def main():
batch_dir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# intialize the BatchLauncher.
from pymatgen.io.abinit.launcher import BatchLauncher
batch = BatchLauncher(workdir=batch_dir)
# Build multiple flows and add them to the BatchLauncher.
for paral_kgb in range(2):
#flow_dir = os.path.join(batch.workdir, "flow_paral_kgb_%d" % paral_kgb)
# Get the SCF and the NSCF input and build the flow.
scf_input, nscf_input = make_scf_nscf_inputs(paral_kgb)
# Each flow will have a unique wordir inside batch.workdir.
# Note that we have to pass workdir=None and use set_name to specify the dir basename
flow = abilab.bandstructure_flow(None, scf_input, nscf_input, allocate=False)
flow.set_name("flow_paral_kgb_%d" % paral_kgb)
batch.add_flow(flow)
# Submit to the queue in batch mode.
# Use abibatch.py to inspect the status or resubmit.
job = batch.submit()
print("batch.submit() returned: ", job.retcode)
return job.retcode
def main():
batch_dir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
# intialize the BatchLauncher.
from pymatgen.io.abinit.launcher import BatchLauncher
batch = BatchLauncher(workdir=batch_dir)
# Build multiple flows and add them to the BatchLauncher.
for paral_kgb in range(2):
#flow_dir = os.path.join(batch.workdir, "flow_paral_kgb_%d" % paral_kgb)
# Get the SCF and the NSCF input and build the flow.
scf_input, nscf_input = make_scf_nscf_inputs(paral_kgb)
# Each flow will have a unique wordir inside batch.workdir.
# Note that we have to pass workdir=None and use set_name to specify the dir basename
flow = abilab.bandstructure_flow(None,
scf_input,
nscf_input,
allocate=False)
flow.set_name("flow_paral_kgb_%d" % paral_kgb)
batch.add_flow(flow)
# Submit to the queue in batch mode.
# Use abibatch.py to inspect the status or resubmit.
job = batch.submit()
print("batch.submit() returned: ", job.retcode)
return job.retcode
def test_batchlauncher(self):
"""Testing BatchLauncher methods."""
# Create the TaskManager.
manager = TaskManager.from_string(self.MANAGER)
print("batch_adapter", manager.batch_adapter)
assert manager.batch_adapter is not None
def build_flow_with_name(name):
"""Build a flow with workdir None and the given name."""
flow = Flow(workdir=None, manager=self.manager)
flow.set_name(name)
flow.register_task(self.fake_input)
work = Work()
work.register_scf_task(self.fake_input)
flow.register_work(work)
return flow
from pymatgen.io.abinit.launcher import BatchLauncher
tmpdir = tempfile.mkdtemp()
batch = BatchLauncher(workdir=tmpdir, manager=manager)
print(batch)
flow0 = build_flow_with_name("flow0")
flow1 = build_flow_with_name("flow1")
flow2_same_name = build_flow_with_name("flow1")
batch.add_flow(flow0)
# Cannot add the same flow twice.
with self.assertRaises(batch.Error):
batch.add_flow(flow0)
batch.add_flow(flow1)
# Cannot add two flows with the same name.
with self.assertRaises(batch.Error):
batch.add_flow(flow2_same_name)
batch.submit(dry_run=True)
for i, flow in enumerate([flow0, flow1]):
assert flow.workdir == os.path.join(batch.workdir, "flow%d" % i)
batch.pickle_dump()
batch_from_pickle = BatchLauncher.pickle_load(batch.workdir)
assert all(f1 == f2 for f1, f2 in zip(batch.flows, batch_from_pickle.flows))
def test_batchlauncher(self):
"""Testing BatchLauncher methods."""
# Create the TaskManager.
manager = TaskManager.from_string(self.MANAGER)
print("batch_adapter", manager.batch_adapter)
assert manager.batch_adapter is not None
def build_flow_with_name(name):
"""Build a flow with workdir None and the given name."""
flow = Flow(workdir=None, manager=self.manager)
flow.set_name(name)
flow.register_task(self.fake_input)
work = Work()
work.register_scf_task(self.fake_input)
flow.register_work(work)
return flow
from pymatgen.io.abinit.launcher import BatchLauncher
tmpdir = tempfile.mkdtemp()
batch = BatchLauncher(workdir=tmpdir, manager=manager)
print(batch)
flow0 = build_flow_with_name("flow0")
flow1 = build_flow_with_name("flow1")
flow2_same_name = build_flow_with_name("flow1")
batch.add_flow(flow0)
# Cannot add the same flow twice.
with self.assertRaises(batch.Error):
batch.add_flow(flow0)
batch.add_flow(flow1)
# Cannot add two flows with the same name.
with self.assertRaises(batch.Error):
batch.add_flow(flow2_same_name)
batch.submit(dry_run=True)
for i, flow in enumerate([flow0, flow1]):
assert flow.workdir == os.path.join(batch.workdir, "flow%d" % i)
batch.pickle_dump()
batch_from_pickle = BatchLauncher.pickle_load(batch.workdir)
assert all(f1 == f2 for f1, f2 in zip(batch.flows, batch_from_pickle.flows))
def main():
def str_examples():
examples = """\
Usage example:\n
abibatch.py sub => Submit all flows located in the current directory
abibatch.py sub flowdir_si_* => Use shell wild cards to select flow directories
abibatch.py load batch_dir => Load BatchLauncher object from batch_dir and show the status of the flows.
Options for developers:
abirun.py prof ABIRUN_ARGS => to profile abirun.py
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Build the main parser.
parser = argparse.ArgumentParser(
epilog=str_examples(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'-v',
'--verbose',
default=0,
action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
parser.add_argument(
'--loglevel',
default="ERROR",
type=str,
help=
"set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG"
)
#parser.add_argument('flowdir', nargs="?", help=("File or directory containing the ABINIT flow"
# "If not given, the first flow in the current workdir is selected"))
timelimit_parser = argparse.ArgumentParser(add_help=False)
timelimit_parser.add_argument(
"-t",
'--timelimit',
default=None,
help=
("Time limit for batch script. "
"Accept int with seconds or string with time given in the slurm convention: "
"`days-hours:minutes:seconds`. If timelimit is None, the default value specified"
" in the `batch_adapter` entry of `manager.yml` is used."))
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command',
help='sub-command help',
description="Valid subcommands")
# Subparser for submit.
p_submit = subparsers.add_parser(
'sub',
parents=[timelimit_parser],
help="Find all flows in dir and submit them")
p_submit.add_argument("-d",
'--dry-run',
default=False,
action="store_true",
help="Dry run mode")
p_submit.add_argument("-w",
'--workdir',
default=None,
help="The workdir of the BatchLauncher")
p_submit.add_argument(
'paths',
nargs="*",
default=".",
help=("Directories containing the object."
"Use current working directory if not specified"))
# Subparser for resubmit.
p_resubmit = subparsers.add_parser(
'resub',
parents=[timelimit_parser],
help="Find all flows in dir and submit them")
p_resubmit.add_argument("-d",
'--dry-run',
default=False,
action="store_true",
help="Dry run mode")
p_resubmit.add_argument('top',
help="File or directory containing the object")
# Subparser for status.
p_status = subparsers.add_parser(
'status', help="Load object from pickle file and show status")
p_status.add_argument('top',
help="File or directory containing the object")
p_status.add_argument('-s',
'--summary',
default=False,
action="store_true",
help="Print short version with status counters.")
p_version = subparsers.add_parser('version',
help="Show version number and exit.")
# Subparser for info.
#p_load = subparsers.add_parser('info', help="Load object from pickle file and show info on the flows..")
#p_load.add_argument('top', help="File or directory containing the object")
# Parse command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
retcode = 0
if options.command == "version":
from abipy.core.release import version
print(version)
return 0
elif options.command == "sub":
#print("paths", options.paths)
workdir = options.workdir
if workdir is None:
workdir = "batch_launcher"
if os.path.exists(workdir):
msg = (
"Directory %s already exists. Cannot overwrite" % workdir +
"Use -w option to specify a not existent directory if you are generating a new BatchLauncher."
"Use abibatch status to inspect the status of an already existing BatchLauncher."
)
raise RuntimeError(msg)
batch = BatchLauncher.from_dir(options.paths,
workdir=workdir,
name=None)
if options.timelimit:
batch.set_timelimit(options.timelimit)
print(batch.to_string())
if not batch.flows:
print("Empty list of flows! Returning")
return 0
job = batch.submit(verbose=options.verbose, dry_run=options.dry_run)
if job.retcode:
print(
"Batch job submission failed. See batch directory for errors")
else:
print("Batch job has been submitted")
elif options.command == "resub":
batch = BatchLauncher.pickle_load(options.top)
batch.show_summary()
if options.timelimit:
batch.set_timelimit(options.timelimit)
job = batch.submit(verbose=options.verbose, dry_run=options.dry_run)
if job.retcode:
print(
"Batch job submission failed. See batch directory for errors")
else:
print("Batch job has been submitted")
elif options.command == "status":
batch = BatchLauncher.pickle_load(options.top)
# Select the method to call.
show_func = batch.show_status if not options.summary else batch.show_summary
show_func(verbose=options.verbose)
else:
raise RuntimeError("Don't know what to do with command %s!" %
options.command)
return retcode
def main():
def str_examples():
examples = """\
Usage example:\n
abibatch.py sub => Submit all flows located in the current directory
abibatch.py sub flowdir_si_* => Use shell wild cards to select flow directories
abibatch.py load batch_dir => Load BatchLauncher object from batch_dir and show the status of the flows.
Options for developers:
abirun.py prof ABIRUN_ARGS => to profile abirun.py
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Build the main parser.
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
parser.add_argument('--loglevel', default="ERROR", type=str,
help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
#parser.add_argument('flowdir', nargs="?", help=("File or directory containing the ABINIT flow"
# "If not given, the first flow in the current workdir is selected"))
timelimit_parser = argparse.ArgumentParser(add_help=False)
timelimit_parser.add_argument("-t", '--timelimit', default=None, help=("Time limit for batch script. "
"Accept int with seconds or string with time given in the slurm convention: "
"`days-hours:minutes:seconds`. If timelimit is None, the default value specified"
" in the `batch_adapter` entry of `manager.yml` is used."))
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for submit.
p_submit = subparsers.add_parser('sub', parents=[timelimit_parser], help="Find all flows in dir and submit them")
p_submit.add_argument("-d", '--dry-run', default=False, action="store_true", help="Dry run mode")
p_submit.add_argument("-w", '--workdir', default=None, help="The workdir of the BatchLauncher")
p_submit.add_argument('paths', nargs="*", default=".", help=("Directories containing the object."
"Use current working directory if not specified"))
# Subparser for resubmit.
p_resubmit = subparsers.add_parser('resub', parents=[timelimit_parser], help="Find all flows in dir and submit them")
p_resubmit.add_argument("-d", '--dry-run', default=False, action="store_true", help="Dry run mode")
p_resubmit.add_argument('top', help="File or directory containing the object")
# Subparser for status.
p_status = subparsers.add_parser('status', help="Load object from pickle file and show status")
p_status.add_argument('top', help="File or directory containing the object")
p_status.add_argument('-s', '--summary', default=False, action="store_true", help="Print short version with status counters.")
p_version = subparsers.add_parser('version', help="Show version number and exit.")
# Subparser for info.
#p_load = subparsers.add_parser('info', help="Load object from pickle file and show info on the flows..")
#p_load.add_argument('top', help="File or directory containing the object")
# Parse command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
retcode = 0
if options.command == "version":
from abipy.core.release import version
print(version)
return 0
elif options.command == "sub":
#print("paths", options.paths)
workdir = options.workdir
if workdir is None:
workdir = "batch_launcher"
if os.path.exists(workdir):
msg = ("Directory %s already exists. Cannot overwrite" % workdir +
"Use -w option to specify a not existent directory if you are generating a new BatchLauncher."
"Use abibatch status to inspect the status of an already existing BatchLauncher."
)
raise RuntimeError(msg)
batch = BatchLauncher.from_dir(options.paths, workdir=workdir, name=None)
if options.timelimit:
batch.set_timelimit(options.timelimit)
print(batch.to_string())
if not batch.flows:
print("Empty list of flows! Returning")
return 0
job = batch.submit(verbose=options.verbose, dry_run=options.dry_run)
if job.retcode:
print("Batch job submission failed. See batch directory for errors")
else:
print("Batch job has been submitted")
elif options.command == "resub":
batch = BatchLauncher.pickle_load(options.top)
batch.show_summary()
if options.timelimit:
batch.set_timelimit(options.timelimit)
job = batch.submit(verbose=options.verbose, dry_run=options.dry_run)
if job.retcode:
print("Batch job submission failed. See batch directory for errors")
else:
print("Batch job has been submitted")
elif options.command == "status":
batch = BatchLauncher.pickle_load(options.top)
# Select the method to call.
show_func = batch.show_status if not options.summary else batch.show_summary
show_func(verbose=options.verbose)
else:
raise RuntimeError("Don't know what to do with command %s!" % options.command)
return retcode