def dispatch(args):
from yank.yank import Yank # TODO: Fix this awkward import syntax.
store_directory = args['--store']
# Set override options.
options = dict()
# Configure MPI, if requested.
mpicomm = None
if args['--mpi']:
mpicomm = utils.initialize_mpi()
logger.info("Initialized MPI on %d processes." % (mpicomm.size))
# Configure logger
utils.config_root_logger(args['--verbose'], mpicomm=mpicomm,
log_file_path=os.path.join(store_directory, 'run.log'))
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--platform'] not in [None, 'None']:
options['platform'] = openmm.Platform.getPlatformByName(args['--platform'])
if args['--precision']:
# We need to modify the Platform object.
if args['--platform'] is None:
raise Exception("The --platform argument must be specified in order to specify platform precision.")
# Set platform precision.
precision = args['--precision']
platform_name = args['--platform']
logger.info("Setting %s platform to use precision model '%s'." % (platform_name, precision))
if precision is not None:
if platform_name == 'CUDA':
options['platform'].setPropertyDefaultValue('CudaPrecision', precision)
elif platform_name == 'OpenCL':
options['platform'].setPropertyDefaultValue('OpenCLPrecision', precision)
elif platform_name == 'CPU':
if precision != 'mixed':
raise Exception("CPU platform does not support precision model '%s'; only 'mixed' is supported." % precision)
elif platform_name == 'Reference':
if precision != 'double':
raise Exception("Reference platform does not support precision model '%s'; only 'double' is supported." % precision)
else:
raise Exception("Platform selection logic is outdated and needs to be updated to add platform '%s'." % platform_name)
# Create YANK object associated with data storage directory.
yank = Yank(store_directory, mpicomm=mpicomm, **options)
# Set YANK to resume from the store file.
phases = None # By default, resume from all phases found in store_directory
if args['--phase']: phases=[args['--phase']]
yank.resume(phases=phases)
# Run simulation.
yank.run()
return True
assert repex.nsteps_per_iteration == 1000000
assert repex.collision_rate == repex.default_parameters['collision_rate']
@tools.raises(TypeError)
def test_unknown_parameters():
"""Test ReplicaExchange raises exception on wrong initialization."""
ReplicaExchange(store_filename='test', wrong_parameter=False)
#=============================================================================================
# MAIN AND TESTS
#=============================================================================================
if __name__ == "__main__":
# Configure logger.
utils.config_root_logger(False)
# Try MPI, if possible.
try:
mpicomm = utils.initialize_mpi()
if mpicomm.rank == 0:
print("MPI initialized successfully.")
except Exception as e:
print(e)
print("Could not start MPI. Using serial code instead.")
mpicomm = None
# Test simple system of harmonic oscillators.
# Disabled until we fix the test
# test_hamiltonian_exchange(mpicomm)
test_replica_exchange(mpicomm)
def dispatch(args):
from yank.yank import Yank # TODO: Fix this awkward import syntax.
store_directory = args['--store']
# Set override options.
options = dict()
# Configure MPI, if requested.
mpicomm = None
if args['--mpi']:
mpicomm = utils.initialize_mpi()
logger.info("Initialized MPI on %d processes." % (mpicomm.size))
# Configure logger
utils.config_root_logger(args['--verbose'],
mpicomm=mpicomm,
log_file_path=os.path.join(
store_directory, 'run.log'))
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--platform'] not in [None, 'None']:
options['platform'] = openmm.Platform.getPlatformByName(
args['--platform'])
if args['--precision']:
# We need to modify the Platform object.
if args['--platform'] is None:
raise Exception(
"The --platform argument must be specified in order to specify platform precision."
)
# Set platform precision.
precision = args['--precision']
platform_name = args['--platform']
logger.info("Setting %s platform to use precision model '%s'." %
(platform_name, precision))
if precision is not None:
if platform_name == 'CUDA':
options['platform'].setPropertyDefaultValue(
'CudaPrecision', precision)
elif platform_name == 'OpenCL':
options['platform'].setPropertyDefaultValue(
'OpenCLPrecision', precision)
elif platform_name == 'CPU':
if precision != 'mixed':
raise Exception(
"CPU platform does not support precision model '%s'; only 'mixed' is supported."
% precision)
elif platform_name == 'Reference':
if precision != 'double':
raise Exception(
"Reference platform does not support precision model '%s'; only 'double' is supported."
% precision)
else:
raise Exception(
"Platform selection logic is outdated and needs to be updated to add platform '%s'."
% platform_name)
# Create YANK object associated with data storage directory.
yank = Yank(store_directory, mpicomm=mpicomm, **options)
# Set YANK to resume from the store file.
phases = None # By default, resume from all phases found in store_directory
if args['--phase']: phases = [args['--phase']]
yank.resume(phases=phases)
# Run simulation.
yank.run()
return True