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ENH: Improve loop timing in DistributedPluginBase #2317

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merged 2 commits into from
Dec 5, 2017
Merged

ENH: Improve loop timing in DistributedPluginBase #2317

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a8a899b
ENH: Improve loop timing in DistributedPluginBase
effigies Nov 29, 2017
89bf38f
STY: Flake8 cleanup
effigies Nov 29, 2017
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28 changes: 17 additions & 11 deletions nipype/pipeline/plugins/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,9 +128,11 @@ def run(self, graph, config, updatehash=False):
old_progress_stats = None
old_presub_stats = None
while not np.all(self.proc_done) or np.any(self.proc_pending):
# Check to see if a job is available (jobs without dependencies not run)
# See https://github.com/nipy/nipype/pull/2200#discussion_r141605722
jobs_ready = np.nonzero(~self.proc_done & (self.depidx.sum(0) == 0))[1]
loop_start = time()
# Check if a job is available (jobs with all dependencies run)
# https://github.com/nipy/nipype/pull/2200#discussion_r141605722
jobs_ready = np.nonzero(~self.proc_done &
(self.depidx.sum(0) == 0))[1]

progress_stats = (len(self.proc_done),
np.sum(self.proc_done ^ self.proc_pending),
Expand Down Expand Up @@ -164,7 +166,8 @@ def run(self, graph, config, updatehash=False):
self._remove_node_dirs()
self._clear_task(taskid)
else:
assert self.proc_done[jobid] and self.proc_pending[jobid]
assert self.proc_done[jobid] and \
self.proc_pending[jobid]
toappend.insert(0, (taskid, jobid))

if toappend:
Expand All @@ -183,7 +186,8 @@ def run(self, graph, config, updatehash=False):
elif display_stats:
logger.debug('Not submitting (max jobs reached)')

sleep(poll_sleep_secs)
sleep_til = loop_start + poll_sleep_secs
sleep(max(0, sleep_til - time()))

self._remove_node_dirs()
report_nodes_not_run(notrun)
Expand Down Expand Up @@ -271,8 +275,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
if (num_jobs >= self.max_jobs) or (slots == 0):
break

# Check to see if a job is available (jobs without dependencies not run)
# See https://github.com/nipy/nipype/pull/2200#discussion_r141605722
# Check if a job is available (jobs with all dependencies run)
# https://github.com/nipy/nipype/pull/2200#discussion_r141605722
jobids = np.nonzero(~self.proc_done & (self.depidx.sum(0) == 0))[1]

if len(jobids) > 0:
Expand Down Expand Up @@ -325,7 +329,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
break

def _local_hash_check(self, jobid, graph):
if not str2bool(self.procs[jobid].config['execution']['local_hash_check']):
if not str2bool(self.procs[jobid].config['execution'][
'local_hash_check']):
return False

logger.debug('Checking hash (%d) locally', jobid)
Expand Down Expand Up @@ -397,8 +402,8 @@ def _remove_node_dirs(self):
"""Removes directories whose outputs have already been used up
"""
if str2bool(self._config['execution']['remove_node_directories']):
for idx in np.nonzero(
(self.refidx.sum(axis=1) == 0).__array__())[0]:
indices = np.nonzero((self.refidx.sum(axis=1) == 0).__array__())[0]
for idx in indices:
if idx in self.mapnodesubids:
continue
if self.proc_done[idx] and (not self.proc_pending[idx]):
Expand Down Expand Up @@ -513,7 +518,8 @@ class GraphPluginBase(PluginBase):

def __init__(self, plugin_args=None):
if plugin_args and plugin_args.get('status_callback'):
logger.warning('status_callback not supported for Graph submission plugins')
logger.warning('status_callback not supported for Graph submission'
' plugins')
super(GraphPluginBase, self).__init__(plugin_args=plugin_args)

def run(self, graph, config, updatehash=False):
Expand Down