w_states
usage:
w_states [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version]
[--show | --append | --replace] [--bstate-file BSTATE_FILE] [--bstate BSTATES]
[--tstate-file TSTATE_FILE] [--tstate TSTATES]
[--serial | --parallel | --work-manager WORK_MANAGER] [--n-workers N_WORKERS]
[--zmq-mode MODE] [--zmq-comm-mode COMM_MODE] [--zmq-write-host-info INFO_FILE]
[--zmq-read-host-info INFO_FILE] [--zmq-upstream-rr-endpoint ENDPOINT]
[--zmq-upstream-ann-endpoint ENDPOINT] [--zmq-downstream-rr-endpoint ENDPOINT]
[--zmq-downstream-ann-endpoint ENDPOINT] [--zmq-master-heartbeat MASTER_HEARTBEAT]
[--zmq-worker-heartbeat WORKER_HEARTBEAT] [--zmq-timeout-factor FACTOR]
[--zmq-startup-timeout STARTUP_TIMEOUT] [--zmq-shutdown-timeout SHUTDOWN_TIMEOUT]
Display or manipulate basis (initial) or target (recycling) states for a WEST simulation. By default,
states are displayed (or dumped to files). If --replace
is specified, all basis/target states are
replaced for the next iteration. If --append
is specified, the given target state(s) are appended to
the list for the next iteration. Appending basis states is not permitted, as this would require
renormalizing basis state probabilities in ways that may be error-prone. Instead, use w_states --show
--bstate-file=bstates.txt
and then edit the resulting bstates.txt
file to include the new desired
basis states, then use w_states --replace --bstate-file=bstates.txt
to update the WEST HDF5 file
appropriately.
optional arguments:
-h, --help show this help message and exit
--bstate-file BSTATE_FILE
Read (--append/--replace) or write (--show) basis state names, probabilities, and
data references from/to BSTATE_FILE.
--bstate BSTATES Add the given basis state (specified as a string 'label,probability[,auxref]') to
the list of basis states (after those specified in --bstate-file, if any). This
argument may be specified more than once, in which case the given states are
appended in the order they are given on the command line.
--tstate-file TSTATE_FILE
Read (--append/--replace) or write (--show) target state names and representative
progress coordinates from/to TSTATE_FILE
--tstate TSTATES Add the given target state (specified as a string 'label,pcoord0[,pcoord1[,...]]')
to the list of target states (after those specified in the file given by
--tstates-from, if any). This argument may be specified more than once, in which
case the given states are appended in the order they appear on the command line.
general options:
-r RCFILE, --rcfile RCFILE
use RCFILE as the WEST run-time configuration file (default: west.cfg)
--quiet emit only essential information
--verbose emit extra information
--debug enable extra checks and emit copious information
--version show program's version number and exit
modes of operation:
--show Display current basis/target states (or dump to files).
--append Append the given basis/target states to those currently in use.
--replace Replace current basis/target states with those specified.
parallelization options:
--serial run in serial mode
--parallel run in parallel mode (using processes)
--work-manager WORK_MANAGER
use the given work manager for parallel task distribution. Available work managers
are ('serial', 'threads', 'processes', 'zmq'); default is 'serial'
--n-workers N_WORKERS
Use up to N_WORKERS on this host, for work managers which support this option. Use
0 for a dedicated server. (Ignored by work managers which do not support this
option.)
options for ZeroMQ (“zmq”) work manager (master or node):
--zmq-mode MODE Operate as a master (server) or a node (workers/client). "server" is a deprecated
synonym for "master" and "client" is a deprecated synonym for "node".
--zmq-comm-mode COMM_MODE
Use the given communication mode -- TCP or IPC (Unix-domain) -- sockets for
communication within a node. IPC (the default) may be more efficient but is not
available on (exceptionally rare) systems without node-local storage (e.g. /tmp);
on such systems, TCP may be used instead.
--zmq-write-host-info INFO_FILE
Store hostname and port information needed to connect to this instance in
INFO_FILE. This allows the master and nodes assisting in coordinating the
communication of other nodes to choose ports randomly. Downstream nodes read this
file with --zmq-read-host-info and know where how to connect.
--zmq-read-host-info INFO_FILE
Read hostname and port information needed to connect to the master (or other
coordinating node) from INFO_FILE. This allows the master and nodes assisting in
coordinating the communication of other nodes to choose ports randomly, writing
that information with --zmq-write-host-info for this instance to read.
--zmq-upstream-rr-endpoint ENDPOINT
ZeroMQ endpoint to which to send request/response (task and result) traffic toward
the master.
--zmq-upstream-ann-endpoint ENDPOINT
ZeroMQ endpoint on which to receive announcement (heartbeat and shutdown
notification) traffic from the master.
--zmq-downstream-rr-endpoint ENDPOINT
ZeroMQ endpoint on which to listen for request/response (task and result) traffic
from subsidiary workers.
--zmq-downstream-ann-endpoint ENDPOINT
ZeroMQ endpoint on which to send announcement (heartbeat and shutdown
notification) traffic toward workers.
--zmq-master-heartbeat MASTER_HEARTBEAT
Every MASTER_HEARTBEAT seconds, the master announces its presence to workers.
--zmq-worker-heartbeat WORKER_HEARTBEAT
Every WORKER_HEARTBEAT seconds, workers announce their presence to the master.
--zmq-timeout-factor FACTOR
Scaling factor for heartbeat timeouts. If the master doesn't hear from a worker in
WORKER_HEARTBEAT*FACTOR, the worker is assumed to have crashed. If a worker
doesn't hear from the master in MASTER_HEARTBEAT*FACTOR seconds, the master is
assumed to have crashed. Both cases result in shutdown.
--zmq-startup-timeout STARTUP_TIMEOUT
Amount of time (in seconds) to wait for communication between the master and at
least one worker. This may need to be changed on very large, heavily-loaded
computer systems that start all processes simultaneously.
--zmq-shutdown-timeout SHUTDOWN_TIMEOUT
Amount of time (in seconds) to wait for workers to shut down.
westpa.cli.core.w_states module
- westpa.cli.core.w_states.make_work_manager()
Using cues from the environment, instantiate a pre-configured work manager.
- class westpa.cli.core.w_states.Segment(n_iter=None, seg_id=None, weight=None, endpoint_type=None, parent_id=None, wtg_parent_ids=None, pcoord=None, status=None, walltime=None, cputime=None, data=None)
Bases:
object
A class wrapping segment data that must be passed through the work manager or data manager. Most fields are self-explanatory. One item worth noting is that a negative parent ID means that the segment starts from the initial state with ID -(segment.parent_id+1)
- SEG_STATUS_UNSET = 0
- SEG_STATUS_PREPARED = 1
- SEG_STATUS_COMPLETE = 2
- SEG_STATUS_FAILED = 3
- SEG_INITPOINT_UNSET = 0
- SEG_INITPOINT_CONTINUES = 1
- SEG_INITPOINT_NEWTRAJ = 2
- SEG_ENDPOINT_UNSET = 0
- SEG_ENDPOINT_CONTINUES = 1
- SEG_ENDPOINT_MERGED = 2
- SEG_ENDPOINT_RECYCLED = 3
- statuses = {'SEG_STATUS_COMPLETE': 2, 'SEG_STATUS_FAILED': 3, 'SEG_STATUS_PREPARED': 1, 'SEG_STATUS_UNSET': 0}
- initpoint_types = {'SEG_INITPOINT_CONTINUES': 1, 'SEG_INITPOINT_NEWTRAJ': 2, 'SEG_INITPOINT_UNSET': 0}
- endpoint_types = {'SEG_ENDPOINT_CONTINUES': 1, 'SEG_ENDPOINT_MERGED': 2, 'SEG_ENDPOINT_RECYCLED': 3, 'SEG_ENDPOINT_UNSET': 0}
- status_names = {0: 'SEG_STATUS_UNSET', 1: 'SEG_STATUS_PREPARED', 2: 'SEG_STATUS_COMPLETE', 3: 'SEG_STATUS_FAILED'}
- initpoint_type_names = {0: 'SEG_INITPOINT_UNSET', 1: 'SEG_INITPOINT_CONTINUES', 2: 'SEG_INITPOINT_NEWTRAJ'}
- endpoint_type_names = {0: 'SEG_ENDPOINT_UNSET', 1: 'SEG_ENDPOINT_CONTINUES', 2: 'SEG_ENDPOINT_MERGED', 3: 'SEG_ENDPOINT_RECYCLED'}
- static initial_pcoord(segment)
Return the initial progress coordinate point of this segment.
- static final_pcoord(segment)
Return the final progress coordinate point of this segment.
- property initpoint_type
- property initial_state_id
- property status_text
- property endpoint_type_text
- class westpa.cli.core.w_states.BasisState(label, probability, pcoord=None, auxref=None, state_id=None)
Bases:
object
Describes an basis (micro)state. These basis states are used to generate initial states for new trajectories, either at the beginning of the simulation (i.e. at w_init) or due to recycling.
- Variables:
state_id – Integer identifier of this state, usually set by the data manager.
label – A descriptive label for this microstate (may be empty)
probability – Probability of this state to be selected when creating a new trajectory.
pcoord – The representative progress coordinate of this state.
auxref – A user-provided (string) reference for locating data associated with this state (usually a filesystem path).
- classmethod states_to_file(states, fileobj)
Write a file defining basis states, which may then be read by states_from_file().
- classmethod states_from_file(statefile)
Read a file defining basis states. Each line defines a state, and contains a label, the probability, and optionally a data reference, separated by whitespace, as in:
unbound 1.0
or:
unbound_0 0.6 state0.pdb unbound_1 0.4 state1.pdb
- as_numpy_record()
Return the data for this state as a numpy record array.
- class westpa.cli.core.w_states.TargetState(label, pcoord, state_id=None)
Bases:
object
Describes a target state.
- Variables:
state_id – Integer identifier of this state, usually set by the data manager.
label – A descriptive label for this microstate (may be empty)
pcoord – The representative progress coordinate of this state.
- classmethod states_to_file(states, fileobj)
Write a file defining basis states, which may then be read by states_from_file().
- classmethod states_from_file(statefile, dtype)
Read a file defining target states. Each line defines a state, and contains a label followed by a representative progress coordinate value, separated by whitespace, as in:
bound 0.02
for a single target and one-dimensional progress coordinates or:
bound 2.7 0.0 drift 100 50.0
for two targets and a two-dimensional progress coordinate.
- westpa.cli.core.w_states.entry_point()
- westpa.cli.core.w_states.initialize(mode, bstates, _bstate_file, tstates, _tstate_file)