def check_links_status(self,
fail_running=False,
fail_pending=False):
""""Check the status of all the jobs run from the
`Link` objects in this `Chain` and return a status
flag that summarizes that.
Parameters
----------
fail_running : `bool`
If True, consider running jobs as failed
fail_pending : `bool`
If True, consider pending jobs as failed
Returns
-------
status : `JobStatus`
Job status flag that summarizes the status of all the jobs,
"""
status_vector = JobStatusVector()
for link in self._links.values():
key = JobDetails.make_fullkey(link.full_linkname)
link_status = link.check_job_status(key,
fail_running=fail_running,
fail_pending=fail_pending)
status_vector[link_status] += 1
return status_vector.get_status()
def run_with_log(self,
dry_run=False,
stage_files=True,
resubmit_failed=False):
"""Runs this link with output sent to a pre-defined logfile
Parameters
-----------
dry_run : bool
Print command but do not run it.
stage_files : bool
Copy files to and from scratch staging area.
resubmit_failed : bool
Flag for sub-classes to resubmit failed jobs.
"""
fullkey = JobDetails.make_fullkey(self.full_linkname)
job_details = self.jobs[fullkey]
odir = os.path.dirname(job_details.logfile)
try:
os.makedirs(odir)
except OSError:
pass
ostream = open(job_details.logfile, 'w')
self.run(ostream, dry_run, stage_files, resubmit_failed)
def check_links_status(self, fail_running=False, fail_pending=False):
""""Check the status of all the jobs run from the
`Link` objects in this `Chain` and return a status
flag that summarizes that.
Parameters
----------
fail_running : `bool`
If True, consider running jobs as failed
fail_pending : `bool`
If True, consider pending jobs as failed
Returns
-------
status : `JobStatus`
Job status flag that summarizes the status of all the jobs,
"""
status_vector = JobStatusVector()
for link in self._links.values():
key = JobDetails.make_fullkey(link.full_linkname)
link_status = link.check_job_status(key,
fail_running=fail_running,
fail_pending=fail_pending)
status_vector[link_status] += 1
return status_vector.get_status()
def _register_self(self, logfile, key=JobDetails.topkey, status=JobStatus.unknown):
"""Runs this link, captures output to logfile,
and records the job in self.jobs"""
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
if fullkey in self.jobs:
job_details = self.jobs[fullkey]
job_details.status = status
else:
job_details = self._register_job(key, self.args, logfile, status)
def _set_status_self(self, key=JobDetails.topkey, status=JobStatus.unknown):
"""Set the status of this job, both in self.jobs and
in the `JobArchive` if it is present. """
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
if fullkey in self.jobs:
self.jobs[fullkey].status = status
if self._job_archive:
self._job_archive.register_job(self.jobs[fullkey])
else:
self._register_self('dummy.log', key, status)
def _set_status_self(self,
key=JobDetails.topkey,
status=JobStatus.unknown):
"""Set the status of this job, both in self.jobs and
in the `JobArchive` if it is present. """
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
if fullkey in self.jobs:
self.jobs[fullkey].status = status
if self._job_archive:
self._job_archive.register_job(self.jobs[fullkey])
else:
self._register_self('dummy.log', key, status)
def _register_self(self,
logfile,
key=JobDetails.topkey,
status=JobStatus.unknown):
"""Runs this link, captures output to logfile,
and records the job in self.jobs"""
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
if fullkey in self.jobs:
job_details = self.jobs[fullkey]
job_details.status = status
else:
job_details = self._register_job(key, self.args, logfile, status)
def print_status(self, indent="", recurse=False):
"""Print a summary of the job status for each `Link` in this `Chain`"""
print ("%s%30s : %15s : %20s" %
(indent, "Linkname", "Link Status", "Jobs Status"))
for link in self._links.values():
if hasattr(link, 'check_status'):
status_vect = link.check_status(
stream=sys.stdout, no_wait=True, do_print=False)
else:
status_vect = None
key = JobDetails.make_fullkey(link.full_linkname)
link_status = JOB_STATUS_STRINGS[link.check_job_status(key)]
if status_vect is None:
jobs_status = JOB_STATUS_STRINGS[link.check_jobs_status()]
else:
jobs_status = status_vect
print ("%s%30s : %15s : %20s" %
(indent, link.linkname, link_status, jobs_status))
if hasattr(link, 'print_status') and recurse:
print ("---------- %30s -----------" % link.linkname)
link.print_status(indent + " ", recurse=True)
print ("------------------------------------------------")
def preconfigure(self, config_yaml):
""" Run any links needed to build files
that are used in _map_arguments """
if self._preconfigured:
return
config_dict = load_yaml(config_yaml)
ttype = config_dict.get('ttype')
self.link_prefix = "%s." % ttype
config_template = config_dict.get('config_template', None)
rosters = config_dict.get('rosters')
alias_dict = config_dict.get('alias_dict', None)
spatial_models = config_dict.get('spatial_models')
sims = config_dict.get('sims', {})
sim_names = []
sim_names += list(sims.keys())
if 'random' in config_dict:
sim_names += ['random']
self._set_link('prepare-targets',
PrepareTargets,
ttype=ttype,
rosters=rosters,
spatial_models=spatial_models,
alias_dict=alias_dict,
sims=sim_names,
config=config_template)
link = self['prepare-targets']
key = JobDetails.make_fullkey(link.full_linkname)
if not link.jobs:
raise ValueError("No Jobs")
link_status = link.check_job_status(key)
if link_status == JobStatus.done:
self._preconfigured = True
return
if link_status == JobStatus.failed:
link.clean_jobs()
link.run_with_log()
self._preconfigured = True
def print_status(self, indent="", recurse=False):
"""Print a summary of the job status for each `Link` in this `Chain`"""
print("%s%30s : %15s : %20s" %
(indent, "Linkname", "Link Status", "Jobs Status"))
for link in self._links.values():
if hasattr(link, 'check_status'):
status_vect = link.check_status(stream=sys.stdout,
no_wait=True,
do_print=False)
else:
status_vect = None
key = JobDetails.make_fullkey(link.full_linkname)
link_status = JOB_STATUS_STRINGS[link.check_job_status(key)]
if status_vect is None:
jobs_status = JOB_STATUS_STRINGS[link.check_jobs_status()]
else:
jobs_status = status_vect
print("%s%30s : %15s : %20s" %
(indent, link.linkname, link_status, jobs_status))
if hasattr(link, 'print_status') and recurse:
print("---------- %30s -----------" % link.linkname)
link.print_status(indent + " ", recurse=True)
print("------------------------------------------------")
def run_with_log(self, dry_run=False, stage_files=True, resubmit_failed=False):
"""Runs this link with output sent to a pre-defined logfile
Parameters
-----------
dry_run : bool
Print command but do not run it.
stage_files : bool
Copy files to and from scratch staging area.
resubmit_failed : bool
Flag for sub-classes to resubmit failed jobs.
"""
fullkey = JobDetails.make_fullkey(self.full_linkname)
job_details = self.jobs[fullkey]
odir = os.path.dirname(job_details.logfile)
try:
os.makedirs(odir)
except OSError:
pass
ostream = open(job_details.logfile, 'w')
self.run(ostream, dry_run, stage_files, resubmit_failed)
def _run_chain(self,
stream=sys.stdout,
dry_run=False,
stage_files=True,
force_run=False,
resubmit_failed=False):
"""Run all the links in the chain
Parameters
-----------
stream : `file`
Stream to print to,
Must have 'write' function
dry_run : bool
Print commands but do not run them
stage_files : bool
Stage files to and from the scratch area
force_run : bool
Run jobs, even if they are marked as done
resubmit_failed : bool
Resubmit failed jobs
"""
self._set_links_job_archive()
failed = False
if self._file_stage is not None:
input_file_mapping, output_file_mapping = self._map_scratch_files(
self.sub_files)
if stage_files:
self._file_stage.make_scratch_dirs(input_file_mapping, dry_run)
self._file_stage.make_scratch_dirs(
output_file_mapping, dry_run)
self._stage_input_files(input_file_mapping, dry_run)
for link in self._links.values():
logfile = os.path.join('logs', "%s.log" % link.full_linkname)
link._archive_self(logfile, status=JobStatus.unknown)
key = JobDetails.make_fullkey(link.full_linkname)
if hasattr(link, 'check_status'):
link.check_status(stream, no_wait=True,
check_once=True, do_print=False)
else:
pass
link_status = link.check_job_status(key)
if link_status in [JobStatus.done]:
if not force_run:
print ("Skipping done link", link.full_linkname)
continue
elif link_status in [JobStatus.running]:
if not force_run and not resubmit_failed:
print ("Skipping running link", link.full_linkname)
continue
elif link_status in [JobStatus.failed,
JobStatus.partial_failed]:
if not resubmit_failed:
print ("Skipping failed link", link.full_linkname)
continue
print ("Running link ", link.full_linkname)
link.run_with_log(dry_run=dry_run, stage_files=False,
resubmit_failed=resubmit_failed)
link_status = link.check_jobs_status()
link._set_status_self(status=link_status)
if link_status in [JobStatus.failed, JobStatus.partial_failed]:
print ("Stoping chain execution at failed link %s" %
link.full_linkname)
failed = True
break
# elif link_status in [JobStatus.partial_failed]:
# print ("Resubmitting partially failed link %s" %
# link.full_linkname)
# link.run_with_log(dry_run=dry_run, stage_files=False,
# resubmit_failed=resubmit_failed)
# link_status = link.check_jobs_status()
# link._set_status_self(status=link_status)
# if link_status in [JobStatus.partial_failed]:
# print ("Stoping chain execution: resubmission failed %s" %
# link.full_linkname)
# failed = True
# break
if self._file_stage is not None and stage_files and not failed:
self._stage_output_files(output_file_mapping, dry_run)
chain_status = self.check_links_status()
print ("Chain status: %s" % (JOB_STATUS_STRINGS[chain_status]))
if chain_status == 5:
job_status = 0
else:
job_status = -1
self._write_status_to_log(job_status, stream)
self._set_status_self(status=chain_status)
if self._job_archive:
self._job_archive.file_archive.update_file_status()
self._job_archive.write_table_file()
def _run_chain(self,
stream=sys.stdout,
dry_run=False,
stage_files=True,
force_run=False,
resubmit_failed=False):
"""Run all the links in the chain
Parameters
-----------
stream : `file`
Stream to print to,
Must have 'write' function
dry_run : bool
Print commands but do not run them
stage_files : bool
Stage files to and from the scratch area
force_run : bool
Run jobs, even if they are marked as done
resubmit_failed : bool
Resubmit failed jobs
"""
self._set_links_job_archive()
failed = False
if self._file_stage is not None:
input_file_mapping, output_file_mapping = self._map_scratch_files(
self.sub_files)
if stage_files:
self._file_stage.make_scratch_dirs(input_file_mapping, dry_run)
self._file_stage.make_scratch_dirs(output_file_mapping,
dry_run)
self._stage_input_files(input_file_mapping, dry_run)
for link in self._links.values():
logfile = os.path.join('logs', "%s.log" % link.full_linkname)
link._archive_self(logfile, status=JobStatus.unknown)
key = JobDetails.make_fullkey(link.full_linkname)
if hasattr(link, 'check_status'):
link.check_status(stream,
no_wait=True,
check_once=True,
do_print=False)
else:
pass
link_status = link.check_job_status(key)
if link_status in [JobStatus.done]:
if not force_run:
print("Skipping done link", link.full_linkname)
continue
elif link_status in [JobStatus.running]:
if not force_run and not resubmit_failed:
print("Skipping running link", link.full_linkname)
continue
elif link_status in [JobStatus.failed, JobStatus.partial_failed]:
if not resubmit_failed:
print("Skipping failed link", link.full_linkname)
continue
print("Running link ", link.full_linkname)
link.run_with_log(dry_run=dry_run,
stage_files=False,
resubmit_failed=resubmit_failed)
link_status = link.check_jobs_status()
link._set_status_self(status=link_status)
if link_status in [JobStatus.failed, JobStatus.partial_failed]:
print("Stoping chain execution at failed link %s" %
link.full_linkname)
failed = True
break
# elif link_status in [JobStatus.partial_failed]:
# print ("Resubmitting partially failed link %s" %
# link.full_linkname)
# link.run_with_log(dry_run=dry_run, stage_files=False,
# resubmit_failed=resubmit_failed)
# link_status = link.check_jobs_status()
# link._set_status_self(status=link_status)
# if link_status in [JobStatus.partial_failed]:
# print ("Stoping chain execution: resubmission failed %s" %
# link.full_linkname)
# failed = True
# break
if self._file_stage is not None and stage_files and not failed:
self._stage_output_files(output_file_mapping, dry_run)
chain_status = self.check_links_status()
print("Chain status: %s" % (JOB_STATUS_STRINGS[chain_status]))
if chain_status == 5:
job_status = 0
else:
job_status = -1
self._write_status_to_log(job_status, stream)
self._set_status_self(status=chain_status)
if self._job_archive:
self._job_archive.file_archive.update_file_status()
self._job_archive.write_table_file()