def Calculate(self, varsByCalc, params=None):
"""
Calculate model predictions for everything in varsByCalc.
varsByCalc is a dictionary of the form:
dict[calc name][dep var] = ind var
The return dictionary is of the form:
dictionary[calc name][dep var][ind var] = result
"""
if params is not None:
self.params.update(params)
results = {}
calcs_to_do = list(varsByCalc.keys())
# Record which calculation each node is doing
calc_assigned = {}
while calcs_to_do:
# The number of calculations to do this round. We want to use
# all the processors if possible.
len_this_block = min(SloppyCell.num_procs, len(calcs_to_do))
for worker in range(1, len_this_block):
calc = calcs_to_do.pop()
calc_assigned[worker] = calc
logger.debug('Assigning calculation %s to worker %i.' %
(calc, worker))
command = 'Network.calculate(net, vars, params)'
args = {
'net': self.get(calc),
'vars': varsByCalc[calc],
'params': self.params
}
comm.send((command, args), dest=worker)
# The master does his share here
calc = calcs_to_do.pop()
# print
# We use the finally statement because we want to ensure that we
# *always* wait for replies from the workers, even if the master
# encounters an exception in his evaluation.
try:
results[calc] = self.get(calc).calculate(
varsByCalc[calc], self.params)
finally:
# Collect results from the workers
for worker in range(1, len_this_block):
logger.debug('Receiving result from worker %i.' % worker)
results[calc_assigned[worker]] = comm.recv(source=worker)
# If the master encounts an exception, we'll break out of the
# function ***here***
# Check the results we received. If any is a SloppyCellException,
# reraise it.
for val in results.values():
if isinstance(val, Utility.SloppyCellException):
raise val
return results
def ensemble_trajs(net, times, ensemble):
"""
Return a list of trajectories evaluated at times for all parameter sets
in ensemble.
"""
traj_set = []
elems_assigned = [ensemble[node::num_procs] for node in range(num_procs)]
for worker in range(1, num_procs):
command = 'Ensembles.few_ensemble_trajs(net, times, elements)'
args = {'net': net, 'times': times, 'elements': elems_assigned[worker]}
comm.send((command, args), dest=worker)
traj_set = few_ensemble_trajs(net, times, elems_assigned[0])
for worker in range(1, num_procs):
traj_set.extend(comm.recv(source=worker))
return traj_set
import SloppyCell.Utility as Utility
class Statement(object):
"""
Class for sending Python statements to workers.
"""
def __init__(self, statement, locals={}):
self.statement = statement
self.locals = locals
while my_rank != 0:
# Wait for a message
message = comm.recv(source=0)
# If the message is a SystemExit exception, exit the code.
if isinstance(message, SystemExit):
sys.exit()
# Exception handling:
# If we catch a SloppyCellException during a eval(), it's probably just
# a numerical issue so we just pass it back to the master to deal with.
# Note that we don't catch SloppyCellExceptions for exec'd things.
# This is because exec'd things shouldn't return anything, thus the
# master won't be waiting for a reply.
# If we catch any other exception, it's probably a bug in the code. Print
# a nice traceback, save results, and exit the code.
try:
if isinstance(message, Statement):
def integrate_sensitivity(net, times, params=None, rtol=None,
fill_traj=False, return_derivs=False,
redirect_msgs=True):
logger.debug('Entering integrate_sens on node %i' % my_rank)
times = np.array(times)
net.compile()
if times[0] == 0:
net.resetDynamicVariables()
if params is not None:
net.update_optimizable_vars(params)
# Assigned variables to process on each node.
vars_assigned = dict([(node, list(net.optimizableVars.keys())[node::num_procs])
for node in range(num_procs)])
# Send out jobs for workers
for worker in range(1, num_procs):
logger.debug('Sending to worker %i: %s' % (worker,
str(vars_assigned[worker])))
command = 'Dynamics.integrate_sens_subset(net, times,'\
'rtol, fill_traj, opt_vars, return_derivs, redirect_msgs=redir)'
args = {'net':net, 'times':times, 'rtol':rtol, 'fill_traj':fill_traj,
'opt_vars':vars_assigned[worker], 'return_derivs':return_derivs,
'redir': redirect_msgs}
comm.send((command, args), dest=worker)
logger.debug('Master doing vars %s' % str(vars_assigned[0]))
try:
result = integrate_sens_subset(net, times, rtol, fill_traj,
vars_assigned[0], return_derivs,
redirect_msgs=redirect_msgs)
except Utility.SloppyCellException:
# If the master encounters an exception, we must still wait and get
# replies from all the workers (even if we do nothing with them) so
# that communication stays synchronized.
for worker in range(1, num_procs):
comm.recv(source=worker)
raise
# Begin pulling results together...
tout = result[0]
# Build the yout array
n_dyn, n_opt = len(net.dynamicVars), len(net.optimizableVars)
yout = np.zeros((len(tout), n_dyn * (n_opt+ 1)), scipy.float_)
# We use the master's result for the non-sensitivity values
yout[:, :n_dyn] = result[1][:, :n_dyn]
if return_derivs:
youtdt = np.zeros((len(tout), n_dyn * (n_opt+ 1)), scipy.float_)
youtdt[:, :n_dyn] = result[2][:, :n_dyn]
else:
youtdt = None
# We use the master's result for events that occurred
event_info = result[-2]
events_occurred = result[-1]
# Copy the sensitivity results into yout and (if necessary) youtdt
# We don't need events_occurred here, because we already have it.
_parse_sens_result(result, net, vars_assigned[0], yout, youtdt)
# Now when we listen to the worker's replies, we store any exception they
# return in exception_raised. We'll reraise that exception after getting
# replies from all the workers.
exception_raised = None
for worker in range(1, num_procs):
logger.debug('Receiving result from worker %i.' % worker)
result = comm.recv(source=worker)
if isinstance(result, Utility.SloppyCellException):
exception_raised = result
continue
if vars_assigned[worker]:
_parse_sens_result(result, net, vars_assigned[worker], yout, youtdt,
events_occurred)
if exception_raised:
raise exception_raised
ddv_dpTrajectory = Trajectory_mod.Trajectory(net, is_sens=True,
holds_dt=return_derivs)
if return_derivs:
yout = np.concatenate((yout, youtdt), axis=1)
ddv_dpTrajectory.appendSensFromODEINT(tout, yout, holds_dt = return_derivs)
ddv_dpTrajectory.events_occurred = events_occurred
ddv_dpTrajectory.event_info = event_info
net.trajectory = ddv_dpTrajectory
return ddv_dpTrajectory
def hessian_log_params(sens_traj, data_ids=None, opt_ids=None,
fixed_sf=False, return_dict=False,
uncert_func=typ_val_uncert(1.0, 1e-14)):
"""
Calculate the "perfect data" hessian in log parameters given a sensitivity
trajectory.
sens_traj Sensitivity trajectory of Network being considered.
data_ids A sequence of variable id's to assume we have data for. If
data_ids is None, all dynamic and assigned variables will be
used.
opt_ids A sequence of parameter id's to calculate derivatives with
respect to. The hessian is (len(opt_ids) x len(opt_ids)).
If opt_ids is None, all optimizable variables are considered.
fixed_sf If True, calculate the hessian assuming fixed scale factors.
return_dict If True, returned values are (hess, hess_dict). hess_dict is a
dictionary keyed on the elements of data_ids; each corresponding
value is the hessian assuming data only on a single variable.
hess is the sum of all these hessians
uncert_func Function that takes in a trajectory and a variable id and
returns what uncertainty should be assumed for that variable,
either as a scalar or a list the same length as the trajectory.
"""
if data_ids is None:
data_ids = sens_traj.dynamicVarKeys + sens_traj.assignedVarKeys
if opt_ids is None:
opt_ids = sens_traj.optimizableVarKeys
data_sigmas = {}
for data_id in data_ids:
ds = uncert_func(sens_traj, data_id)
if np.isscalar(ds):
ds = np.zeros(len(sens_traj), scipy.float_) + ds
data_sigmas[data_id] = ds
vars_assigned = [data_ids[node::num_procs] for node in range(num_procs)]
for worker in range(1, num_procs):
logger.debug('Sending to worker %i.' % worker)
# reduce the amount we have to pickle
# The only things the worker needs in the sens_traj are those that
# refer to data_ids it has to deal with.
vars_needed = set(sens_traj.optimizableVarKeys)
vars_needed.union_update(vars_assigned[worker])
for var in vars_assigned[worker]:
vars_needed.union_update([(var, ov) for ov in opt_ids])
worker_traj = sens_traj.copy_subset(vars_needed)
# And the only uncertainties it needs have to do with those data_ids
worker_ds = dict([(var, data_sigmas[var])
for var in vars_assigned[worker]])
command = 'PerfectData.compute_sf_LMHessian_conts(sens_traj, data_ids,'\
'data_sigmas, opt_ids, fixed_sf)'
args = {'sens_traj': worker_traj, 'data_ids': vars_assigned[worker],
'data_sigmas': worker_ds, 'opt_ids': opt_ids,
'fixed_sf': fixed_sf}
comm.send((command, args), dest=worker)
hess_dict = compute_sf_LMHessian_conts(sens_traj, vars_assigned[0],
data_sigmas, opt_ids, fixed_sf)
for worker in range(1, num_procs):
logger.debug('Receiving from worker %i.' % worker)
hess_dict.update(comm.recv(source=worker))
hess = np.sum(list(hess_dict.values()), axis=0)
if return_dict:
return hess, hess_dict
else:
return hess