From 3edfa390f7abc902cbb1a2c66423f5228cd7b467 Mon Sep 17 00:00:00 2001
From: Andrew Williams <williamsa89@cardiff.ac.uk>
Date: Mon, 15 Aug 2016 11:19:40 +0100
Subject: [PATCH] Basic package file for plumed and boilerplate for external
intel mpi
---
etc/spack/packages.yaml | 5 +
.../builtin/packages/intelmpi/package.py | 17 +++
.../repos/builtin/packages/plumed/package.py | 100 +++++-------------
3 files changed, 46 insertions(+), 76 deletions(-)
create mode 100644 etc/spack/packages.yaml
create mode 100644 var/spack/repos/builtin/packages/intelmpi/package.py
diff --git a/etc/spack/packages.yaml b/etc/spack/packages.yaml
new file mode 100644
index 0000000000..41d8c5f9f6
--- /dev/null
+++ b/etc/spack/packages.yaml
@@ -0,0 +1,5 @@
+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
+ buildable: False
diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py
new file mode 100644
index 0000000000..16cfbab260
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intelmpi/package.py
@@ -0,0 +1,17 @@
+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 install(self, spec, prefix):
+# configure("--prefix=%s" % prefix)
+# make()
+# make("install")
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index b670b4c2b8..b179076b7f 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -22,91 +22,39 @@
# 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
-
+#
+# This is a template package file for Spack. We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+# spack install plumed
+#
+# You can edit this file again by typing:
+#
+# spack edit plumed
+#
+# See the Spack documentation for more information on packaging.
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
from spack import *
class Plumed(Package):
"""PLUMED is an open source library for free energy calculations in
- molecular systems which works together with some of the most popular
- molecular dynamics engines.
-
- Free energy calculations can be performed as a function of many order
- parameters with a particular focus on biological problems, using state
- of the art methods such as metadynamics, umbrella sampling and
- Jarzynski-equation based steered MD.
+ molecular systems which works together with some of the most popular
+ molecular dynamics engines."""
- The software, written in C++, can be easily interfaced with both fortran
- and C/C++ codes.
- """
- homepage = 'http://www.plumed.org/'
- url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
+ # FIXME: Add a proper url for your package's homepage here.
+ homepage = "http://www.plumed.org/home"
+ 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')
- variant('shared', default=True, description='Builds shared libraries')
- variant('mpi', default=True, description='Activates MPI support')
- variant('gsl', default=True, description='Activates GSL support')
-
- depends_on('zlib')
- depends_on('blas')
- depends_on('lapack')
-
- 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'))
+ # FIXME: Add additional dependencies if required.
+ depends_on('intelmpi')
def install(self, spec, prefix):
- # From plumed docs :
- # Also consider that this is different with respect to what some other
- # configure script does in that variables such as MPICXX are
- # completely ignored here. In case you work on a machine where CXX is
- # set to a serial compiler and MPICXX to a MPI compiler, to compile
- # with MPI you should use:
- #
- # > ./configure CXX="$MPICXX"
- configure_opts = [
- 'CXX={0}'.format(spec['mpi'].mpicxx)
- ] if '+mpi' in self.spec else []
-
- 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')
- ])
-
- configure(*configure_opts)
+ # FIXME: Unknown build system
make()
make('install')
--
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