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raise Exception("Platform selection logic is outdated and needs to be updated to add platform '%s'."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
def dispatch(args):
from yank.yank import Yank # TODO: Fix this awkward import syntax.
# Create YANK object associated with data storage directory.
store_directory = args["--store"]
yank = Yank(store_directory)
# Set override options.
options = dict()
if args["--iterations"]:
options["niterations"] = int(args["--iterations"])
if args["--verbose"]:
options["verbose"] = True
if args["--online-analysis"]:
options["online_analysis"] = True
if args["--platform"] != "None":
options["platform"] = openmm.Platform.getPlatformByName(args["--platform"])
# 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)
# Configure MPI, if requested.
mpicomm = None
if args["--mpi"]:
# Initialize MPI.
from mpi4py import MPI
hostname = os.uname()[1]
if not MPI.COMM_WORLD.rank == 0:
yank.verbose = False
MPI.COMM_WORLD.barrier()
if MPI.COMM_WORLD.rank == 0:
print "Initialized MPI on %d processes." % (MPI.COMM_WORLD.size)
mpicomm = MPI
# Run simulation.
yank.run(mpicomm, options=options)
return True
def dispatch(args):
from yank.yank import Yank # TODO: Fix this awkward import syntax.
# Create YANK object associated with data storage directory.
store_directory = args['--store']
yank = Yank(store_directory)
# Set override options.
options = dict()
if args['--iterations']:
options['niterations'] = int(args['--iterations'])
if args['--verbose']:
options['verbose'] = True
if args['--online-analysis']:
options['online_analysis'] = True
if args['--platform'] != 'None':
options['platform'] = openmm.Platform.getPlatformByName(args['--platform'])
# 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)
# Configure MPI, if requested.
mpicomm = None
if args['--mpi']:
# Initialize MPI.
from mpi4py import MPI
hostname = os.uname()[1]
if not MPI.COMM_WORLD.rank == 0:
yank.verbose = False
MPI.COMM_WORLD.barrier()
if MPI.COMM_WORLD.rank == 0: print "Initialized MPI on %d processes." % (MPI.COMM_WORLD.size)
mpicomm = MPI
# Run simulation.
yank.run(mpicomm, options=options)
return True
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']:
# Initialize MPI.
from mpi4py import MPI
hostname = os.uname()[1]
MPI.COMM_WORLD.barrier()
logger.info("Initialized MPI on %d processes." % (MPI.COMM_WORLD.size))
mpicomm = MPI.COMM_WORLD
# 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
