def test_runner_equals_fake_runner_should_create_fake_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = "fake_runner"
with mock.patch("meld.system.runner.FakeSystemRunner") as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_fake_runner_should_create_fake_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = 'fake_runner'
with mock.patch('meld.system.runner.FakeSystemRunner') as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_openmm_should_create_openmm_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = "openmm"
with mock.patch("meld.system.openmm_runner.runner.OpenMMRunner") as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_openmm_should_create_openmm_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = 'openmm'
with mock.patch('meld.system.runner.OpenMMRunner') as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def launch_multiplex(platform: str,
console_handler: Handler,
debug: bool = False) -> None:
logger.info("Loading data store")
store = vault.DataStore.load_data_store()
#
# Setup logging
#
level = logging.DEBUG if debug else logging.INFO
fmt = "%(asctime)s %(name)s: %(message)s"
datefmt = "%Y-%m-%d %H:%M:%S"
meld_logger = logging.getLogger("meld")
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
handler = logging.FileHandler(filename=os.path.join(
store.log_dir, "remd.log"),
mode="a")
handler.setFormatter(formatter)
handler.setLevel(level)
meld_logger.addHandler(handler)
meld_logger.setLevel(level)
logger.info("Launching replica exchange")
log_versions()
system = store.load_system()
options = store.load_run_options()
system_runner = get_runner(system, options, None, platform)
store.initialize(mode="a")
remd_runner = store.load_remd_runner()
runner = multiplex_runner.MultiplexReplicaExchangeRunner(
remd_runner.n_replicas,
remd_runner.max_steps,
remd_runner.ladder,
remd_runner.adaptor,
remd_runner._step,
)
runner.run(system_runner, store)
def launch_multiplex(console_handler, debug=False):
logger.info('Loading data store')
store = vault.DataStore.load_data_store()
#
# Setup logging
#
level = logging.DEBUG if debug else logging.INFO
fmt = '%(asctime)s %(name)s: %(message)s'
datefmt = '%Y-%m-%d %H:%M:%S'
meld_logger = logging.getLogger('meld')
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
handler = logging.FileHandler(filename='remd.log', mode='a')
handler.setFormatter(formatter)
handler.setLevel(level)
meld_logger.addHandler(handler)
meld_logger.setLevel(level)
logger.info('Launching replica exchange')
log_versions()
system = store.load_system()
options = store.load_run_options()
system_runner = get_runner(system, options, None)
store.initialize(mode='a')
remd_runner = store.load_remd_runner()
runner = multiplex_runner.MultiplexReplicaExchangeRunner(remd_runner.n_replicas, remd_runner.max_steps,
remd_runner.ladder, remd_runner.adaptor,
remd_runner._step)
runner.run(system_runner, store)
def launch_multiplex(console_handler, debug=False):
logger.info('Loading data store')
store = vault.DataStore.load_data_store()
#
# Setup logging
#
level = logging.DEBUG if debug else logging.INFO
fmt = '%(asctime)s %(name)s: %(message)s'
datefmt = '%Y-%m-%d %H:%M:%S'
meld_logger = logging.getLogger('meld')
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
handler = logging.FileHandler(filename='remd.log', mode='a')
handler.setFormatter(formatter)
handler.setLevel(level)
meld_logger.addHandler(handler)
meld_logger.setLevel(level)
logger.info('Launching replica exchange')
log_versions()
system = store.load_system()
options = store.load_run_options()
system_runner = get_runner(system, options, None)
store.initialize(mode='a')
remd_runner = store.load_remd_runner()
runner = multiplex_runner.MultiplexReplicaExchangeRunner(
remd_runner.n_replicas, remd_runner.max_steps, remd_runner.ladder,
remd_runner.adaptor, remd_runner._step)
runner.run(system_runner, store)
def launch(console_handler, debug=False, console_log=False):
logger.info('loading data store')
store = vault.DataStore.load_data_store()
logger.info('initializing communicator')
communicator = store.load_communicator()
communicator.initialize()
#
# setup logging
#
hostname = socket.gethostname()
hostid = '{}:{}'.format(hostname, communicator.rank)
meld_logger = logging.getLogger('meld')
# this filter adds the hostid to each logging record so
# it gets printed out as part of the logging output
hostid_log_filter = util.HostNameContextFilter(hostid)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
if not console_log:
if communicator.is_master():
# start logging server
abort_queue = multiprocessing.Queue()
socket_queue = multiprocessing.Queue()
process = multiprocessing.Process(target=util.configure_logging_and_launch_listener,
args=(hostname, abort_queue, socket_queue))
process.start()
# communicate address to slaves
logger_address = socket_queue.get(block=True, timeout=60)
communicator.broadcast_logger_address_to_slaves(logger_address)
else:
# get port from master
logger_address = communicator.receive_logger_address_from_master()
# create SocketHandler to write logging over network
handler = logging.handlers.SocketHandler(logger_address[0], logger_address[1])
else:
fmt = '%(hostid)s %(asctime)s %(levelname)s %(name)s: %(message)s'.format(hostid)
datefmt = '%Y-%m-%d %H:%M:%S'
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
handler = logging.StreamHandler()
handler.setFormatter(formatter)
meld_logger.addHandler(handler)
handler.addFilter(hostid_log_filter)
level = logging.DEBUG if debug else logging.INFO
handler.setLevel(level)
meld_logger.setLevel(level)
meld_logger.propagate = False
if communicator.is_master():
logger.info('Launching replica exchange on master')
else:
logger.info('Launching replica exchange on slave')
log_versions()
logger.info('Loading system')
system = store.load_system()
logger.info('Loading run options')
options = store.load_run_options()
system_runner = get_runner(system, options, communicator)
if communicator.is_master():
store.initialize(mode='a')
remd_runner = store.load_remd_runner()
remd_runner.run(communicator, system_runner, store)
else:
remd_runner = store.load_remd_runner().to_slave()
remd_runner.run(communicator, system_runner)
if (not console_log) and communicator.is_master():
# pause and then shutdown logging server
abort_queue.put(1)
process.join()
def launch(
platform: str,
console_handler: Handler,
debug: bool = False,
console_log: bool = False,
) -> None:
logger.info("loading data store")
store = vault.DataStore.load_data_store()
logger.info("initializing communicator")
communicator = store.load_communicator()
communicator.initialize()
#
# setup logging
#
hostname = socket.gethostname()
hostid = f"{hostname}:{communicator.rank:03d}"
meld_logger = logging.getLogger("meld")
# this filter adds the hostid to each logging record so
# it gets printed out as part of the logging output
hostid_log_filter = util.HostNameContextFilter(hostid)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
if not console_log:
# setup file
log_path = os.path.join(store.log_dir,
f"remd_{communicator.rank:03d}.log")
handler: Handler = logging.FileHandler(
filename=log_path,
mode="a",
)
else:
fmt = "%(hostid)s %(asctime)s %(levelname)s %(name)s: %(message)s"
fmt = fmt.format(hostid)
datefmt = "%Y-%m-%d %H:%M:%S"
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
handler = logging.StreamHandler()
handler.setFormatter(formatter)
meld_logger.addHandler(handler)
handler.addFilter(hostid_log_filter)
level = logging.DEBUG if debug else logging.INFO
handler.setLevel(level)
meld_logger.setLevel(level)
meld_logger.propagate = False
if communicator.is_leader():
logger.info("Launching replica exchange on leader")
else:
logger.info("Launching replica exchange on follower")
log_versions()
logger.info("Loading system")
system = store.load_system()
logger.info("Loading run options")
options = store.load_run_options()
system_runner = get_runner(system,
options,
comm=communicator,
platform=platform)
if communicator.is_leader():
store.initialize(mode="a")
remd_runner = store.load_remd_runner()
remd_runner.run(communicator, system_runner, store)
else:
remd_runner = store.load_remd_runner().to_follower()
remd_runner.run(communicator, system_runner)
def launch(
console_handler: Handler,
debug: bool = False,
console_log: bool = False,
) -> None:
logger.info("loading data store")
store = vault.DataStore.load_data_store()
logger.info("initializing communicator")
communicator = store.load_communicator()
communicator.initialize()
#
# setup logging
#
hostname = socket.gethostname()
hostid = f"{hostname}:{communicator.rank:03d}"
meld_logger = logging.getLogger("meld")
# this filter adds the hostid to each logging record so
# it gets printed out as part of the logging output
hostid_log_filter = util.HostNameContextFilter(hostid)
# remove the console handler, so that
# we can add a new handler below without
# duplicate logging messages
meld_logger.removeHandler(console_handler)
if not console_log:
if communicator.is_master():
# start logging server
abort_queue: mp.Queue[int] = mp.Queue()
socket_queue: mp.Queue[Tuple[str, int]] = mp.Queue()
process = mp.Process(
target=util.configure_logging_and_launch_listener,
args=(hostname, abort_queue, socket_queue),
)
process.start()
# communicate address to slaves
logger_address = socket_queue.get(block=True, timeout=60)
communicator.broadcast_logger_address_to_slaves(logger_address)
else:
# get port from master
logger_address = communicator.receive_logger_address_from_master()
# create SocketHandler to write logging over network
handler: Handler = logging.handlers.SocketHandler(
logger_address[0], logger_address[1])
else:
fmt = "%(hostid)s %(asctime)s %(levelname)s %(name)s: %(message)s"
fmt = fmt.format(hostid)
datefmt = "%Y-%m-%d %H:%M:%S"
formatter = logging.Formatter(fmt=fmt, datefmt=datefmt)
handler = logging.StreamHandler()
handler.setFormatter(formatter)
meld_logger.addHandler(handler)
handler.addFilter(hostid_log_filter)
level = logging.DEBUG if debug else logging.INFO
handler.setLevel(level)
meld_logger.setLevel(level)
meld_logger.propagate = False
if communicator.is_master():
logger.info("Launching replica exchange on master")
else:
logger.info("Launching replica exchange on slave")
log_versions()
logger.info("Loading system")
system = store.load_system()
logger.info("Loading run options")
options = store.load_run_options()
system_runner = get_runner(system, options, communicator)
if communicator.is_master():
store.initialize(mode="a")
remd_runner = store.load_remd_runner()
remd_runner.run(communicator, system_runner, store)
else:
remd_runner = store.load_remd_runner().to_slave()
remd_runner.run(communicator, system_runner)
if (not console_log) and communicator.is_master():
# pause and then shutdown logging server
abort_queue.put(1)
process.join()
