def _work_queue_submit_wait(task_queue=multiprocessing.Queue(),
launch_cmd=None,
env=None,
collector_queue=multiprocessing.Queue(),
data_dir=".",
full=False,
shared_fs=False,
autolabel=False,
autolabel_window=None,
autocategory=False,
should_stop=None,
port=WORK_QUEUE_DEFAULT_PORT,
wq_log_dir=None,
project_password_file=None,
project_name=None):
"""Thread to handle Parsl app submissions to the Work Queue objects.
Takes in Parsl functions submitted using submit(), and creates a
Work Queue task with the appropriate specifications, which is then
submitted to Work Queue. After tasks are completed, processes the
exit status and exit code of the task, and sends results to the
Work Queue collector thread.
To avoid python's global interpreter lock with work queue's wait, this
function should be launched as a process, not as a lightweight thread. This
means that any communication should be done using the multiprocessing
module capabilities, rather than shared memory.
"""
logger.debug("Starting WorkQueue Submit/Wait Process")
# Enable debugging flags and create logging file
wq_debug_log = None
if wq_log_dir is not None:
logger.debug("Setting debugging flags and creating logging file")
wq_debug_log = os.path.join(wq_log_dir, "debug_log")
# Create WorkQueue queue object
logger.debug("Creating WorkQueue Object")
try:
logger.debug("Listening on port {}".format(port))
q = WorkQueue(port, debug_log=wq_debug_log)
except Exception as e:
logger.error("Unable to create WorkQueue object: {}".format(e))
raise e
# Specify WorkQueue queue attributes
if project_name:
q.specify_name(project_name)
if project_password_file:
q.specify_password_file(project_password_file)
if autolabel:
q.enable_monitoring()
if autolabel_window is not None:
q.tune('category-steady-n-tasks', autolabel_window)
# Only write logs when the wq_log_dir is specified, which it most likely will be
if wq_log_dir is not None:
wq_master_log = os.path.join(wq_log_dir, "master_log")
wq_trans_log = os.path.join(wq_log_dir, "transaction_log")
if full:
wq_resource_log = os.path.join(wq_log_dir, "resource_logs")
q.enable_monitoring_full(dirname=wq_resource_log)
q.specify_log(wq_master_log)
q.specify_transactions_log(wq_trans_log)
orig_ppid = os.getppid()
result_file_of_task_id = {
} # Mapping taskid -> result file for active tasks.
while not should_stop.value:
# Monitor the task queue
ppid = os.getppid()
if ppid != orig_ppid:
logger.debug("new Process")
break
# Submit tasks
while task_queue.qsize() > 0 and not should_stop.value:
# Obtain task from task_queue
try:
task = task_queue.get(timeout=1)
logger.debug("Removing task from queue")
except queue.Empty:
continue
pkg_pfx = ""
if task.env_pkg is not None:
pkg_pfx = "./{} -e {} ".format(
os.path.basename(package_run_script),
os.path.basename(task.env_pkg))
# Create command string
logger.debug(launch_cmd)
command_str = launch_cmd.format(
package_prefix=pkg_pfx,
mapping=os.path.basename(task.map_file),
function=os.path.basename(task.function_file),
result=os.path.basename(task.result_file))
logger.debug(command_str)
# Create WorkQueue task for the command
logger.debug("Sending task {} with command: {}".format(
task.id, command_str))
try:
t = Task(command_str)
except Exception as e:
logger.error("Unable to create task: {}".format(e))
collector_queue.put_nowait(
WqTaskToParsl(
id=task.id,
result_received=False,
result=None,
reason="task could not be created by work queue",
status=-1))
continue
t.specify_category(task.category)
if autolabel:
q.specify_category_mode(
task.category, WORK_QUEUE_ALLOCATION_MODE_MAX_THROUGHPUT)
# Specify environment variables for the task
if env is not None:
for var in env:
t.specify_environment_variable(var, env[var])
if task.env_pkg is not None:
t.specify_input_file(package_run_script, cache=True)
t.specify_input_file(task.env_pkg, cache=True)
# Specify script, and data/result files for task
t.specify_input_file(exec_parsl_function.__file__, cache=True)
t.specify_input_file(task.function_file, cache=False)
t.specify_input_file(task.map_file, cache=False)
t.specify_output_file(task.result_file, cache=False)
t.specify_tag(str(task.id))
result_file_of_task_id[str(task.id)] = task.result_file
logger.debug("Parsl ID: {}".format(task.id))
# Specify input/output files that need to be staged.
# Absolute paths are assumed to be in shared filesystem, and thus
# not staged by work queue.
if not shared_fs:
for spec in task.input_files:
if spec.stage:
t.specify_input_file(spec.parsl_name,
spec.parsl_name,
cache=spec.cache)
for spec in task.output_files:
if spec.stage:
t.specify_output_file(spec.parsl_name,
spec.parsl_name,
cache=spec.cache)
# Submit the task to the WorkQueue object
logger.debug("Submitting task {} to WorkQueue".format(task.id))
try:
wq_id = q.submit(t)
except Exception as e:
logger.error(
"Unable to submit task to work queue: {}".format(e))
collector_queue.put_nowait(
WqTaskToParsl(
id=task.id,
result_received=False,
result=None,
reason="task could not be submited to work queue",
status=-1))
continue
logger.debug("Task {} submitted to WorkQueue with id {}".format(
task.id, wq_id))
# If the queue is not empty wait on the WorkQueue queue for a task
task_found = True
if not q.empty():
while task_found and not should_stop.value:
# Obtain the task from the queue
t = q.wait(1)
if t is None:
task_found = False
continue
# When a task is found:
parsl_id = t.tag
logger.debug(
"Completed WorkQueue task {}, parsl task {}".format(
t.id, t.tag))
result_file = result_file_of_task_id.pop(t.tag)
# A tasks completes 'succesfully' if it has result file,
# and it can be loaded. This may mean that the 'success' is
# an exception.
logger.debug("Looking for result in {}".format(result_file))
try:
with open(result_file, "rb") as f_in:
result = pickle.load(f_in)
logger.debug("Found result in {}".format(result_file))
collector_queue.put_nowait(
WqTaskToParsl(id=parsl_id,
result_received=True,
result=result,
reason=None,
status=t.return_status))
# If a result file could not be generated, explain the
# failure according to work queue error codes. We generate
# an exception and wrap it with RemoteExceptionWrapper, to
# match the positive case.
except Exception as e:
reason = _explain_work_queue_result(t)
logger.debug(
"Did not find result in {}".format(result_file))
logger.debug(
"Wrapper Script status: {}\nWorkQueue Status: {}".
format(t.return_status, t.result))
logger.debug(
"Task with id parsl {} / wq {} failed because:\n{}".
format(parsl_id, t.id, reason))
collector_queue.put_nowait(
WqTaskToParsl(id=parsl_id,
result_received=False,
result=e,
reason=reason,
status=t.return_status))
logger.debug("Exiting WorkQueue Monitoring Process")
return 0
def WorkQueueSubmitThread(task_queue=multiprocessing.Queue(),
queue_lock=threading.Lock(),
launch_cmd=None,
env=None,
collector_queue=multiprocessing.Queue(),
see_worker_output=False,
data_dir=".",
full=False,
autolabel=False,
autolabel_window=None,
autocategory=False,
cancel_value=multiprocessing.Value('i', 1),
port=WORK_QUEUE_DEFAULT_PORT,
wq_log_dir=None,
project_password=None,
project_password_file=None,
project_name=None):
"""Thread to handle Parsl app submissions to the Work Queue objects.
Takes in Parsl functions submitted using submit(), and creates a
Work Queue task with the appropriate specifications, which is then
submitted to Work Queue. After tasks are completed, processes the
exit status and exit code of the task, and sends results to the
Work Queue collector thread.
"""
logger.debug("Starting WorkQueue Submit/Wait Process")
# Enable debugging flags and create logging file
if wq_log_dir is not None:
logger.debug("Setting debugging flags and creating logging file")
wq_debug_log = os.path.join(wq_log_dir, "debug_log")
cctools_debug_flags_set("all")
cctools_debug_config_file(wq_debug_log)
# Create WorkQueue queue object
logger.debug("Creating WorkQueue Object")
try:
logger.debug("Listening on port {}".format(port))
q = WorkQueue(port)
except Exception as e:
logger.error("Unable to create WorkQueue object: {}".format(e))
raise e
# Specify WorkQueue queue attributes
if project_name:
q.specify_name(project_name)
if project_password:
q.specify_password(project_password)
elif project_password_file:
q.specify_password_file(project_password_file)
if autolabel:
q.enable_monitoring()
if autolabel_window is not None:
q.tune('category-steady-n-tasks', autolabel_window)
# Only write logs when the wq_log_dir is specified, which it most likely will be
if wq_log_dir is not None:
wq_master_log = os.path.join(wq_log_dir, "master_log")
wq_trans_log = os.path.join(wq_log_dir, "transaction_log")
if full:
wq_resource_log = os.path.join(wq_log_dir, "resource_logs")
q.enable_monitoring_full(dirname=wq_resource_log)
q.specify_log(wq_master_log)
q.specify_transactions_log(wq_trans_log)
wq_tasks = set()
orig_ppid = os.getppid()
continue_running = True
result_file_of_task_id = {
} # Mapping taskid -> result file for active tasks.
while (continue_running):
# Monitor the task queue
ppid = os.getppid()
if ppid != orig_ppid:
logger.debug("new Process")
continue_running = False
continue
# Submit tasks
while task_queue.qsize() > 0:
if cancel_value.value == 0:
logger.debug("cancel value set to cancel")
continue_running = False
break
# Obtain task from task_queue
try:
item = task_queue.get(timeout=1)
logger.debug("Removing task from queue")
except queue.Empty:
continue
parsl_id = item["task_id"]
# Extract information about the task
function_data_loc = item["data_loc"]
function_data_loc_remote = function_data_loc.split("/")[-1]
function_result_loc = item["result_loc"]
function_result_loc_remote = function_result_loc.split("/")[-1]
input_files = item["input_files"]
output_files = item["output_files"]
std_files = item["std_files"]
category = item["category"]
full_script_name = workqueue_worker.__file__
script_name = full_script_name.split("/")[-1]
remapping_string = ""
std_string = ""
# Parse input file information
logger.debug("Looking at input")
for item in input_files:
if item[3] == "std":
std_string += "mv " + item[1] + " " + item[0] + "; "
else:
remapping_string += item[0] + ":" + item[1] + ","
logger.debug(remapping_string)
# Parse output file information
logger.debug("Looking at output")
for item in output_files:
remapping_string += item[0] + ":" + item[1] + ","
logger.debug(remapping_string)
if len(input_files) + len(output_files) > 0:
remapping_string = "-r " + remapping_string
remapping_string = remapping_string[:-1]
# Create command string
logger.debug(launch_cmd)
command_str = launch_cmd.format(
input_file=function_data_loc_remote,
output_file=function_result_loc_remote,
remapping_string=remapping_string)
command_str = std_string + command_str
logger.debug(command_str)
# Create WorkQueue task for the command
logger.debug("Sending task {} with command: {}".format(
parsl_id, command_str))
try:
t = Task(command_str)
except Exception as e:
logger.error("Unable to create task: {}".format(e))
continue
t.specify_category(category)
if autolabel:
q.specify_category_mode(
category, WORK_QUEUE_ALLOCATION_MODE_MAX_THROUGHPUT)
# Specify environment variables for the task
if env is not None:
for var in env:
t.specify_environment_variable(var, env[var])
# Specify script, and data/result files for task
t.specify_file(full_script_name,
script_name,
WORK_QUEUE_INPUT,
cache=True)
t.specify_file(function_data_loc,
function_data_loc_remote,
WORK_QUEUE_INPUT,
cache=False)
t.specify_file(function_result_loc,
function_result_loc_remote,
WORK_QUEUE_OUTPUT,
cache=False)
t.specify_tag(str(parsl_id))
result_file_of_task_id[str(parsl_id)] = function_result_loc
logger.debug("Parsl ID: {}".format(parsl_id))
# Specify all input/output files for task
for item in input_files:
t.specify_file(item[0],
item[1],
WORK_QUEUE_INPUT,
cache=item[2])
for item in output_files:
t.specify_file(item[0],
item[1],
WORK_QUEUE_OUTPUT,
cache=item[2])
for item in std_files:
t.specify_file(item[0],
item[1],
WORK_QUEUE_OUTPUT,
cache=item[2])
# Submit the task to the WorkQueue object
logger.debug("Submitting task {} to WorkQueue".format(parsl_id))
try:
wq_id = q.submit(t)
wq_tasks.add(wq_id)
except Exception as e:
logger.error("Unable to create task: {}".format(e))
msg = {
"tid": parsl_id,
"result_received": False,
"reason": "Workqueue Task Start Failure",
"status": 1
}
collector_queue.put_nowait(msg)
continue
logger.debug("Task {} submitted to WorkQueue with id {}".format(
parsl_id, wq_id))
if cancel_value.value == 0:
continue_running = False
# If the queue is not empty wait on the WorkQueue queue for a task
task_found = True
if not q.empty() and continue_running:
while task_found is True:
if cancel_value.value == 0:
continue_running = False
task_found = False
continue
# Obtain the task from the queue
t = q.wait(1)
if t is None:
task_found = False
continue
else:
parsl_tid = t.tag
logger.debug(
"Completed WorkQueue task {}, parsl task {}".format(
t.id, parsl_tid))
status = t.return_status
task_result = t.result
msg = None
# Task failure
if status != 0 or (task_result != WORK_QUEUE_RESULT_SUCCESS
and task_result !=
WORK_QUEUE_RESULT_OUTPUT_MISSING):
logger.debug(
"Wrapper Script status: {}\nWorkQueue Status: {}".
format(status, task_result))
reason = explain_task_exit_status(t, parsl_tid)
logger.debug(
"WorkQueue runner script failed for parsl task {} (wq {}) because:\n{}"
.format(parsl_id, t.id, reason))
msg = {
"tid": parsl_tid,
"result_received": False,
"reason": reason,
"status": status
}
collector_queue.put_nowait(msg)
# Task Success
else:
# Print the output from the task
if see_worker_output:
print(t.output)
# Load result into result file. The tag of the task is the parsl_id.
result_loc = result_file_of_task_id.pop(t.tag)
logger.debug(
"Looking for result in {}".format(result_loc))
f = open(result_loc, "rb")
result = pickle.load(f)
f.close()
msg = {
"tid": parsl_tid,
"result_received": True,
"result": result
}
wq_tasks.remove(t.id)
collector_queue.put_nowait(msg)
if continue_running is False:
logger.debug("Exiting WorkQueue Master Thread event loop")
break
# Remove all WorkQueue tasks that remain in the queue object
for wq_task in wq_tasks:
logger.debug("Cancelling WorkQueue Task {}".format(wq_task))
q.cancel_by_taskid(wq_task)
logger.debug("Exiting WorkQueue Monitoring Process")
return 0
