else '-imd',
+            '+manyrestraints' if (
+                '+manyrestraints' in spec) else '-manyrestraints'
+        ])
+
+        # If we have specified any optional modules then add the argument to
+        # enable or disable them.
+        if module_opts:
+            configure_opts.extend([
+                '--enable-modules={0}'.format("".join(module_opts))])
+
         configure(*configure_opts)
         make()
         make('install')