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plumed: reworked patching applications, added new version (#5680)

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closes #5506

The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.

All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
This commit is contained in:
Massimiliano Culpo 2017-10-10 21:35:53 +02:00 committed by Todd Gamblin
parent e3053d7425
commit a3bbe066b3
1 changed files with 31 additions and 47 deletions
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78
var/spack/repos/builtin/packages/plumed/package.py
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@ -22,7 +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
import collections
from spack import *
@ -43,6 +43,7 @@ class Plumed(AutotoolsPackage):
homepage = 'http://www.plumed.org/'
url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
version('2.3.3', '9f5729e406e79a06a16976fcb020e024')
version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5')
version('2.2.4', 'afb00da25a3fbd47acf377e53342059d')
version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
@ -73,58 +74,41 @@ class Plumed(AutotoolsPackage):
depends_on('automake', type='build')
depends_on('libtool', type='build')
# Dictionary mapping PLUMED versions to the patches it provides
# interactively
plumed_patches = {
'2.3.0': {
'amber-14': '1',
'gromacs-2016.1': '2',
'gromacs-4.5.7': '3',
'gromacs-5.0.7': '4',
'gromacs-5.1.4': '5',
'lammps-6Apr13': '6',
'namd-2.8': '7',
'namd-2.9': '8',
'espresso-5.0.2': '9'
},
'2.2.4': {
'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'
},
'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'
}
}
force_autoreconf = True
parallel = False
def apply_patch(self, other):
plumed = subprocess.Popen(
[join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'],
stdin=subprocess.PIPE
# The name of MD engines differ slightly from the ones used in Spack
format_strings = collections.defaultdict(
lambda: '{0.name}-{0.version}'
)
opts = Plumed.plumed_patches[str(self.version)]
search = '{0.name}-{0.version}'.format(other)
choice = opts[search] + '\n'
plumed.stdin.write(choice)
plumed.wait()
format_strings['espresso'] = 'q{0.name}-{0.version}'
format_strings['amber'] = '{0.name}{0.version}'
get_md = lambda x: format_strings[x.name].format(x)
# Get available patches
plumed_patch = Executable(
join_path(self.spec.prefix.bin, 'plumed-patch')
)
out = plumed_patch('-q', '-l', output=str)
available = out.split(':')[-1].split()
# Check that `other` is among the patchable applications
if get_md(other) not in available:
msg = '{0.name}@{0.version} is not among the MD engine'
msg += ' that can be patched by {1.name}@{1.version}.\n'
msg += 'Supported engines are:\n'
for x in available:
msg += x + '\n'
raise RuntimeError(msg.format(other, self.spec))
# Call plumed-patch to patch executables
target = format_strings[other.name].format(other)
plumed_patch('-p', '-e', target)
def setup_dependent_package(self, module, dependent_spec):
# Make plumed visible from dependent packages