def submitJob(ini):
if not args.dryrun:
print('Submitting...' + ini)
else:
print('... ' + ini)
iniFiles.append(ini)
if args.combine_one_job_name:
return
if len(iniFiles) >= args.runs_per_job:
if args.runs_per_job > 1:
print('--> jobName: ', jobName())
jobqueue.submitJob(jobName(), iniFiles, **args.__dict__)
iniFiles.clear()
def submitJob(ini):
global iniFiles
ini = ini.replace('.ini', '').replace(".yaml", "")
if not args.dryrun:
print('Submitting...' + ini)
else:
print('... ' + ini)
iniFiles.append(ini)
if args.combine_one_job_name:
return
if len(iniFiles) >= args.runs_per_job:
if args.runs_per_job > 1:
print('--> jobName: ', jobName())
jobqueue.submitJob(jobName(), iniFiles, **args.__dict__)
iniFiles = []
def run():
warn_deprecation()
Opts = batchjob_args.batchArgs(
'Submit jobs to run chains or importance sample',
notExist=True,
notall=True,
converge=True)
jobqueue.addArguments(Opts.parser, combinedJobs=True)
Opts.parser.add_argument('--subitems',
action='store_true',
help='include sub-grid items')
Opts.parser.add_argument('--not_queued', action='store_true')
Opts.parser.add_argument('--minimize',
action='store_true',
help='Run minimization jobs')
Opts.parser.add_argument('--importance_minimize',
action='store_true',
help=('Run minimization jobs for chains '
'that are importance sampled'))
Opts.parser.add_argument('--minimize_failed',
action='store_true',
help='run where minimization previously failed')
Opts.parser.add_argument(
'--checkpoint_run',
nargs='?',
default=None,
const=0,
type=float,
help=('run if stopped and not finished; if optional value '
'given then only run chains with convergence worse than '
'the given value'))
Opts.parser.add_argument(
'--importance_ready',
action='store_true',
help='where parent chain has converged and stopped')
Opts.parser.add_argument(
'--importance_changed',
action='store_true',
help=('run importance jobs where the parent chain has '
'changed since last run'))
Opts.parser.add_argument(
'--parent_converge',
type=float,
default=0,
help='minimum R-1 convergence for importance job parent')
Opts.parser.add_argument(
'--parent_stopped',
action='store_true',
help='only run if parent chain is not still running')
(batch, args) = Opts.parseForBatch()
if args.not_queued:
print('Getting queued names...')
queued = jobqueue.queue_job_names(args.batchPath)
def notQueued(name):
for job in queued:
if name in job:
# print 'Already running:', name
return False
return True
variant = ''
if args.importance_minimize:
variant = '_minimize'
if args.importance is None:
args.importance = []
if args.minimize:
args.noimportance = True
variant = '_minimize'
if args.importance is None:
if args.importance_changed or args.importance_ready:
args.importance = []
else:
args.noimportance = True
isMinimize = args.importance_minimize or args.minimize
if args.combine_one_job_name:
print('Combining multiple (hopefully fast) into single job script: ' +
args.combine_one_job_name)
global iniFiles
iniFiles = []
jobqueue.checkArguments(**args.__dict__)
def jobName():
s = "-".join(
[os.path.splitext(os.path.basename(ini))[0] for ini in iniFiles])
if len(iniFiles) < 2 or len(s) < 70:
return s
base = os.path.basename(iniFiles[0])
if len(base) > 70:
base = base[:70]
return base + '__' + hashlib.md5(s).hexdigest()[:16]
def submitJob(ini):
global iniFiles
if not args.dryrun:
print('Submitting...' + ini)
else:
print('... ' + ini)
iniFiles.append(ini)
if args.combine_one_job_name:
return
if len(iniFiles) >= args.runs_per_job:
if args.runs_per_job > 1:
print('--> jobName: ', jobName())
jobqueue.submitJob(jobName(), iniFiles, **args.__dict__)
iniFiles = []
for jobItem in Opts.filteredBatchItems(wantSubItems=args.subitems):
if ((not args.notexist or isMinimize and not jobItem.chainMinimumExists()
or not isMinimize and not jobItem.chainExists()) and (
not args.minimize_failed or not jobItem.chainMinimumConverged())
and (isMinimize or args.notall is None or not jobItem.allChainExists(args.notall))) \
and (not isMinimize or getattr(jobItem, 'want_minimize', True)):
if not args.parent_converge or not jobItem.isImportanceJob or jobItem.parent.hasConvergeBetterThan(
args.parent_converge):
if args.converge == 0 or not jobItem.hasConvergeBetterThan(
args.converge, returnNotExist=True):
if args.checkpoint_run is None or jobItem.wantCheckpointContinue(
args.checkpoint_run) and jobItem.notRunning():
if (not jobItem.isImportanceJob or isMinimize
or (args.importance_ready
and jobItem.parent.chainFinished()
or not args.importance_ready
and jobItem.parent.chainExists()) and
(not args.importance_changed
or jobItem.parentChanged()) and
(not args.parent_stopped
or jobItem.parent.notRunning())):
if not args.not_queued or notQueued(jobItem.name):
submitJob(jobItem.iniFile(variant))
if len(iniFiles) > 0:
if args.runs_per_job > 1: print('--> jobName: ', jobName())
jobqueue.submitJob(args.combine_one_job_name or jobName(),
iniFiles,
sequential=args.combine_one_job_name is not None,
**args.__dict__)
