import re
from functools import partial
import pkg_resources # part of setuptools
+import Queue
+import time
from cwltool.errors import WorkflowException
import cwltool.main
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache
from .perf import Perf
from .pathmapper import NoFollowPathMapper
+from .task_queue import TaskQueue
from ._version import __version__
from cwltool.pack import pack
"""
- def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None, num_retries=4):
+ def __init__(self, api_client, work_api=None, keep_client=None,
+ output_name=None, output_tags=None, num_retries=4):
self.api = api_client
self.processes = {}
- self.in_flight = 0
self.workflow_eval_lock = threading.Condition(threading.RLock())
self.final_output = None
self.final_status = None
self.intermediate_output_ttl = 0
self.intermediate_output_collections = []
self.trash_intermediate = False
+ self.thread_count = 4
+ self.poll_interval = 12
if keep_client is not None:
self.keep_client = keep_client
return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs)
def output_callback(self, out, processStatus):
- if processStatus == "success":
- logger.info("Overall process status is %s", processStatus)
- if self.pipeline:
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Complete"}).execute(num_retries=self.num_retries)
- else:
- logger.warn("Overall process status is %s", processStatus)
- if self.pipeline:
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Failed"}).execute(num_retries=self.num_retries)
- self.final_status = processStatus
- self.final_output = out
+ with self.workflow_eval_lock:
+ if processStatus == "success":
+ logger.info("Overall process status is %s", processStatus)
+ if self.pipeline:
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Complete"}).execute(num_retries=self.num_retries)
+ else:
+ logger.warn("Overall process status is %s", processStatus)
+ if self.pipeline:
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ self.final_status = processStatus
+ self.final_output = out
+ self.workflow_eval_lock.notifyAll()
+
def start_run(self, runnable, kwargs):
- with self.workflow_eval_lock:
- self.in_flight += 1
- runnable.run(**kwargs)
+ self.task_queue.add(partial(runnable.run, **kwargs))
def process_submitted(self, container):
with self.workflow_eval_lock:
self.processes[container.uuid] = container
- self.in_flight -= 1
def process_done(self, uuid):
with self.workflow_eval_lock:
if uuid in self.processes:
del self.processes[uuid]
+ def wrapped_callback(self, cb, obj, st):
+ with self.workflow_eval_lock:
+ cb(obj, st)
+ self.workflow_eval_lock.notifyAll()
+
+ def get_wrapped_callback(self, cb):
+ return partial(self.wrapped_callback, cb)
+
def on_message(self, event):
if "object_uuid" in event:
if event["object_uuid"] in self.processes and event["event_type"] == "update":
- if event["properties"]["new_attributes"]["state"] == "Running" and self.processes[event["object_uuid"]].running is False:
- uuid = event["object_uuid"]
+ uuid = event["object_uuid"]
+ if event["properties"]["new_attributes"]["state"] == "Running":
with self.workflow_eval_lock:
j = self.processes[uuid]
- logger.info("%s %s is Running", self.label(j), uuid)
- j.running = True
- j.update_pipeline_component(event["properties"]["new_attributes"])
+ if j.running is False:
+ j.running = True
+ j.update_pipeline_component(event["properties"]["new_attributes"])
+ logger.info("%s %s is Running", self.label(j), uuid)
elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
- uuid = event["object_uuid"]
with self.workflow_eval_lock:
j = self.processes[uuid]
- logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
- with Perf(metrics, "done %s" % j.name):
- j.done(event["properties"]["new_attributes"])
- self.workflow_eval_lock.notify()
+ self.task_queue.add(partial(j.done, event["properties"]["new_attributes"]))
+ logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
def label(self, obj):
return "[%s %s]" % (self.work_api[0:-1], obj.name)
"""
try:
+ remain_wait = self.poll_interval
while True:
- self.stop_polling.wait(15)
+ if remain_wait > 0:
+ self.stop_polling.wait(remain_wait)
if self.stop_polling.is_set():
break
with self.workflow_eval_lock:
keys = list(self.processes.keys())
if not keys:
+ remain_wait = self.poll_interval
continue
+ begin_poll = time.time()
if self.work_api == "containers":
table = self.poll_api.container_requests()
elif self.work_api == "jobs":
proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
except Exception as e:
logger.warn("Error checking states on API server: %s", e)
+ remain_wait = self.poll_interval
continue
for p in proc_states["items"]:
"new_attributes": p
}
})
+ finish_poll = time.time()
+ remain_wait = self.poll_interval - (finish_poll - begin_poll)
except:
- logger.error("Fatal error in state polling thread.", exc_info=(sys.exc_info()[1] if self.debug else False))
- with workflow_eval_lock:
+ logger.exception("Fatal error in state polling thread.")
+ with self.workflow_eval_lock:
self.processes.clear()
- self.workflow_eval_lock.notify()
+ self.workflow_eval_lock.notifyAll()
finally:
self.stop_polling.set()
collection_cache=self.collection_cache)
self.fs_access = make_fs_access(kwargs["basedir"])
self.secret_store = kwargs.get("secret_store")
+ self.thread_count = kwargs.get("thread_count", 4)
self.trash_intermediate = kwargs["trash_intermediate"]
if self.trash_intermediate and self.work_api != "containers":
logger.info("Pipeline instance %s", self.pipeline["uuid"])
if runnerjob and not kwargs.get("wait"):
- runnerjob.run(wait=kwargs.get("wait"))
+ runnerjob.run(**kwargs)
return (runnerjob.uuid, "success")
self.poll_api = arvados.api('v1')
self.polling_thread = threading.Thread(target=self.poll_states)
self.polling_thread.start()
+ self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
+
if runnerjob:
jobiter = iter((runnerjob,))
else:
if self.stop_polling.is_set():
break
+ if self.task_queue.error is not None:
+ raise self.task_queue.error
+
if runnable:
with Perf(metrics, "run"):
self.start_run(runnable, kwargs)
else:
- if (self.in_flight + len(self.processes)) > 0:
- self.workflow_eval_lock.wait(1)
+ if (self.task_queue.in_flight + len(self.processes)) > 0:
+ self.workflow_eval_lock.wait(3)
else:
- logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
+ logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pendingjobs.")
break
loopperf.__enter__()
loopperf.__exit__()
- while self.processes:
- self.workflow_eval_lock.wait(1)
+ while (self.task_queue.in_flight + len(self.processes)) > 0:
+ if self.task_queue.error is not None:
+ raise self.task_queue.error
+ self.workflow_eval_lock.wait(3)
except UnsupportedRequirement:
raise
body={"priority": "0"}).execute(num_retries=self.num_retries)
finally:
self.workflow_eval_lock.release()
+ self.task_queue.drain()
self.stop_polling.set()
self.polling_thread.join()
+ self.task_queue.join()
if self.final_status == "UnsupportedRequirement":
raise UnsupportedRequirement("Check log for details.")
action="store_true", default=False,
help=argparse.SUPPRESS)
+ parser.add_argument("--thread-count", type=int,
+ default=4, help="Number of threads to use for job submit and output collection.")
+
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--trash-intermediate", action="store_true",
default=False, dest="trash_intermediate",
projects / arvados.git / blobdiff