def init_stage(homepath,
step,
stage,
model,
n_jobs=1,
progressbar=False,
update=None,
rm_flag=False):
"""
Examine starting point of sampling, reload stages and initialise steps.
"""
if stage is not None:
if stage == '0':
# continue or start initial stage
step.stage = int(stage)
stage_path = os.path.join(homepath, 'stage_%i' % step.stage)
draws = 1
elif stage == 'final':
# continue sampling final stage
last = backend.get_highest_sampled_stage(homepath)
logger.info('Loading parameters from completed stage_%i' % last)
project_dir = os.path.dirname(homepath)
mode = os.path.basename(homepath)
step, updates = backend.load_sampler_params(
project_dir, str(last), mode)
if update is not None:
update.apply(updates)
stage_path = os.path.join(homepath, 'stage_final')
draws = step.n_steps
else:
# continue sampling intermediate
stage = int(stage)
logger.info('Loading parameters from completed stage_%i' %
(stage - 1))
project_dir = os.path.dirname(homepath)
mode = os.path.basename(homepath)
step, updates = backend.load_sampler_params(
project_dir, str(stage - 1), mode)
if update is not None:
update.apply(updates)
step.stage += 1
stage_path = os.path.join(homepath, 'stage_%i' % step.stage)
draws = step.n_steps
if rm_flag:
chains = None
if os.path.exists(stage_path):
logger.info('Removing previous sampling results ... '
'%s' % stage_path)
shutil.rmtree(stage_path)
else:
with model:
if os.path.exists(stage_path):
# load incomplete stage results
logger.info('Reloading existing results ...')
mtrace = backend.load(stage_path, model=model)
if len(mtrace.chains) > 0:
# continue sampling if traces exist
logger.info('Checking for corrupted files ...')
chains = backend.check_multitrace(
mtrace, draws=draws, n_chains=step.n_chains)
rest = len(chains) % n_jobs
if rest > 0.:
logger.info('Fixing %i chains ...' % rest)
rest_chains = utility.split_off_list(chains, rest)
# process traces that are not a multiple of n_jobs
sample_args = {
'draws': draws,
'step': step,
'stage_path': stage_path,
'progressbar': progressbar,
'model': model,
'n_jobs': rest,
'chains': rest_chains
}
_iter_parallel_chains(**sample_args)
logger.info('Back to normal!')
else:
logger.info('Init new trace!')
chains = None
else:
logger.info('Init new trace!')
chains = None
else:
raise Exception('stage has to be not None!')
return chains, step, update
def iter_parallel_chains(draws,
step,
stage_path,
progressbar,
model,
n_jobs,
chains=None,
initializer=None,
initargs=(),
chunksize=None):
"""
Do Metropolis sampling over all the chains with each chain being
sampled 'draws' times. Parallel execution according to n_jobs.
If jobs hang for any reason they are being killed after an estimated
timeout. The chains in question are being rerun and the estimated timeout
is added again.
Parameters
----------
draws : int
number of steps that are taken within each Markov Chain
step : step object of the sampler class, e.g.:
:class:`beat.sampler.Metropolis`, :class:`beat.sampler.SMC`
stage_path : str
with absolute path to the directory where to store the sampling results
progressbar : boolean
flag for displaying a progressbar
model : :class:`pymc3.model.Model` instance
holds definition of the forward problem
n_jobs : int
number of jobs to run in parallel, must not be higher than the
number of CPUs
chains : list
of integers to the chain numbers, if None then all chains from the
step object are sampled
initializer : function
to run before execution of each sampling process
initargs : tuple
of arguments for the initializer
chunksize : int
number of chains to sample within each process
Returns
-------
MultiTrace object
"""
timeout = 0
if chains is None:
chains = list(range(step.n_chains))
n_chains = len(chains)
if n_chains == 0:
mtrace = backend.load_multitrace(dirname=stage_path, model=model)
# while is necessary if any worker times out - rerun in case
while n_chains > 0:
trace_list = []
logger.info('Initialising %i chain traces ...' % n_chains)
for chain in chains:
trace_list.append(backend.TextChain(stage_path, model=model))
max_int = np.iinfo(np.int32).max
random_seeds = [randint(max_int) for _ in range(n_chains)]
work = [
(draws, step, step.population[step.resampling_indexes[chain]],
trace, chain, None, progressbar, model, rseed)
for chain, rseed, trace in zip(chains, random_seeds, trace_list)
]
tps = step.time_per_sample(np.minimum(n_jobs, 10))
logger.info('Serial time per sample: %f' % tps)
if chunksize is None:
if draws < 10:
chunksize = int(np.ceil(float(n_chains) / n_jobs))
elif draws > 10 and tps < 1.:
chunksize = int(np.ceil(float(n_chains) / n_jobs))
else:
chunksize = n_jobs
timeout += int(np.ceil(tps * draws)) * n_jobs + 10
if n_jobs > 1:
shared_params = [
sparam for sparam in step.logp_forw.get_shared()
if sparam.name in parallel._tobememshared
]
logger.info('Data to be memory shared: %s' %
list2string(shared_params))
if len(shared_params) > 0:
if len(parallel._shared_memory.keys()) == 0:
logger.info('Putting data into shared memory ...')
parallel.memshare_sparams(shared_params)
else:
logger.info('Data already in shared memory!')
else:
logger.info('No data to be memshared!')
else:
logger.info('Not using shared memory.')
p = parallel.paripool(_sample,
work,
chunksize=chunksize,
timeout=timeout,
nprocs=n_jobs,
initializer=initializer,
initargs=initargs)
logger.info('Sampling ...')
for res in p:
pass
# return chain indexes that have been corrupted
mtrace = backend.load_multitrace(dirname=stage_path, model=model)
corrupted_chains = backend.check_multitrace(mtrace,
draws=draws,
n_chains=step.n_chains)
n_chains = len(corrupted_chains)
if n_chains > 0:
logger.warning('%i Chains not finished sampling,'
' restarting ...' % n_chains)
chains = corrupted_chains
return mtrace
def _iter_parallel_chains(
draws, step, stage_path, progressbar, model, n_jobs,
chains=None):
"""
Do Metropolis sampling over all the chains with each chain being
sampled 'draws' times. Parallel execution according to n_jobs.
If jobs hang for any reason they are being killed after an estimated
timeout. The chains in question are being rerun and the estimated timeout
is added again.
"""
timeout = 0
if chains is None:
chains = list(range(step.n_chains))
n_chains = len(chains)
if n_chains == 0:
mtrace = backend.load_multitrace(dirname=stage_path, model=model)
# while is necessary if any worker times out - rerun in case
while n_chains > 0:
trace_list = []
logger.info('Initialising %i chain traces ...' % n_chains)
for chain in chains:
trace_list.append(backend.TextChain(stage_path, model=model))
max_int = np.iinfo(np.int32).max
random_seeds = [randint(max_int) for _ in range(n_chains)]
work = [(draws, step, step.population[step.resampling_indexes[chain]],
trace, chain, None, progressbar, model, rseed)
for chain, rseed, trace in zip(
chains, random_seeds, trace_list)]
tps = step.time_per_sample(10)
if draws < 10:
chunksize = int(np.ceil(float(n_chains) / n_jobs))
tps += 5.
elif draws > 10 and tps < 1.:
chunksize = int(np.ceil(float(n_chains) / n_jobs))
else:
chunksize = n_jobs
timeout += int(np.ceil(tps * draws)) * n_jobs
p = paripool.paripool(
_sample, work, chunksize=chunksize, timeout=timeout, nprocs=n_jobs)
logger.info('Sampling ...')
for res in p:
pass
# return chain indexes that have been corrupted
mtrace = backend.load_multitrace(dirname=stage_path, model=model)
corrupted_chains = backend.check_multitrace(
mtrace, draws=draws, n_chains=step.n_chains)
n_chains = len(corrupted_chains)
if n_chains > 0:
logger.warning(
'%i Chains not finished sampling,'
' restarting ...' % n_chains)
chains = corrupted_chains
return mtrace
