def parse_wf_for_latt_constants(wf_id):
lpad = LaunchPad().from_file(lpad_file_path)
wf = lpad.get_wf_by_fw_id(wf_id)
lattdata = {}
print('{} workflow retrieved with {} fws in it'.format(
wf.name, len(wf.fws)))
for fw in wf.fws:
print('\t{}'.format(fw.name))
if 'structure optimization' not in fw.name:
raise ValueError("Not a recognized firework!")
elif fw.state != 'COMPLETED':
print('\t\tstatus = {}, so skipping'.format(fw.state))
continue
pat = fw.launches[-1].launch_dir
s = Poscar.from_file(os.path.join(pat, 'CONTCAR.relax2.gz')).structure
nom = s.composition.reduced_formula
if nom in lattdata:
raise ValueError("{} already exists in lattdata??".format(nom))
elif (max(s.lattice.abc) - min(s.lattice.abc)) > 0.00001 or (
max(s.lattice.angles) - min(s.lattice.angles)) > 0.00001:
raise ValueError("Error occured with lattice relaxation??".format(
s.lattice))
else:
lattdata.update({nom: s.lattice.abc[0]})
print('\nFinalized lattice constant set:\n{}'.format(lattdata))
return lattdata
def do_launch(args):
if not args.launchpad_file and os.path.exists(
os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
elif not args.launchpad_file:
args.launchpad_file = LAUNCHPAD_LOC
if not args.fworker_file and os.path.exists(
os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
elif not args.fworker_file:
args.fworker_file = FWORKER_LOC
if not args.queueadapter_file and os.path.exists(
os.path.join(args.config_dir, 'my_qadapter.yaml')):
args.queueadapter_file = os.path.join(args.config_dir, 'my_qadapter.yaml')
elif not args.queueadapter_file:
args.queueadapter_file = QUEUEADAPTER_LOC
launchpad = LaunchPad.from_file(
args.launchpad_file) if args.launchpad_file else LaunchPad(
strm_lvl=args.loglvl)
fworker = FWorker.from_file(
args.fworker_file) if args.fworker_file else FWorker()
queueadapter = load_object_from_file(args.queueadapter_file)
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'rapidfire':
rapidfire(launchpad, fworker=fworker, qadapter=queueadapter, launch_dir=args.launch_dir,
nlaunches=args.nlaunches, njobs_queue=args.maxjobs_queue,
njobs_block=args.maxjobs_block, sleep_time=args.sleep,
reserve=args.reserve, strm_lvl=args.loglvl, timeout=args.timeout, fill_mode=args.fill_mode)
else:
launch_rocket_to_queue(launchpad, fworker, queueadapter,
args.launch_dir, args.reserve, args.loglvl, False, args.fill_mode, args.fw_id)
def do_launch(args):
if not args.launchpad_file and os.path.exists(
os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and os.path.exists(
os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
if not args.queueadapter_file and os.path.exists(
os.path.join(args.config_dir, 'my_qadapter.yaml')):
args.queueadapter_file = os.path.join(args.config_dir,
'my_qadapter.yaml')
launchpad = LaunchPad.from_file(
args.launchpad_file) if args.launchpad_file else LaunchPad(
strm_lvl=args.loglvl)
fworker = FWorker.from_file(
args.fworker_file) if args.fworker_file else FWorker()
queueadapter = load_object_from_file(args.queueadapter_file)
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'rapidfire':
rapidfire(launchpad, fworker, queueadapter, args.launch_dir,
args.nlaunches, args.maxjobs_queue,
args.maxjobs_block, args.sleep, args.reserve, args.loglvl)
else:
launch_rocket_to_queue(launchpad, fworker, queueadapter,
args.launch_dir, args.reserve, args.loglvl, False)
def launchpad():
"""Get a launchpad"""
# Manually add the package to be included
fw_config.USER_PACKAGES = [
'fireworks.user_objects', 'fireworks.utilities.tests', 'fw_tutorials',
'fireworks.features'
]
lpd = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
lpd.reset(password=None, require_password=False)
yield lpd
lpd.connection.drop_database(TESTDB_NAME)
def perturb_wf_setup(perovskite,
structure_type='111',
Nstruct=100,
perturbamnt=None,
max_strain=0.06,
nimages=8,
tags=[]):
if perturbamnt is None:
perturbamnt = perovskite.lattconst * 0.04
print(
"Setting up {} different perturbation polarization approaches\nMax strain = {}, "
"Perturbation amount = {}".format(Nstruct, max_strain, perturbamnt))
allowed_struct_type = ['111', '211', 's2s21', 's2s22']
if structure_type not in allowed_struct_type:
raise ValueError("{} not in {}".format(structure_type,
allowed_struct_type))
fws = []
pert_N_structs = [
perovskite.get_struct_from_structure_type(structure_type).as_dict()
]
user_incar_settings = {"ADDGRID": True, 'EDIFF': 1e-8, "NELMIN": 6}
for nind in range(Nstruct):
sclass = PerfectPerovskite(Asite=perovskite.eltA,
Bsite=perovskite.eltB,
Osite=perovskite.eltC,
lattconst=perovskite.lattconst)
strain_class = StrainedPerovskite.generate_random_strain(
sclass,
structure_type=structure_type,
max_strain=max_strain,
perturb_amnt=perturbamnt)
tmp_wf = polarization_wf(strain_class.structure,
strain_class.base,
submit=False,
nimages=nimages,
user_incar_settings=user_incar_settings,
tags=tags)
fws.extend(tmp_wf.fws)
pert_N_structs.append(strain_class.structure.as_dict())
print("Submitting Polarization workflow with {} fireworks".format(
len(fws)))
wf = Workflow(fws)
lp = LaunchPad().from_file(lpad_file_path)
lp.add_wf(wf)
def mlaunch():
m_description = 'This program launches multiple Rockets simultaneously'
parser = ArgumentParser(description=m_description)
parser.add_argument('num_jobs', help='the number of jobs to run in parallel', type=int)
parser.add_argument('--nlaunches', help='number of FireWorks to run in series per parallel job (int or "infinite"; default 0 is all jobs in DB)', default=0)
parser.add_argument('--sleep', help='sleep time between loops in infinite launch mode (secs)', default=None, type=int)
parser.add_argument('-l', '--launchpad_file', help='path to launchpad file',
default=LAUNCHPAD_LOC)
parser.add_argument('-w', '--fworker_file', help='path to fworker file',
default=FWORKER_LOC)
parser.add_argument('-c', '--config_dir', help='path to a directory containing the config file (used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl', help='level to print log messages', default='INFO')
parser.add_argument('-s', '--silencer', help='shortcut to mute log messages', action='store_true')
parser.add_argument('--nodefile', help='nodefile name or environment variable name containing the node file name (for populating FWData only)', default=None, type=str)
parser.add_argument('--ppn', help='processors per node (for populating FWData only)', default=1, type=int)
args = parser.parse_args()
if not args.launchpad_file and args.config_dir and os.path.exists(os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and args.config_dir and os.path.exists(os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(strm_lvl=args.loglvl)
if args.fworker_file:
fworker = FWorker.from_file(args.fworker_file)
else:
fworker = FWorker()
total_node_list = None
if args.nodefile:
if args.nodefile in os.environ:
args.nodefile = os.environ[args.nodefile]
with open(args.nodefile, 'r') as f:
total_node_list = [line.strip() for line in f.readlines()]
launch_multiprocess(launchpad, fworker, args.loglvl, args.nlaunches, args.num_jobs,
args.sleep, total_node_list, args.ppn)
def born():
fw = Firework(
[
Cry(),
Eat(),
Sleep(),
Poop(),
],
spec={"name": "BabyJain"}
)
launchpad = LaunchPad()
launchpad.add_wf(Workflow([fw]))
def clear_env():
sma = SubmissionMongoAdapter.auto_load()
lp = LaunchPad.auto_load()
snl = SNLMongoAdapter.auto_load()
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
with open(db_path) as f:
db_creds = json.load(f)
sma._reset()
lp.reset('', require_password=False)
snl._reset()
conn = MongoClient(db_creds['host'], db_creds['port'])
db = conn[db_creds['database']]
db.authenticate(db_creds['admin_user'], db_creds['admin_password'])
db.tasks.remove()
db.boltztrap.remove()
db.counter.remove()
db['dos_fs.chunks'].remove()
db['dos_fs.files'].remove()
db['band_structure_fs.files'].remove()
db['band_structure_fs.files'].remove()
def clear_env():
sma = SubmissionMongoAdapter.auto_load()
lp = LaunchPad.auto_load()
snl = SNLMongoAdapter.auto_load()
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
with open(db_path) as f:
db_creds = json.load(f)
sma._reset()
lp.reset('', require_password=False)
snl._reset()
conn = MongoClient(db_creds['host'], db_creds['port'])
db = conn[db_creds['database']]
db.authenticate(db_creds['admin_user'], db_creds['admin_password'])
db.tasks.remove()
db.boltztrap.remove()
db.counter.remove()
db['dos_fs.chunks'].remove()
db['dos_fs.files'].remove()
db['band_structure_fs.files'].remove()
db['band_structure_fs.files'].remove()
def run_task(self, fw_spec):
# the FW.json/yaml file is mandatory to get the fw_id
# no need to deserialize the whole FW
if '_add_launchpad_and_fw_id' in fw_spec:
lp = self.launchpad
fw_id = self.fw_id
else:
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError("Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
deleted_files = []
# iterate over all the fws and launches
for fw_id, fw in wf.id_fw.items():
for l in fw.launches+fw.archived_launches:
l_dir = l.launch_dir
deleted_files.extend(self.delete_files(os.path.join(l_dir, TMPDIR_NAME)))
deleted_files.extend(self.delete_files(os.path.join(l_dir, INDIR_NAME)))
deleted_files.extend(self.delete_files(os.path.join(l_dir, OUTDIR_NAME), self.out_exts))
logging.info("Deleted files:\n {}".format("\n".join(deleted_files)))
return FWAction(stored_data={'deleted_files': deleted_files})
def do_launch(args):
if not args.launchpad_file and os.path.exists(
os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
elif not args.launchpad_file:
args.launchpad_file = LAUNCHPAD_LOC
if not args.fworker_file and os.path.exists(
os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
elif not args.fworker_file:
args.fworker_file = FWORKER_LOC
if not args.queueadapter_file and os.path.exists(
os.path.join(args.config_dir, 'my_qadapter.yaml')):
args.queueadapter_file = os.path.join(args.config_dir, 'my_qadapter.yaml')
elif not args.queueadapter_file:
args.queueadapter_file = QUEUEADAPTER_LOC
launchpad = LaunchPad.from_file(
args.launchpad_file) if args.launchpad_file else LaunchPad(
strm_lvl=args.loglvl)
fworker = FWorker.from_file(
args.fworker_file) if args.fworker_file else FWorker()
queueadapter = load_object_from_file(args.queueadapter_file)
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'rapidfire':
rapidfire(launchpad, fworker=fworker, qadapter=queueadapter, launch_dir=args.launch_dir,
nlaunches=args.nlaunches, njobs_queue=args.maxjobs_queue,
njobs_block=args.maxjobs_block, sleep_time=args.sleep,
reserve=args.reserve, strm_lvl=args.loglvl, timeout=args.timeout, fill_mode=args.fill_mode)
else:
launch_rocket_to_queue(launchpad, fworker, queueadapter,
args.launch_dir, args.reserve, args.loglvl, False, args.fill_mode)
def run_task(self, fw_spec):
self.db_data.connect_mongoengine()
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError(
"No FW.json nor FW.yaml file present: impossible to determine fw_id"
)
fw_id = fw_dict['fw_id']
lp = LaunchPad.auto_load()
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
get_results_method = getattr(wf_class, 'get_mongoengine_results')
#TODO extend for multiple documents?
document = get_results_method(wf)
with self.db_data.switch_collection(
document.__class__) as document.__class__:
#TODO it would be better to try to remove automatically the FileFields already saved if the save of
# the document fails.
document.save()
def get_lp(args):
try:
if not args.launchpad_file and os.path.exists(os.path.join(args.config_dir, DEFAULT_LPAD_YAML)):
args.launchpad_file = os.path.join(args.config_dir, DEFAULT_LPAD_YAML)
if args.launchpad_file:
return LaunchPad.from_file(args.launchpad_file)
else:
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
return LaunchPad(logdir=args.logdir, strm_lvl=args.loglvl)
except:
traceback.print_exc()
err_message = 'FireWorks was not able to connect to MongoDB. Is the server running? The database file specified was {}.'.format(args.launchpad_file)
if not args.launchpad_file:
err_message += ' Type "lpad init" if you would like to set up a file that specifies location and credentials of your Mongo database (otherwise use default localhost configuration).'
raise ValueError(err_message)
def run_task(self, fw_spec):
# the FW.json/yaml file is mandatory to get the fw_id
# no need to deserialize the whole FW
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError("No FW.json nor FW.yaml file present: impossible to determine fw_id")
fw_id = fw_dict['fw_id']
lp = LaunchPad.auto_load()
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
get_results_method = getattr(wf_class, 'get_final_structure_and_history')
#TODO: make this more general ... just to test right now ...
results = get_results_method(wf)
database = MongoDatabase.from_dict(fw_spec['mongo_database'])
database.insert_entry({'structure': results['structure'], 'history': results['history']})
logging.info("Inserted data:\n something")
return FWAction()
def rlaunch():
m_description = 'This program launches one or more Rockets. A Rocket grabs a job from the central database and ' \
'runs it. The "single-shot" option launches a single Rocket, ' \
'whereas the "rapidfire" option loops until all FireWorks are completed.'
parser = ArgumentParser(description=m_description)
subparsers = parser.add_subparsers(help='command', dest='command')
single_parser = subparsers.add_parser('singleshot', help='launch a single Rocket')
rapid_parser = subparsers.add_parser('rapidfire',
help='launch multiple Rockets (loop until all FireWorks complete)')
single_parser.add_argument('-f', '--fw_id', help='specific fw_id to run', default=None, type=int)
single_parser.add_argument('--offline', help='run in offline mode (FW.json required)', action='store_true')
rapid_parser.add_argument('--nlaunches', help='num_launches (int or "infinite"; default 0 is all jobs in DB)', default=0)
rapid_parser.add_argument('--sleep', help='sleep time between loops (secs)', default=None, type=int)
parser.add_argument('-l', '--launchpad_file', help='path to launchpad file', default=LAUNCHPAD_LOC)
parser.add_argument('-w', '--fworker_file', help='path to fworker file', default=FWORKER_LOC)
parser.add_argument('-c', '--config_dir', help='path to a directory containing the config file (used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl', help='level to print log messages', default='INFO')
parser.add_argument('-s', '--silencer', help='shortcut to mute log messages', action='store_true')
args = parser.parse_args()
signal.signal(signal.SIGINT, handle_interrupt) # graceful exist on ^C
if not args.launchpad_file and os.path.exists(os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and os.path.exists(os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'singleshot' and args.offline:
launchpad = None
else:
launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(strm_lvl=args.loglvl)
if args.fworker_file:
fworker = FWorker.from_file(args.fworker_file)
else:
fworker = FWorker()
# prime addr lookups
_log = get_fw_logger("rlaunch", stream_level="INFO")
_log.info("Hostname/IP lookup (this will take a few seconds)")
get_my_host()
get_my_ip()
if args.command == 'rapidfire':
rapidfire(launchpad, fworker, None, args.nlaunches, -1, args.sleep, args.loglvl)
else:
launch_rocket(launchpad, fworker, args.fw_id, args.loglvl)
def rlaunch():
m_description = 'This program launches one or more Rockets. A Rocket grabs a job from the central database and ' \
'runs it. The "single-shot" option launches a single Rocket, ' \
'whereas the "rapidfire" option loops until all FireWorks are completed.'
parser = ArgumentParser(description=m_description)
subparsers = parser.add_subparsers(help='command', dest='command')
single_parser = subparsers.add_parser('singleshot', help='launch a single Rocket')
rapid_parser = subparsers.add_parser('rapidfire',
help='launch multiple Rockets (loop until all FireWorks complete)')
single_parser.add_argument('-f', '--fw_id', help='specific fw_id to run', default=None, type=int)
single_parser.add_argument('--offline', help='run in offline mode (FW.json required)', action='store_true')
rapid_parser.add_argument('--nlaunches', help='num_launches (int or "infinite"; default 0 is all jobs in DB)', default=0)
rapid_parser.add_argument('--sleep', help='sleep time between loops (secs)', default=None, type=int)
parser.add_argument('-l', '--launchpad_file', help='path to launchpad file', default=LAUNCHPAD_LOC)
parser.add_argument('-w', '--fworker_file', help='path to fworker file', default=FWORKER_LOC)
parser.add_argument('-c', '--config_dir', help='path to a directory containing the config file (used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl', help='level to print log messages', default='INFO')
parser.add_argument('-s', '--silencer', help='shortcut to mute log messages', action='store_true')
args = parser.parse_args()
signal.signal(signal.SIGINT, handle_interrupt) # graceful exist on ^C
if not args.launchpad_file and os.path.exists(os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and os.path.exists(os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'singleshot' and args.offline:
launchpad = None
else:
launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(strm_lvl=args.loglvl)
if args.fworker_file:
fworker = FWorker.from_file(args.fworker_file)
else:
fworker = FWorker()
# prime addr lookups
_log = get_fw_logger("rlaunch", stream_level="INFO")
_log.info("Hostname/IP lookup (this will take a few seconds)")
get_my_host()
get_my_ip()
if args.command == 'rapidfire':
rapidfire(launchpad, fworker, None, args.nlaunches, -1, args.sleep, args.loglvl)
else:
launch_rocket(launchpad, fworker, args.fw_id, args.loglvl)
def get_lp_and_fw_id_from_task(task, fw_spec):
"""
Given an instance of a running task and its spec, tries to load the LaunchPad and the current fw_id.
It will first check for "_add_launchpad_and_fw_id", then try to load from FW.json/FW.yaml file.
Should be used inside tasks that require to access to the LaunchPad and to the whole workflow.
Args:
task: An instance of a running task
fw_spec: The spec of the task
Returns:
an instance of LaunchPah and the fw_id of the current task
"""
if '_add_launchpad_and_fw_id' in fw_spec:
lp = task.launchpad
fw_id = task.fw_id
# lp may be None in offline mode
if lp is None:
raise RuntimeError("The LaunchPad in spec is None.")
else:
try:
with open('FW.json', "rt") as fh:
fw_dict = json.load(fh, cls=MontyDecoder)
except IOError:
try:
with open('FW.yaml', "rt") as fh:
fw_dict = yaml.load(fh)
except IOError:
raise RuntimeError("Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
logger.warning("LaunchPad not available from spec. Generated with auto_load.")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
# since it is not given that the LaunchPad is the correct one, try to verify if the workflow
# and the fw_id are being accessed correctly
try:
fw = lp.get_fw_by_id(fw_id)
except ValueError as e:
traceback.print_exc()
raise RuntimeError("The firework with id {} is not present in the LaunchPad {}. The LaunchPad is "
"probably incorrect.". format(fw_id, lp))
if fw.state != "RUNNING":
raise RuntimeError("The firework with id {} from LaunchPad {} is {}. There might be an error in the "
"selection of the LaunchPad". format(fw_id, lp, fw.state))
if len(fw.tasks) != len(fw_dict['spec']['_tasks']):
raise RuntimeError("The firework with id {} from LaunchPad {} is has different number of tasks "
"from the current.".format(fw_id, lp))
for db_t, dict_t in zip(fw.tasks, fw_dict['spec']['_tasks']):
if db_t.fw_name != dict_t['_fw_name']:
raise RuntimeError("The firework with id {} from LaunchPad {} has task that don't match: "
"{} and {}.".format(fw_id, lp, db_t.fw_name, dict_t['fw_name']))
return lp, fw_id
def auto_load(cls):
sma = SubmissionMongoAdapter.auto_load()
l_dir = FWConfig().CONFIG_FILE_DIR
l_file = os.path.join(l_dir, 'my_launchpad.yaml')
lp = LaunchPad.from_file(l_file)
return SubmissionProcessor(sma, lp)
def setUpClass(cls):
cls.lp = None
cls.fworker = FWorker()
try:
cls.lp = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
cls.lp.reset(password=None, require_password=False)
except:
raise unittest.SkipTest('MongoDB is not running in localhost:27017! Skipping tests.')
def polarization_wf(polar_structure,
nonpolar_structure,
submit=False,
nimages=8,
user_incar_settings={},
tags=[]):
"""
:param polar_structure: structure of polar structure
:param nonpolar_structure: structure of nonpolar structure
:param submit: boolean for submitting
:param tags: list of string tags
:return:
"""
if polar_structure.species != nonpolar_structure.species:
raise ValueError("WRONG ORDER OF SPECIES: {} vs {}".format(
polar_structure.species, nonpolar_structure.species))
vasp_input_set_params = {'user_incar_settings': user_incar_settings}
wf = get_wf_ferroelectric(
polar_structure,
nonpolar_structure,
vasp_cmd=">>vasp_cmd<<",
db_file='>>db_file<<',
vasp_input_set_polar="MPStaticSet",
vasp_input_set_nonpolar="MPStaticSet",
relax=False,
vasp_relax_input_set_polar=vasp_input_set_params,
vasp_relax_input_set_nonpolar=vasp_input_set_params,
nimages=nimages,
hse=False,
add_analysis_task=True,
tags=tags)
print('workflow created with {} fws'.format(len(wf.fws)))
if submit:
print("\tSubmitting Polarization workflow")
lp = LaunchPad().from_file(lpad_file_path)
lp.add_wf(wf)
else:
return wf
def update_checkpoint(launchpad: LaunchPad, launch_dir: str, launch_id: int, checkpoint: Dict[str, any]) -> None:
"""
Helper function to update checkpoint
Args:
launchpad (LaunchPad): LaunchPad to ping with checkpoint data
launch_dir (str): directory in which FW_offline.json was created
launch_id (int): launch id to update
checkpoint (dict): checkpoint data
"""
if launchpad:
launchpad.ping_launch(launch_id, checkpoint=checkpoint)
else:
fpath = zpath(os.path.join(launch_dir, "FW_offline.json"))
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d["checkpoint"] = checkpoint
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
def bootstrap_app(*args, **kwargs):
"""Pass instead of `app` to a forking process.
This is so a server process will re-initialize a MongoDB client
connection after forking. This is useful to avoid deadlock when
using pymongo with multiprocessing.
"""
import fireworks.flask_site.app
fireworks.flask_site.app.lp = LaunchPad.from_dict(
json.loads(os.environ["FWDB_CONFIG"]))
return app(*args, **kwargs)
def bootstrap_app(*args, **kwargs):
"""Pass instead of `app` to a forking process.
This is so a server process will re-initialize a MongoDB client
connection after forking. This is useful to avoid deadlock when
using pymongo with multiprocessing.
"""
import fireworks.flask_site.app
fireworks.flask_site.app.lp = LaunchPad.from_dict(
json.loads(os.environ["FWDB_CONFIG"]))
return app(*args, **kwargs)
def __init__(self, launchpad=None):
super().__init__()
# Here store the launchpad in the class attribute so it can be reused....
if launchpad is not None:
self.lpad = launchpad
# Keep the launchpad
FwScheduler._lpad = launchpad
else:
# Create and save the launchpad
if FwScheduler._lpad is None:
FwScheduler._lpad = LaunchPad.from_file(LAUNCHPAD_LOC)
self.lpad = FwScheduler._lpad
def setup_fireworks(cls):
"""
Sets up the fworker and launchpad if a connection to a local mongodb is available.
cls.lp is set to None if not available
"""
cls.fworker = FWorker()
try:
cls.lp = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
cls.lp.reset(password=None, require_password=False)
except:
cls.lp = None
def setUp(self):
if os.path.exists(self.scratch_dir):
shutil.rmtree(self.scratch_dir)
os.makedirs(self.scratch_dir)
os.chdir(self.scratch_dir)
try:
self.lp = LaunchPad.from_file(os.path.join(db_dir, "my_launchpad.yaml"))
self.lp.reset("", require_password=False)
except:
raise unittest.SkipTest(
'Cannot connect to MongoDB! Is the database server running? '
'Are the credentials correct?')
def init_yaml(args):
fields = (("host", "localhost"), ("port", 27017), ("name", "fireworks"), ("username", None), ("password", None))
doc = {}
print("Please supply the following configuration values")
print("(press Enter if you want to accept the defaults)\n")
for k, v in fields:
val = input("Enter {} (default: {}) : ".format(k, v))
doc[k] = val if val else v
doc["port"] = int(doc["port"]) # enforce the port as an int
with open(args.config_file, "w") as f:
import yaml
yaml.dump(LaunchPad.from_dict(doc).to_dict(), f)
print("\nConfiguration written to {}!".format(args.config_file))
def init_yaml(args):
fields = (("host", "localhost"), ("port", 27017), ("name", "fireworks"),
("username", None), ("password", None))
doc = {}
print("Please supply the following configuration values")
print("(press Enter if you want to accept the defaults)\n")
for k, v in fields:
val = input("Enter {} (default: {}) : ".format(k, v))
doc[k] = val if val else v
doc["port"] = int(doc["port"]) # enforce the port as an int
with open(args.config_file, "w") as f:
import yaml
yaml.dump(LaunchPad.from_dict(doc).to_dict(), f)
print("\nConfiguration written to {}!".format(args.config_file))
def mlaunch():
m_description = 'This program launches multiple Rockets simultaneously'
parser = ArgumentParser(description=m_description)
parser.add_argument('num_jobs', help='the number of jobs to run in parallel', type=int)
parser.add_argument('--nlaunches', help='number of FireWorks to run in series per parallel job (int or "infinite"; default 0 is all jobs in DB)', default=0)
parser.add_argument('--sleep', help='sleep time between loops in infinite launch mode (secs)', default=None, type=int)
parser.add_argument('--timeout', help='timeout (secs) after which to quit (default None)', default=None, type=int)
parser.add_argument('-l', '--launchpad_file', help='path to launchpad file',
default=LAUNCHPAD_LOC)
parser.add_argument('-w', '--fworker_file', help='path to fworker file',
default=FWORKER_LOC)
parser.add_argument('-c', '--config_dir', help='path to a directory containing the config file (used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl', help='level to print log messages', default='INFO')
parser.add_argument('-s', '--silencer', help='shortcut to mute log messages', action='store_true')
parser.add_argument('--nodefile', help='nodefile name or environment variable name containing the node file name (for populating FWData only)', default=None, type=str)
parser.add_argument('--ppn', help='processors per node (for populating FWData only)', default=1, type=int)
args = parser.parse_args()
if not args.launchpad_file and args.config_dir and os.path.exists(os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and args.config_dir and os.path.exists(os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(strm_lvl=args.loglvl)
if args.fworker_file:
fworker = FWorker.from_file(args.fworker_file)
else:
fworker = FWorker()
total_node_list = None
if args.nodefile:
if args.nodefile in os.environ:
args.nodefile = os.environ[args.nodefile]
with open(args.nodefile, 'r') as f:
total_node_list = [line.strip() for line in f.readlines()]
launch_multiprocess(launchpad, fworker, args.loglvl, args.nlaunches, args.num_jobs,
args.sleep, total_node_list, args.ppn, timeout=args.timeout)
def restart_fizzled():
module_dir = os.path.dirname(os.path.abspath(__file__))
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
for fw in lpdb.fireworks.find({"state": "FIZZLED"}, {"fw_id": 1, "spec.task_type": 1}):
fw_id = fw['fw_id']
task_type = fw['spec']['task_type']
restart_id = fw_id
if 'VASP db insertion' in task_type:
restart_id = fw_id - 1
elif 'Controller' in task_type:
restart_id = fw_id - 2
lpdb.rerun_fw(restart_id)
def get_lp(args):
try:
if not args.launchpad_file and os.path.exists(os.path.join(args.config_dir, DEFAULT_LPAD_YAML)):
args.launchpad_file = os.path.join(args.config_dir, DEFAULT_LPAD_YAML)
if args.launchpad_file:
return LaunchPad.from_file(args.launchpad_file)
else:
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
return LaunchPad(logdir=args.logdir, strm_lvl=args.loglvl)
except:
traceback.print_exc()
err_message = 'FireWorks was not able to connect to MongoDB. Is the server running? The database file specified was {}.'.format(args.launchpad_file)
if not args.launchpad_file:
err_message += ' Type "lpad init" if you would like to set up a file that specifies location and credentials of your Mongo database (otherwise use default localhost configuration).'
raise ValueError(err_message)
def run_task(self, fw_spec):
# the FW.json/yaml file is mandatory to get the fw_id
# no need to deserialize the whole FW
if '_add_launchpad_and_fw_id' in fw_spec:
lp = self.launchpad
fw_id = self.fw_id
else:
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError(
"Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
wf = lp.get_wf_by_fw_id(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
database = fw_spec['mongo_database']
if self.criteria is not None:
entry = database.get_entry(criteria=self.criteria)
else:
entry = {}
inserted = []
for root_key, method_name in self.insertion_data.items():
get_results_method = getattr(wf_class, method_name)
results = get_results_method(wf)
for key, val in results.items():
entry[key] = jsanitize(val)
inserted.append(key)
if self.criteria is not None:
database.save_entry(entry=entry)
else:
database.insert_entry(entry=entry)
logging.info("Inserted data:\n{}".format('- {}\n'.join(inserted)))
return FWAction()
def archive_deprecated_fws():
# find all snlgroups that are deprecated, and archive all WFs that have deprecated fw_ids so we don't run them
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snlgroups = snldb.snlgroups
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
for g in snlgroups.find({'canonical_snl.about.remarks':'DEPRECATED'}, {'snlgroup_id': 1}):
while lpdb.fireworks.find_one({'spec.snlgroup_id': g['snlgroup_id'], 'state': {'$ne': 'ARCHIVED'}}, {'fw_id': 1}):
fw = lpdb.fireworks.find_one({'spec.snlgroup_id': g['snlgroup_id'], 'state': {'$ne': 'ARCHIVED'}}, {'fw_id': 1})
print fw['fw_id']
lpdb.archive_wf(fw['fw_id'])
print 'DONE'
def run_task(self, fw_spec):
# the FW.json/yaml file is mandatory to get the fw_id
# no need to deserialize the whole FW
if '_add_launchpad_and_fw_id' in fw_spec:
lp = self.launchpad
fw_id = self.fw_id
else:
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError("Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
wf = lp.get_wf_by_fw_id(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
database = fw_spec['mongo_database']
if self.criteria is not None:
entry = database.get_entry(criteria=self.criteria)
else:
entry = {}
inserted = []
for root_key, method_name in self.insertion_data.items():
get_results_method = getattr(wf_class, method_name)
results = get_results_method(wf)
for key, val in results.items():
entry[key] = jsanitize(val)
inserted.append(key)
if self.criteria is not None:
database.save_entry(entry=entry)
else:
database.insert_entry(entry=entry)
logging.info("Inserted data:\n{}".format('- {}\n'.join(inserted)))
return FWAction()
def get_colls():
colls = namedtuple('Collections', ['snl', 'snlgroups'])
sma = SNLMongoAdapter.from_file(snl_f)
lp = LaunchPad.from_file(fw_f)
colls.snl = sma.snl
colls.snlgroups = sma.snlgroups
colls.fireworks = lp.fireworks
colls.launches = lp.launches
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
colls.tasks = db['tasks']
return colls
def run_task(self, fw_spec):
# the FW.json/yaml file is mandatory to get the fw_id
# no need to deserialize the whole FW
if '_add_launchpad_and_fw_id' in fw_spec:
lp = self.launchpad
fw_id = self.fw_id
else:
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError(
"Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
deleted_files = []
# iterate over all the fws and launches
for fw_id, fw in wf.id_fw.items():
for l in fw.launches + fw.archived_launches:
l_dir = l.launch_dir
deleted_files.extend(
self.delete_files(os.path.join(l_dir, TMPDIR_NAME)))
deleted_files.extend(
self.delete_files(os.path.join(l_dir, INDIR_NAME)))
deleted_files.extend(
self.delete_files(os.path.join(l_dir, OUTDIR_NAME),
self.out_exts))
logging.info("Deleted files:\n {}".format("\n".join(deleted_files)))
return FWAction(stored_data={'deleted_files': deleted_files})
def process_task(self, data):
try:
dir_name = data[0]
parse_dos = data[1]
prev_info = self.tasks.find_one({'dir_name_full': dir_name}, {'task_type': 1, 'snl_final': 1, 'snlgroup_id_final': 1, 'snlgroup_changed': 1})
drone = MPVaspDrone(
host=self.host, port=self.port,
database=self.database, user=self.admin_user,
password=self.admin_password,
collection=self.collection, parse_dos=parse_dos,
additional_fields={},
update_duplicates=True)
t_id, d = drone.assimilate(dir_name, launches_coll=LaunchPad.auto_load().launches)
self.tasks.update({"task_id": t_id}, {"$set": {"snl_final": prev_info['snl_final'], "snlgroup_id_final": prev_info['snlgroup_id_final'], "snlgroup_changed": prev_info['snlgroup_changed']}})
print 'FINISHED', t_id
except:
print '-----'
print 'ENCOUNTERED AN EXCEPTION!!!', data[0]
traceback.print_exc()
print '-----'
x = tdb.tasks.find_one({"fw_id": fw_id}, {"analysis": 1})
warnings = x['analysis'].get('warnings', [])
warnings.extend(x['analysis']['errors_MP']['signals'])
errors = x['analysis'].get('errors', [])
errors.extend(x['analysis']['errors_MP']['critical_signals'])
warnings = set(warnings)
errors = set(errors)
warnings = warnings.difference(errors)
return set(warnings), set(errors)
if __name__ == '__main__':
module_dir = os.path.dirname(os.path.abspath(__file__))
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
tasks_f = os.path.join(module_dir, 'tasks_read.yaml')
creds = {}
with open(tasks_f) as f:
creds = yaml.load(f)
connection = MongoClient(creds['host'], creds['port'])
tdb = connection[creds['db']]
tdb.authenticate(creds['username'], creds['password'])
except_dict = defaultdict(int)
fizzled_fws = []
def arlaunch():
"""
Function rapid-fire job launching
"""
m_description = 'This program launches one or more Rockets. A Rocket retrieves a job from the ' \
'central database and runs it. The "single-shot" option launches a single Rocket, ' \
'whereas the "rapidfire" option loops until all FireWorks are completed.'
parser = ArgumentParser(description=m_description)
subparsers = parser.add_subparsers(help='command', dest='command')
single_parser = subparsers.add_parser('singleshot',
help='launch a single Rocket')
rapid_parser = subparsers.add_parser(
'rapidfire',
help='launch multiple Rockets (loop until all FireWorks complete)')
multi_parser = subparsers.add_parser(
'multi', help='launches multiple Rockets simultaneously')
single_parser.add_argument('-f',
'--fw_id',
help='specific fw_id to run',
default=None,
type=int)
single_parser.add_argument('--offline',
help='run in offline mode (FW.json required)',
action='store_true')
single_parser.add_argument('--pdb',
help='shortcut to invoke debugger on error',
action='store_true')
rapid_parser.add_argument('--nlaunches',
help='num_launches (int or "infinite"; '
'default 0 is all jobs in DB)',
default=0)
rapid_parser.add_argument(
'--timeout',
help='timeout (secs) after which to quit (default None)',
default=None,
type=int)
rapid_parser.add_argument(
'--max_loops',
help='after this many sleep loops, quit even in '
'infinite nlaunches mode (default -1 is infinite loops)',
default=-1,
type=int)
rapid_parser.add_argument('--sleep',
help='sleep time between loops (secs)',
default=None,
type=int)
rapid_parser.add_argument(
'--local_redirect',
help="Redirect stdout and stderr to the launch directory",
action="store_true")
multi_parser.add_argument('num_jobs',
help='the number of jobs to run in parallel',
type=int)
multi_parser.add_argument('--nlaunches',
help='number of FireWorks to run in series per '
'parallel job (int or "infinite"; default 0 is '
'all jobs in DB)',
default=0)
multi_parser.add_argument(
'--sleep',
help='sleep time between loops in infinite launch mode'
'(secs)',
default=None,
type=int)
multi_parser.add_argument(
'--timeout',
help='timeout (secs) after which to quit (default None)',
default=None,
type=int)
multi_parser.add_argument(
'--nodefile',
help='nodefile name or environment variable name '
'containing the node file name (for populating'
' FWData only)',
default=None,
type=str)
multi_parser.add_argument(
'--ppn',
help='processors per node (for populating FWData only)',
default=1,
type=int)
multi_parser.add_argument('--exclude_current_node',
help="Don't use the script launching node"
"as compute node",
action="store_true")
multi_parser.add_argument(
'--local_redirect',
help="Redirect stdout and stderr to the launch directory",
action="store_true")
parser.add_argument('-l',
'--launchpad_file',
help='path to launchpad file')
parser.add_argument('-w',
'--fworker_file',
required=True,
help='path to fworker file')
parser.add_argument('-c',
'--config_dir',
help='path to a directory containing the config file '
'(used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl',
help='level to print log messages',
default='INFO')
parser.add_argument('-s',
'--silencer',
help='shortcut to mute log messages',
action='store_true')
try:
import argcomplete
argcomplete.autocomplete(parser)
# This supports bash autocompletion. To enable this, pip install
# argcomplete, activate global completion, or add
# eval "$(register-python-argcomplete rlaunch)"
# into your .bash_profile or .bashrc
except ImportError:
pass
args = parser.parse_args()
signal.signal(signal.SIGINT, handle_interrupt) # graceful exit on ^C
if not args.launchpad_file and os.path.exists(
os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir,
'my_launchpad.yaml')
elif not args.launchpad_file:
args.launchpad_file = LAUNCHPAD_LOC
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'singleshot' and args.offline:
launchpad = None
else:
launchpad = LaunchPad.from_file(
args.launchpad_file) if args.launchpad_file else LaunchPad(
strm_lvl=args.loglvl)
fworker = AiiDAFWorker.from_file(args.fworker_file)
# prime addr lookups
_log = get_fw_logger("rlaunch", stream_level="INFO")
_log.info("Hostname/IP lookup (this will take a few seconds)")
get_my_host()
get_my_ip()
if args.command == 'rapidfire':
rapidfire(launchpad,
fworker=fworker,
m_dir=None,
nlaunches=args.nlaunches,
max_loops=args.max_loops,
sleep_time=args.sleep,
strm_lvl=args.loglvl,
timeout=args.timeout,
local_redirect=args.local_redirect)
elif args.command == 'multi':
total_node_list = None
if args.nodefile:
if args.nodefile in os.environ:
args.nodefile = os.environ[args.nodefile]
with open(args.nodefile, 'r') as fhandle:
total_node_list = [
line.strip() for line in fhandle.readlines()
]
launch_multiprocess(launchpad,
fworker,
args.loglvl,
args.nlaunches,
args.num_jobs,
args.sleep,
total_node_list,
args.ppn,
timeout=args.timeout,
exclude_current_node=args.exclude_current_node,
local_redirect=args.local_redirect)
else:
launch_rocket(launchpad,
fworker,
args.fw_id,
args.loglvl,
pdb_on_exception=args.pdb)
def rlaunch():
m_description = 'This program launches one or more Rockets. A Rocket grabs a job from the ' \
'central database and runs it. The "single-shot" option launches a single Rocket, ' \
'whereas the "rapidfire" option loops until all FireWorks are completed.'
parser = ArgumentParser(description=m_description)
subparsers = parser.add_subparsers(help='command', dest='command')
single_parser = subparsers.add_parser('singleshot', help='launch a single Rocket')
rapid_parser = subparsers.add_parser('rapidfire',
help='launch multiple Rockets (loop until all FireWorks complete)')
multi_parser = subparsers.add_parser('multi',
help='launches multiple Rockets simultaneously')
single_parser.add_argument('-f', '--fw_id', help='specific fw_id to run', default=None, type=int)
single_parser.add_argument('--offline', help='run in offline mode (FW.json required)', action='store_true')
rapid_parser.add_argument('--nlaunches', help='num_launches (int or "infinite"; '
'default 0 is all jobs in DB)', default=0)
rapid_parser.add_argument('--timeout', help='timeout (secs) after which to quit (default None)',
default=None, type=int)
rapid_parser.add_argument('--max_loops', help='after this many sleep loops, quit even in '
'infinite nlaunches mode (default -1 is infinite loops)',
default=-1, type=int)
rapid_parser.add_argument('--sleep', help='sleep time between loops (secs)', default=None,
type=int)
multi_parser.add_argument('num_jobs', help='the number of jobs to run in parallel', type=int)
multi_parser.add_argument('--nlaunches', help='number of FireWorks to run in series per '
'parallel job (int or "infinite"; default 0 is '
'all jobs in DB)',
default=0)
multi_parser.add_argument('--sleep', help='sleep time between loops in infinite launch mode'
'(secs)',
default=None, type=int)
multi_parser.add_argument('--timeout', help='timeout (secs) after which to quit (default None)',
default=None, type=int)
multi_parser.add_argument('--nodefile', help='nodefile name or environment variable name '
'containing the node file name (for populating'
' FWData only)',
default=None, type=str)
multi_parser.add_argument('--ppn', help='processors per node (for populating FWData only)',
default=1, type=int)
multi_parser.add_argument('--exclude_current_node', help="Don't use the script launching node"
"as compute node",
action="store_true")
parser.add_argument('-l', '--launchpad_file', help='path to launchpad file', default=LAUNCHPAD_LOC)
parser.add_argument('-w', '--fworker_file', help='path to fworker file', default=FWORKER_LOC)
parser.add_argument('-c', '--config_dir', help='path to a directory containing the config file '
'(used if -l, -w unspecified)',
default=CONFIG_FILE_DIR)
parser.add_argument('--loglvl', help='level to print log messages', default='INFO')
parser.add_argument('-s', '--silencer', help='shortcut to mute log messages', action='store_true')
args = parser.parse_args()
signal.signal(signal.SIGINT, handle_interrupt) # graceful exit on ^C
if not args.launchpad_file and os.path.exists(os.path.join(args.config_dir, 'my_launchpad.yaml')):
args.launchpad_file = os.path.join(args.config_dir, 'my_launchpad.yaml')
if not args.fworker_file and os.path.exists(os.path.join(args.config_dir, 'my_fworker.yaml')):
args.fworker_file = os.path.join(args.config_dir, 'my_fworker.yaml')
args.loglvl = 'CRITICAL' if args.silencer else args.loglvl
if args.command == 'singleshot' and args.offline:
launchpad = None
else:
launchpad = LaunchPad.from_file(args.launchpad_file) if args.launchpad_file else LaunchPad(
strm_lvl=args.loglvl)
if args.fworker_file:
fworker = FWorker.from_file(args.fworker_file)
else:
fworker = FWorker()
# prime addr lookups
_log = get_fw_logger("rlaunch", stream_level="INFO")
_log.info("Hostname/IP lookup (this will take a few seconds)")
get_my_host()
get_my_ip()
if args.command == 'rapidfire':
rapidfire(launchpad, fworker=fworker, m_dir=None, nlaunches=args.nlaunches,
max_loops=args.max_loops, sleep_time=args.sleep, strm_lvl=args.loglvl,
timeout=args.timeout)
elif args.command == 'multi':
total_node_list = None
if args.nodefile:
if args.nodefile in os.environ:
args.nodefile = os.environ[args.nodefile]
with open(args.nodefile, 'r') as f:
total_node_list = [line.strip() for line in f.readlines()]
launch_multiprocess(launchpad, fworker, args.loglvl, args.nlaunches, args.num_jobs,
args.sleep, total_node_list, args.ppn, timeout=args.timeout,
exclude_current_node=args.exclude_current_node)
else:
launch_rocket(launchpad, fworker, args.fw_id, args.loglvl)
from fireworks.core.launchpad import LaunchPad
from fireworks.core.firework import Firework, Workflow
from mpworks.firetasks.controller_tasks import AddEStructureTask
from fireworks.utilities.fw_utilities import get_slug
from mpworks.snl_utils.snl_mongo import SNLMongoAdapter
from pymongo import MongoClient
from collections import Counter
from datetime import datetime
from fnmatch import fnmatch
from custodian.vasp.handlers import VaspErrorHandler
cwd = os.getcwd()
# DONE manually: "mp-987" -> fw_id: 119629
lpdb = LaunchPad.from_file(
'/global/homes/m/matcomp/mp_prod/config/config_Mendel/my_launchpad.yaml')
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': 100000
}
sma = SNLMongoAdapter.from_file(
'/global/homes/m/matcomp/mp_prod/config/dbs/snl_db.yaml')
with open('/global/homes/m/matcomp/mp_prod/materials_db_prod.yaml') as f:
creds = yaml.load(f)
client = MongoClient(creds['host'], creds['port'])
db = client[creds['db']]
db.authenticate(creds['username'], creds['password'])
materials = db['materials']
tasks = db['tasks']
print materials.count()
from atomate.qchem.workflows.base.FF_then_fragment import get_wf_FF_then_fragment
from fireworks.core.launchpad import LaunchPad
from pymatgen.core import Molecule
mol = Molecule.from_file("BF4-.xyz")
wf = get_wf_FF_then_fragment(molecule=mol, max_cores=32)
lp = LaunchPad.auto_load()
lp.add_wf(wf)
def auto_load(cls):
spsma = SPSubmissionsMongoAdapter.auto_load()
lp = LaunchPad.auto_load()
return SPSubmissionProcessor(spsma, lp)
def run(self, pdb_on_exception=False):
"""
Run the rocket (check out a job from the database and execute it)
Args:
pdb_on_exception (bool): whether to invoke the debugger on
a caught exception. Default False.
"""
all_stored_data = {} # combined stored data for *all* the Tasks
all_update_spec = {} # combined update_spec for *all* the Tasks
all_mod_spec = [] # combined mod_spec for *all* the Tasks
lp = self.launchpad
launch_dir = os.path.abspath(os.getcwd())
logdir = lp.get_logdir() if lp else None
l_logger = get_fw_logger('rocket.launcher', l_dir=logdir,
stream_level=ROCKET_STREAM_LOGLEVEL)
# check a FW job out of the launchpad
if lp:
m_fw, launch_id = lp.checkout_fw(self.fworker, launch_dir, self.fw_id)
else: # offline mode
m_fw = Firework.from_file(os.path.join(os.getcwd(), "FW.json"))
# set the run start time
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['started_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
launch_id = None # we don't need this in offline mode...
if not m_fw:
print("No FireWorks are ready to run and match query! {}".format(self.fworker.query))
return False
final_state = None
ping_stop = None
btask_stops = []
try:
if '_launch_dir' in m_fw.spec and lp:
prev_dir = launch_dir
launch_dir = os.path.expandvars(m_fw.spec['_launch_dir'])
if not os.path.abspath(launch_dir):
launch_dir = os.path.normpath(os.path.join(os.getcwd(), launch_dir))
# thread-safe "mkdir -p"
try:
os.makedirs(launch_dir)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
os.chdir(launch_dir)
if not os.path.samefile(launch_dir, prev_dir):
lp.change_launch_dir(launch_id, launch_dir)
if not os.listdir(prev_dir) and REMOVE_USELESS_DIRS:
try:
os.rmdir(prev_dir)
except:
pass
recovery = m_fw.spec.get('_recovery', None)
if recovery:
recovery_dir = recovery.get('_prev_dir')
recovery_mode = recovery.get('_mode')
starting_task = recovery.get('_task_n')
all_stored_data.update(recovery.get('_all_stored_data'))
all_update_spec.update(recovery.get('_all_update_spec'))
all_mod_spec.extend(recovery.get('_all_mod_spec'))
if lp:
l_logger.log(
logging.INFO,
'Recovering from task number {} in folder {}.'.format(starting_task,
recovery_dir))
if recovery_mode == 'cp' and launch_dir != recovery_dir:
if lp:
l_logger.log(
logging.INFO,
'Copying data from recovery folder {} to folder {}.'.format(recovery_dir,
launch_dir))
distutils.dir_util.copy_tree(recovery_dir, launch_dir, update=1)
else:
starting_task = 0
files_in = m_fw.spec.get("_files_in", {})
prev_files = m_fw.spec.get("_files_prev", {})
for f in set(files_in.keys()).intersection(prev_files.keys()):
# We use zopen for the file objects for transparent handling
# of zipped files. shutil.copyfileobj does the actual copy
# in chunks that avoid memory issues.
with zopen(prev_files[f], "rb") as fin, zopen(files_in[f], "wb") as fout:
shutil.copyfileobj(fin, fout)
if lp:
message = 'RUNNING fw_id: {} in directory: {}'.\
format(m_fw.fw_id, os.getcwd())
l_logger.log(logging.INFO, message)
# write FW.json and/or FW.yaml to the directory
if PRINT_FW_JSON:
m_fw.to_file('FW.json', indent=4)
if PRINT_FW_YAML:
m_fw.to_file('FW.yaml')
my_spec = dict(m_fw.spec) # make a copy of spec, don't override original
my_spec["_fw_env"] = self.fworker.env
# set up heartbeat (pinging the server that we're still alive)
ping_stop = start_ping_launch(lp, launch_id)
# start background tasks
if '_background_tasks' in my_spec:
for bt in my_spec['_background_tasks']:
btask_stops.append(start_background_task(bt, m_fw.spec))
# execute the Firetasks!
for t_counter, t in enumerate(m_fw.tasks[starting_task:], start=starting_task):
checkpoint = {'_task_n': t_counter,
'_all_stored_data': all_stored_data,
'_all_update_spec': all_update_spec,
'_all_mod_spec': all_mod_spec}
Rocket.update_checkpoint(lp, launch_dir, launch_id, checkpoint)
if lp:
l_logger.log(logging.INFO, "Task started: %s." % t.fw_name)
if my_spec.get("_add_launchpad_and_fw_id"):
t.fw_id = m_fw.fw_id
if FWData().MULTIPROCESSING:
# hack because AutoProxy manager can't access attributes
t.launchpad = LaunchPad.from_dict(self.launchpad.to_dict())
else:
t.launchpad = self.launchpad
if my_spec.get("_add_fworker"):
t.fworker = self.fworker
try:
m_action = t.run_task(my_spec)
except BaseException as e:
traceback.print_exc()
tb = traceback.format_exc()
stop_backgrounds(ping_stop, btask_stops)
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# If the exception is serializable, save its details
if pdb_on_exception:
pdb.post_mortem()
try:
exception_details = e.to_dict()
except AttributeError:
exception_details = None
except BaseException as e:
if lp:
l_logger.log(logging.WARNING,
"Exception couldn't be serialized: %s " % e)
exception_details = None
try:
m_task = t.to_dict()
except:
m_task = None
m_action = FWAction(stored_data={'_message': 'runtime error during task',
'_task': m_task,
'_exception': {'_stacktrace': tb,
'_details': exception_details}},
exit=True)
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
if lp:
final_state = 'FIZZLED'
lp.complete_launch(launch_id, m_action, final_state)
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
# read in a FWAction from a file, in case the task is not Python and cannot return
# it explicitly
if os.path.exists('FWAction.json'):
m_action = FWAction.from_file('FWAction.json')
elif os.path.exists('FWAction.yaml'):
m_action = FWAction.from_file('FWAction.yaml')
if not m_action:
m_action = FWAction()
# update the global stored data with the data to store and update from this
# particular Task
all_stored_data.update(m_action.stored_data)
all_update_spec.update(m_action.update_spec)
all_mod_spec.extend(m_action.mod_spec)
# update spec for next task as well
my_spec.update(m_action.update_spec)
for mod in m_action.mod_spec:
apply_mod(mod, my_spec)
if lp:
l_logger.log(logging.INFO, "Task completed: %s " % t.fw_name)
if m_action.skip_remaining_tasks:
break
# add job packing info if this is needed
if FWData().MULTIPROCESSING and STORE_PACKING_INFO:
all_stored_data['multiprocess_name'] = multiprocessing.current_process().name
# perform finishing operation
stop_backgrounds(ping_stop, btask_stops)
for b in btask_stops:
b.set()
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# last background monitors
if '_background_tasks' in my_spec:
for bt in my_spec['_background_tasks']:
if bt.run_on_finish:
for task in bt.tasks:
task.run_task(m_fw.spec)
m_action.stored_data = all_stored_data
m_action.mod_spec = all_mod_spec
m_action.update_spec = all_update_spec
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
if lp:
final_state = 'COMPLETED'
lp.complete_launch(launch_id, m_action, final_state)
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'COMPLETED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
except LockedWorkflowError as e:
l_logger.log(logging.DEBUG, traceback.format_exc())
l_logger.log(logging.WARNING,
"Firework {} reached final state {} but couldn't complete the update of "
"the database. Reason: {}\nRefresh the WF to recover the result "
"(lpad admin refresh -i {}).".format(
self.fw_id, final_state, e, self.fw_id))
return True
except:
# problems while processing the results. high probability of malformed data.
traceback.print_exc()
stop_backgrounds(ping_stop, btask_stops)
# restore initial state to prevent the raise of further exceptions
if lp:
lp.restore_backup_data(launch_id, m_fw.fw_id)
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# the action produced by the task is discarded
m_action = FWAction(stored_data={'_message': 'runtime error during task', '_task': None,
'_exception': {'_stacktrace': traceback.format_exc(),
'_details': None}},
exit=True)
try:
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
except:
traceback.print_exc()
if lp:
try:
lp.complete_launch(launch_id, m_action, 'FIZZLED')
except LockedWorkflowError as e:
l_logger.log(logging.DEBUG, traceback.format_exc())
l_logger.log(logging.WARNING,
"Firework {} fizzled but couldn't complete the update of the database."
" Reason: {}\nRefresh the WF to recover the result "
"(lpad admin refresh -i {}).".format(
self.fw_id, final_state, e, self.fw_id))
return True
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
def run_task(self, fw_spec):
# Get the fw_id and launchpad
if '_add_launchpad_and_fw_id' in fw_spec:
lp = self.launchpad
fw_id = self.fw_id
else:
try:
fw_dict = loadfn('FW.json')
except IOError:
try:
fw_dict = loadfn('FW.yaml')
except IOError:
raise RuntimeError("Launchpad/fw_id not present in spec and No FW.json nor FW.yaml file present: "
"impossible to determine fw_id")
lp = LaunchPad.auto_load()
fw_id = fw_dict['fw_id']
# Treat the case where there was some error that led to a fizzled state
if '_fizzled_parents' in fw_spec:
if len(fw_spec['_fizzled_parents']) != 1:
raise ValueError('CheckTask\'s Firework should have exactly one parent firework')
# Get the fizzled fw
fizzled_fw_id = fw_spec['_fizzled_parents'][0]['fw_id']
fizzled_fw = lp.get_fw_by_id(fizzled_fw_id)
# Sort handlers by their priority
sorted_handlers = sorted([h for h in self.handlers if h.allow_fizzled], key=lambda x: x.handler_priority)
# Get the corrections for all the handlers
corrections = []
for handler in sorted_handlers:
# Set needed data for the handlers (the spec of this check task/fw and the fw that has to be checked)
handler.src_setup(fw_spec=fw_spec, fw_to_check=fizzled_fw)
if handler.check():
corrections.append(handler.correct())
if handler.skip_remaining_handlers:
break
# In case of a fizzled parent, at least one correction is needed !
if len(corrections) == 0:
raise RuntimeError('No corrections found for fizzled firework ...')
# Apply the corrections
fw_action = self.apply_corrections(fw_to_correct=fizzled_fw, corrections=corrections)
return fw_action
# Treat the case where there was no fizzled parents => forward "needed" outputs of the previous firework to the
# next one.
else:
# Get the previous fw
this_lzy_wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
parents_fw_ids = this_lzy_wf.links.parent_links[fw_id]
if len(parents_fw_ids) != 1:
raise ValueError('CheckTask\'s Firework should have exactly one parent firework')
run_fw = lp.get_fw_by_id(parents_fw_ids[0])
# Get the corrections for all the handlers
# Sort handlers by their priority
if self.handlers is not None:
sorted_handlers = sorted([h for h in self.handlers if h.allow_completed],
key=lambda x: x.handler_priority)
else:
sorted_handlers = []
# Get the corrections for all the handlers
corrections = []
for handler in sorted_handlers:
# Set needed data for the handlers (the spec of this check task/fw and the fw that has to be checked)
handler.src_setup(fw_spec=fw_spec, fw_to_check=run_fw)
if handler.check():
corrections.append(handler.correct())
if handler.skip_remaining_handlers:
break
# If some corrections are found, apply and return the FWAction
if len(corrections) > 0:
fw_action = self.apply_corrections(fw_to_correct=run_fw, corrections=corrections)
return fw_action
# Validate the results if no error was found
validators = self.validators if self.validators is not None else []
for validator in validators:
if not validator.check():
raise RuntimeError('Validator invalidate results ...')
stored_data = {}
update_spec = {}
mod_spec = []
for task_type, task_info in fw_spec['previous_fws'].items():
mod_spec.append({'_push_all': {'previous_fws->'+task_type: task_info}})
return FWAction(stored_data=stored_data, update_spec=update_spec, mod_spec=mod_spec)
def add_to_db(self, lpad=None):
if not lpad:
lpad = LaunchPad.auto_load()
return lpad.add_wf(self.wf)
def add_to_db(self):
from fireworks.core.launchpad import LaunchPad
launchpad_file = os.path.join(os.environ['FW_CONFIG_DIR'], 'my_launchpad.yaml')
lp = LaunchPad.from_file(launchpad_file)
lp.add_wf(self.wf)
def auto_load(cls):
sma = SubmissionMongoAdapterEG.auto_load()
lp = LaunchPad.auto_load()
return SubmissionProcessorEG(sma, lp)
def random_launch(lp_creds):
lp = LaunchPad.from_dict(lp_creds)
while lp.run_exists(None):
launch_rocket(lp)
time.sleep(random.random()/3+0.1)
def launch_workflow(
self,
launchpad_dir="",
k_product=50,
job=None,
user_incar_settings=None,
potcar_functional="PBE",
additional_handlers=[],
):
"""
Creates a list of Fireworks. Each Firework represents calculations
that will be done on a slab system of a compound in a specific
orientation. Each Firework contains a oriented unit cell relaxation job
and a WriteSlabVaspInputs which creates os. Firework(s) depending
on whether or not Termination=True. Vasp outputs from all slab and
oriented unit cell calculations will then be inserted into a database.
Args:
launchpad_dir (str path): The path to my_launchpad.yaml. Defaults to
the current working directory containing your runs
k_product: kpts[0][0]*a. Decide k density without
kpoint0, default to 50
cwd: (str path): The curent working directory. Location of where you
want your vasp outputs to be.
job (VaspJob): The command (cmd) entered into VaspJob object. Default
is specifically set for running vasp jobs on Carver at NERSC
(use aprun for Hopper or Edison).
user_incar_settings(dict): A dict specifying additional incar
settings, default to None (ediff_per_atom=False)
potcar_functional (str): default to PBE
"""
launchpad = LaunchPad.from_file(os.path.join(os.environ["HOME"], launchpad_dir, "my_launchpad.yaml"))
if self.reset:
launchpad.reset("", require_password=False)
# Scratch directory reffered to by custodian.
# May be different on non-Nersc systems.
if not job:
job = VaspJob(["mpirun", "-n", "64", "vasp"], auto_npar=False, copy_magmom=True)
handlers = [
VaspErrorHandler(),
NonConvergingErrorHandler(),
UnconvergedErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(timeout=3600),
]
if additional_handlers:
handlers.extend(additional_handlers)
cust_params = {
"custodian_params": {"scratch_dir": os.path.join("/global/scratch2/sd/", os.environ["USER"])},
"jobs": job.double_relaxation_run(job.vasp_cmd, auto_npar=False),
"handlers": handlers,
"max_errors": 100,
} # will return a list of jobs
# instead of just being one job
fws = []
for key in self.miller_dict.keys():
# Enumerate through all compounds in the dictionary,
# the key is the compositional formula of the compound
print key
for miller_index in self.miller_dict[key]:
# Enumerates through all miller indices we
# want to create slabs of that compound from
print str(miller_index)
max_norm = max(miller_index) if self.max_normal_search else None
# Whether or not we want to use the
# max_normal_search algorithm from surface.py
print "true or false max norm is ", max_norm, self.max_normal_search
slab = SlabGenerator(
self.unit_cells_dict[key][0], miller_index, self.ssize, self.vsize, max_normal_search=max_norm
)
oriented_uc = slab.oriented_unit_cell
if self.fail_safe and len(oriented_uc) > 199:
break
# This method only creates the oriented unit cell, the
# slabs are created in the WriteSlabVaspInputs task.
# WriteSlabVaspInputs will create the slabs from
# the contcar of the oriented unit cell calculation
handler = []
tasks = []
folderbulk = "/%s_%s_k%s_s%sv%s_%s%s%s" % (
oriented_uc.composition.reduced_formula,
"bulk",
k_product,
self.ssize,
self.vsize,
str(miller_index[0]),
str(miller_index[1]),
str(miller_index[2]),
)
cwd = os.getcwd()
if self.get_bulk_e:
tasks.extend(
[
WriteUCVaspInputs(
oriented_ucell=oriented_uc,
folder=folderbulk,
cwd=cwd,
user_incar_settings=user_incar_settings,
potcar_functional=potcar_functional,
k_product=k_product,
),
RunCustodianTask(dir=folderbulk, cwd=cwd, **cust_params),
VaspSlabDBInsertTask(
struct_type="oriented_unit_cell",
loc=folderbulk,
cwd=cwd,
miller_index=miller_index,
**self.vaspdbinsert_params
),
]
)
# Slab will inherit average final magnetic moment
# of the bulk from outcar, will have to generalize
# this for systems with different elements later
# element = oriented_uc.species[0]
# out = Outcar(cwd+folderbulk)
# out_mag = out.magnetization
# tot_mag = [mag['tot'] for mag in out_mag]
# magmom = np.mean(tot_mag)
# user_incar_settings['MAGMOM'] = {element: magmom}
tasks.append(
WriteSlabVaspInputs(
folder=folderbulk,
cwd=cwd,
user_incar_settings=user_incar_settings,
terminations=self.terminations,
custodian_params=cust_params,
vaspdbinsert_parameters=self.vaspdbinsert_params,
potcar_functional=potcar_functional,
k_product=k_product,
miller_index=miller_index,
min_slab_size=self.ssize,
min_vacuum_size=self.vsize,
ucell=self.unit_cells_dict[key][0],
)
)
fw = Firework(tasks, name=folderbulk)
fws.append(fw)
wf = Workflow(fws, name="Surface Calculations")
launchpad.add_wf(wf)
def fix():
# initialize databases
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snl = snldb.snl
snlgroups = snldb.snlgroups
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
fws = lpdb.fireworks
launches = lpdb.launches
sb_f = os.path.join(module_dir, 'submission.yaml')
sbdb = SubmissionMongoAdapter.from_file(sb_f)
submissions = sbdb.jobs
bad_crystal_ids = []
crystals_file = os.path.join(module_dir, 'bad_crystals.txt')
with open(crystals_file) as f:
for line in f:
bad_crystal_ids.append(int(line.strip()))
for c_id in bad_crystal_ids:
if c_id == 100892 or c_id == 100202:
print 'SKIP'
else:
# FIX SNL
for s in snl.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snl_id': 1}):
snl.update({'snl_id': s['snl_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SNLGROUPS
for s in snlgroups.find({'canonical_snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snlgroup_id': 1}):
snlgroups.update({'snlgroup_id': s['snlgroup_id']}, {'$pushAll': {"canonical_snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 1
for s in fws.find({'spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 2
for s in fws.find({'spec.force_mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.force_mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX Launches
for s in launches.find({'action.update_spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'launch_id': 1}):
launches.update({'launch_id': s['launch_id']}, {'$pushAll': {"action.update_spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX TASKS
for s in tasks.find({'snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'task_id': 1}):
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl_final.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SUBMISSIONS
for s in submissions.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'submission_id': 1}):
submissions.update({'submission_id': s['submission_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
print 'FIXED', c_id
from flask import Flask, render_template, request, jsonify
from flask import redirect, url_for, abort
from fireworks import Firework
from fireworks.utilities.fw_serializers import DATETIME_HANDLER
from pymongo import DESCENDING
import os, json
from fireworks.core.launchpad import LaunchPad
from flask.ext.paginate import Pagination
app = Flask(__name__)
app.use_reloader=True
hello = __name__
lp = LaunchPad.from_dict(json.loads(os.environ["FWDB_CONFIG"]))
PER_PAGE = 20
STATES = Firework.STATE_RANKS.keys()
@app.template_filter('datetime')
def datetime(value):
import datetime as dt
date = dt.datetime.strptime(value, '%Y-%m-%dT%H:%M:%S.%f')
return date.strftime('%m/%d/%Y')
@app.template_filter('pluralize')
def pluralize(number, singular='', plural='s'):
if number == 1:
return singular
else:
return plural
def run(self, pdb_on_exception=False):
"""
Run the rocket (check out a job from the database and execute it)
Args:
pdb_on_exception (bool): whether to invoke the debugger on
a caught exception. Default False.
"""
all_stored_data = {} # combined stored data for *all* the Tasks
all_update_spec = {} # combined update_spec for *all* the Tasks
all_mod_spec = [] # combined mod_spec for *all* the Tasks
lp = self.launchpad
launch_dir = os.path.abspath(os.getcwd())
logdir = lp.get_logdir() if lp else None
l_logger = get_fw_logger('rocket.launcher', l_dir=logdir,
stream_level=ROCKET_STREAM_LOGLEVEL)
# check a FW job out of the launchpad
if lp:
m_fw, launch_id = lp.checkout_fw(self.fworker, launch_dir, self.fw_id)
else: # offline mode
m_fw = Firework.from_file(os.path.join(os.getcwd(), "FW.json"))
# set the run start time
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['started_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
launch_id = None # we don't need this in offline mode...
if not m_fw:
print("No FireWorks are ready to run and match query! {}".format(self.fworker.query))
return False
final_state = None
ping_stop = None
btask_stops = []
try:
if '_launch_dir' in m_fw.spec and lp:
prev_dir = launch_dir
launch_dir = os.path.expandvars(m_fw.spec['_launch_dir'])
if not os.path.abspath(launch_dir):
launch_dir = os.path.normpath(os.path.join(os.getcwd(), launch_dir))
# thread-safe "mkdir -p"
try:
os.makedirs(launch_dir)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
os.chdir(launch_dir)
if not os.path.samefile(launch_dir, prev_dir):
lp.change_launch_dir(launch_id, launch_dir)
if not os.listdir(prev_dir) and REMOVE_USELESS_DIRS:
try:
os.rmdir(prev_dir)
except Exception:
pass
recovery = m_fw.spec.get('_recovery', None)
if recovery:
recovery_dir = recovery.get('_prev_dir')
recovery_mode = recovery.get('_mode')
starting_task = recovery.get('_task_n')
all_stored_data.update(recovery.get('_all_stored_data'))
all_update_spec.update(recovery.get('_all_update_spec'))
all_mod_spec.extend(recovery.get('_all_mod_spec'))
if lp:
l_logger.log(
logging.INFO,
'Recovering from task number {} in folder {}.'.format(starting_task,
recovery_dir))
if recovery_mode == 'cp' and launch_dir != recovery_dir:
if lp:
l_logger.log(
logging.INFO,
'Copying data from recovery folder {} to folder {}.'.format(recovery_dir,
launch_dir))
distutils.dir_util.copy_tree(recovery_dir, launch_dir, update=1)
else:
starting_task = 0
files_in = m_fw.spec.get("_files_in", {})
prev_files = m_fw.spec.get("_files_prev", {})
for f in set(files_in.keys()).intersection(prev_files.keys()):
# We use zopen for the file objects for transparent handling
# of zipped files. shutil.copyfileobj does the actual copy
# in chunks that avoid memory issues.
with zopen(prev_files[f], "rb") as fin, zopen(files_in[f], "wb") as fout:
shutil.copyfileobj(fin, fout)
if lp:
message = 'RUNNING fw_id: {} in directory: {}'. \
format(m_fw.fw_id, os.getcwd())
l_logger.log(logging.INFO, message)
# write FW.json and/or FW.yaml to the directory
if PRINT_FW_JSON:
m_fw.to_file('FW.json', indent=4)
if PRINT_FW_YAML:
m_fw.to_file('FW.yaml')
my_spec = dict(m_fw.spec) # make a copy of spec, don't override original
my_spec["_fw_env"] = self.fworker.env
# set up heartbeat (pinging the server that we're still alive)
ping_stop = start_ping_launch(lp, launch_id)
# start background tasks
if '_background_tasks' in my_spec:
for bt in my_spec['_background_tasks']:
btask_stops.append(start_background_task(bt, m_fw.spec))
# execute the Firetasks!
for t_counter, t in enumerate(m_fw.tasks[starting_task:], start=starting_task):
checkpoint = {'_task_n': t_counter,
'_all_stored_data': all_stored_data,
'_all_update_spec': all_update_spec,
'_all_mod_spec': all_mod_spec}
Rocket.update_checkpoint(lp, launch_dir, launch_id, checkpoint)
if lp:
l_logger.log(logging.INFO, "Task started: %s." % t.fw_name)
if my_spec.get("_add_launchpad_and_fw_id"):
t.fw_id = m_fw.fw_id
if FWData().MULTIPROCESSING:
# hack because AutoProxy manager can't access attributes
t.launchpad = LaunchPad.from_dict(self.launchpad.to_dict())
else:
t.launchpad = self.launchpad
if my_spec.get("_add_fworker"):
t.fworker = self.fworker
try:
m_action = t.run_task(my_spec)
except BaseException as e:
traceback.print_exc()
tb = traceback.format_exc()
stop_backgrounds(ping_stop, btask_stops)
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# If the exception is serializable, save its details
if pdb_on_exception:
pdb.post_mortem()
try:
exception_details = e.to_dict()
except AttributeError:
exception_details = None
except BaseException as e:
if lp:
l_logger.log(logging.WARNING,
"Exception couldn't be serialized: %s " % e)
exception_details = None
try:
m_task = t.to_dict()
except Exception:
m_task = None
m_action = FWAction(stored_data={'_message': 'runtime error during task',
'_task': m_task,
'_exception': {'_stacktrace': tb,
'_details': exception_details}},
exit=True)
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
if lp:
final_state = 'FIZZLED'
lp.complete_launch(launch_id, m_action, final_state)
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
# read in a FWAction from a file, in case the task is not Python and cannot return
# it explicitly
if os.path.exists('FWAction.json'):
m_action = FWAction.from_file('FWAction.json')
elif os.path.exists('FWAction.yaml'):
m_action = FWAction.from_file('FWAction.yaml')
if not m_action:
m_action = FWAction()
# update the global stored data with the data to store and update from this
# particular Task
all_stored_data.update(m_action.stored_data)
all_update_spec.update(m_action.update_spec)
all_mod_spec.extend(m_action.mod_spec)
# update spec for next task as well
my_spec.update(m_action.update_spec)
for mod in m_action.mod_spec:
apply_mod(mod, my_spec)
if lp:
l_logger.log(logging.INFO, "Task completed: %s " % t.fw_name)
if m_action.skip_remaining_tasks:
break
# add job packing info if this is needed
if FWData().MULTIPROCESSING and STORE_PACKING_INFO:
all_stored_data['multiprocess_name'] = multiprocessing.current_process().name
# perform finishing operation
stop_backgrounds(ping_stop, btask_stops)
for b in btask_stops:
b.set()
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# last background monitors
if '_background_tasks' in my_spec:
for bt in my_spec['_background_tasks']:
if bt.run_on_finish:
for task in bt.tasks:
task.run_task(m_fw.spec)
m_action.stored_data = all_stored_data
m_action.mod_spec = all_mod_spec
m_action.update_spec = all_update_spec
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
if lp:
final_state = 'COMPLETED'
lp.complete_launch(launch_id, m_action, final_state)
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'COMPLETED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
except LockedWorkflowError as e:
l_logger.log(logging.DEBUG, traceback.format_exc())
l_logger.log(logging.WARNING,
"Firework {} reached final state {} but couldn't complete the update of "
"the database. Reason: {}\nRefresh the WF to recover the result "
"(lpad admin refresh -i {}).".format(
self.fw_id, final_state, e, self.fw_id))
return True
except Exception:
# problems while processing the results. high probability of malformed data.
traceback.print_exc()
stop_backgrounds(ping_stop, btask_stops)
# restore initial state to prevent the raise of further exceptions
if lp:
lp.restore_backup_data(launch_id, m_fw.fw_id)
do_ping(lp, launch_id) # one last ping, esp if there is a monitor
# the action produced by the task is discarded
m_action = FWAction(stored_data={'_message': 'runtime error during task', '_task': None,
'_exception': {'_stacktrace': traceback.format_exc(),
'_details': None}},
exit=True)
try:
m_action = self.decorate_fwaction(m_action, my_spec, m_fw, launch_dir)
except Exception:
traceback.print_exc()
if lp:
try:
lp.complete_launch(launch_id, m_action, 'FIZZLED')
except LockedWorkflowError as e:
l_logger.log(logging.DEBUG, traceback.format_exc())
l_logger.log(logging.WARNING,
"Firework {} fizzled but couldn't complete the update of the database."
" Reason: {}\nRefresh the WF to recover the result "
"(lpad admin refresh -i {}).".format(
self.fw_id, final_state, e, self.fw_id))
return True
else:
fpath = zpath("FW_offline.json")
with zopen(fpath) as f_in:
d = json.loads(f_in.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
d['completed_on'] = datetime.utcnow().isoformat()
with zopen(fpath, "wt") as f_out:
f_out.write(json.dumps(d, ensure_ascii=False))
return True
def random_launch(lp_creds):
lp = LaunchPad.from_dict(lp_creds)
while lp.run_exists(None):
launch_rocket(lp)
time.sleep(random.random()/3+0.1)