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gmxapi-50 enable MPI domain decomposition with plugins #15

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gmxapi-50 enable MPI domain decomposition with plugins #15

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84 changes: 44 additions & 40 deletions tests/test_binding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,13 +233,16 @@ def test_ensemble_potential_nompi():
@withmpi_only
@pytest.mark.usefixtures("cleandir")
def test_ensemble_potential_withmpi():
logger.debug("Entering test_ensemble_potential_withmpi")
import gmx
import os
import shutil
import myplugin

logger.debug("Importing mpi4py.MPI")
from mpi4py import MPI
rank = MPI.COMM_WORLD.Get_rank()
logger.debug("test_ensemble_potential_withmpi on rank {} in directory {}".format(rank, os.getcwd()))

tests_dir = os.path.dirname(__file__)
water = os.path.join(tests_dir, 'data', 'water.gro')
Expand All @@ -250,46 +253,47 @@ def test_ensemble_potential_withmpi():
shutil.copy(water, rank_dir)

# In MPI, this never makes it to grompp. We should get rid of this...
try:
# use GromacsWrapper if available
import gromacs
import gromacs.formats
from gromacs.tools import Solvate as solvate
solvate(o=os.path.join(rank_dir, 'water.gro'), box=[5,5,5])
mdpparams = [('integrator', 'md'),
('nsteps', 1000),
('nstxout', 100),
('nstvout', 100),
('nstfout', 100),
('tcoupl', 'v-rescale'),
('tc-grps', 'System'),
('tau-t', 1),
('ref-t', 298)]
mdp = gromacs.formats.MDP()
for param, value in mdpparams:
mdp[param] = value
mdp.write(os.path.join(rank_dir, 'water.mdp'))
with open(os.path.join(rank_dir, 'input.top'), 'w') as fh:
fh.write("""#include "gromos43a1.ff/forcefield.itp"
#include "gromos43a1.ff/spc.itp"

[ system ]
; Name
spc

[ molecules ]
; Compound #mols
SOL 4055
""")
gromacs.grompp(f=os.path.join(rank_dir, 'water.mdp'),
c=os.path.join(rank_dir, 'water.gro'),
po=os.path.join(rank_dir, 'water.mdp'),
pp=os.path.join(rank_dir, 'water.top'),
o=os.path.join(rank_dir, 'water.tpr'),
p=os.path.join(rank_dir, 'input.top'))
tpr_filename = os.path.join(rank_dir, 'water.tpr')
except:
from gmx.data import tpr_filename
# try:
# # use GromacsWrapper if available
# import gromacs
# import gromacs.formats
# from gromacs.tools import Solvate as solvate
# solvate(o=os.path.join(rank_dir, 'water.gro'), box=[5,5,5])
# mdpparams = [('integrator', 'md'),
# ('nsteps', 1000),
# ('nstxout', 100),
# ('nstvout', 100),
# ('nstfout', 100),
# ('tcoupl', 'v-rescale'),
# ('tc-grps', 'System'),
# ('tau-t', 1),
# ('ref-t', 298)]
# mdp = gromacs.formats.MDP()
# for param, value in mdpparams:
# mdp[param] = value
# mdp.write(os.path.join(rank_dir, 'water.mdp'))
# with open(os.path.join(rank_dir, 'input.top'), 'w') as fh:
# fh.write("""#include "gromos43a1.ff/forcefield.itp"
# #include "gromos43a1.ff/spc.itp"
#
# [ system ]
# ; Name
# spc
#
# [ molecules ]
# ; Compound #mols
# SOL 4055
# """)
# gromacs.grompp(f=os.path.join(rank_dir, 'water.mdp'),
# c=os.path.join(rank_dir, 'water.gro'),
# po=os.path.join(rank_dir, 'water.mdp'),
# pp=os.path.join(rank_dir, 'water.top'),
# o=os.path.join(rank_dir, 'water.tpr'),
# p=os.path.join(rank_dir, 'input.top'))
# tpr_filename = os.path.join(rank_dir, 'water.tpr')
# except:
# from gmx.data import tpr_filename
from gmx.data import tpr_filename
logger.info("Testing plugin potential with input file {}".format(os.path.abspath(tpr_filename)))

assert gmx.version.api_is_at_least(0,0,5)
Expand Down