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 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 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 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 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 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 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 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 '-----'
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 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:
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")
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)
# coding: utf-8
from __future__ import division, print_function, unicode_literals, absolute_import
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):
sma = SubmissionMongoAdapterEG.auto_load()
lp = LaunchPad.auto_load()
return SubmissionProcessorEG(sma, lp)
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, lpad=None):
if not lpad:
lpad = LaunchPad.auto_load()
return lpad.add_wf(self.wf)
def add_to_db(self):
lpad = LaunchPad.auto_load()
lpad.add_wf(self.wf)
def run_task(self, fw_spec):
if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec:
prev_dir = get_loc(
fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir'])
update_spec = {} # add this later when creating new FW
fizzled_parent = True
parse_dos = False
else:
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
update_spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['prev_task_type'],
'run_tags': fw_spec['run_tags'],
'parameters': fw_spec.get('parameters')
}
fizzled_parent = False
parse_dos = 'Uniform' in fw_spec['prev_task_type']
if 'run_tags' in fw_spec:
self.additional_fields['run_tags'] = fw_spec['run_tags']
else:
self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][
0]['spec']['run_tags']
if MOVE_TO_GARDEN_DEV:
prev_dir = move_to_garden(prev_dir, prod=False)
elif MOVE_TO_GARDEN_PROD:
prev_dir = move_to_garden(prev_dir, prod=True)
# get the directory containing the db file
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('MPVaspDrone')
logger.setLevel(logging.INFO)
sh = logging.StreamHandler(stream=sys.stdout)
sh.setLevel(getattr(logging, 'INFO'))
logger.addHandler(sh)
with open(db_path) as f:
db_creds = json.load(f)
drone = MPVaspDrone(host=db_creds['host'],
port=db_creds['port'],
database=db_creds['database'],
user=db_creds['admin_user'],
password=db_creds['admin_password'],
collection=db_creds['collection'],
parse_dos=parse_dos,
additional_fields=self.additional_fields,
update_duplicates=self.update_duplicates)
t_id, d = drone.assimilate(
prev_dir, launches_coll=LaunchPad.auto_load().launches)
mpsnl = d['snl_final'] if 'snl_final' in d else d['snl']
snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d[
'snlgroup_id']
update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id})
print 'ENTERED task id:', t_id
stored_data = {'task_id': t_id}
if d['state'] == 'successful':
update_spec['analysis'] = d['analysis']
update_spec['output'] = d['output']
update_spec['vasp'] = {
'incar': d['calculations'][-1]['input']['incar'],
'kpoints': d['calculations'][-1]['input']['kpoints']
}
update_spec["task_id"] = t_id
return FWAction(stored_data=stored_data, update_spec=update_spec)
# not successful - first test to see if UnconvergedHandler is needed
if not fizzled_parent:
unconverged_tag = 'unconverged_handler--{}'.format(
fw_spec['prev_task_type'])
output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml'))
ueh = UnconvergedErrorHandler(output_filename=output_dir)
# TODO: make this a little more flexible
if ueh.check() and unconverged_tag not in fw_spec['run_tags']:
print 'Unconverged run! Creating dynamic FW...'
spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['task_type'],
'mpsnl': mpsnl,
'snlgroup_id': snlgroup_id,
'task_type': fw_spec['prev_task_type'],
'run_tags': list(fw_spec['run_tags']),
'parameters': fw_spec.get('parameters'),
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': fw_spec['_priority']
}
# Pass elastic tensor spec
if 'deformation_matrix' in fw_spec.keys():
spec['deformation_matrix'] = fw_spec['deformation_matrix']
spec['original_task_id'] = fw_spec['original_task_id']
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition(snl.structure.composition.reduced_formula
).alphabetical_formula
fws.append(
Firework([
VaspCopyTask({
'files': [
'INCAR', 'KPOINTS', 'POSCAR', 'POTCAR',
'CONTCAR'
],
'use_CONTCAR':
False
}),
SetupUnconvergedHandlerTask(),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-2))
spec = {
'task_type': 'VASP db insertion',
'_allow_fizzled_parents': True,
'_priority': fw_spec['_priority'],
'_queueadapter': QA_DB,
'run_tags': list(fw_spec['run_tags'])
}
if 'deformation_matrix' in fw_spec.keys():
spec['deformation_matrix'] = fw_spec['deformation_matrix']
spec['original_task_id'] = fw_spec['original_task_id']
spec['run_tags'].append(unconverged_tag)
fws.append(
Firework([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-1))
connections[-2] = -1
wf = Workflow(fws, connections)
return FWAction(detours=wf)
# not successful and not due to convergence problem - FIZZLE
raise ValueError("DB insertion successful, but don't know how to \
fix this Firework! Can't continue with workflow...")
def auto_load(cls):
spsma = SPSubmissionsMongoAdapter.auto_load()
lp = LaunchPad.auto_load()
return SPSubmissionProcessor(spsma, lp)
def auto_load(cls):
spsma = SPSubmissionsMongoAdapter.auto_load()
lp = LaunchPad.auto_load()
return SPSubmissionProcessor(spsma, lp)
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 add_to_db(self):
lpad = LaunchPad.auto_load()
lpad.add_wf(self.wf)
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 run_task(self, fw_spec):
if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec:
prev_dir = get_loc(fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir'])
update_spec = {} # add this later when creating new FW
fizzled_parent = True
parse_dos = False
else:
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
update_spec = {'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['prev_task_type'],
'run_tags': fw_spec['run_tags'], 'parameters': fw_spec.get('parameters')}
fizzled_parent = False
parse_dos = 'Uniform' in fw_spec['prev_task_type']
if 'run_tags' in fw_spec:
self.additional_fields['run_tags'] = fw_spec['run_tags']
else:
self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][0]['spec']['run_tags']
if MOVE_TO_GARDEN_DEV:
prev_dir = move_to_garden(prev_dir, prod=False)
elif MOVE_TO_GARDEN_PROD:
prev_dir = move_to_garden(prev_dir, prod=True)
# get the directory containing the db file
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('MPVaspDrone')
logger.setLevel(logging.INFO)
sh = logging.StreamHandler(stream=sys.stdout)
sh.setLevel(getattr(logging, 'INFO'))
logger.addHandler(sh)
with open(db_path) as f:
db_creds = json.load(f)
drone = MPVaspDrone(
host=db_creds['host'], port=db_creds['port'],
database=db_creds['database'], user=db_creds['admin_user'],
password=db_creds['admin_password'],
collection=db_creds['collection'], parse_dos=parse_dos,
additional_fields=self.additional_fields,
update_duplicates=self.update_duplicates)
t_id, d = drone.assimilate(prev_dir, launches_coll=LaunchPad.auto_load().launches)
mpsnl = d['snl_final'] if 'snl_final' in d else d['snl']
snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d['snlgroup_id']
update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id})
print 'ENTERED task id:', t_id
stored_data = {'task_id': t_id}
if d['state'] == 'successful':
update_spec['analysis'] = d['analysis']
update_spec['output'] = d['output']
return FWAction(stored_data=stored_data, update_spec=update_spec)
# not successful - first test to see if UnconvergedHandler is needed
if not fizzled_parent:
unconverged_tag = 'unconverged_handler--{}'.format(fw_spec['prev_task_type'])
output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml'))
ueh = UnconvergedErrorHandler(output_filename=output_dir)
if ueh.check() and unconverged_tag not in fw_spec['run_tags']:
print 'Unconverged run! Creating dynamic FW...'
spec = {'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['task_type'],
'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id,
'task_type': fw_spec['prev_task_type'],
'run_tags': list(fw_spec['run_tags']),
'parameters': fw_spec.get('parameters'),
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': fw_spec['_priority']}
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula
fws.append(FireWork(
[VaspCopyTask({'files': ['INCAR', 'KPOINTS', 'POSCAR', 'POTCAR', 'CONTCAR'],
'use_CONTCAR': False}), SetupUnconvergedHandlerTask(),
get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']),
fw_id=-2))
spec = {'task_type': 'VASP db insertion', '_allow_fizzled_parents': True,
'_priority': fw_spec['_priority'], '_queueadapter': QA_DB,
'run_tags': list(fw_spec['run_tags'])}
spec['run_tags'].append(unconverged_tag)
fws.append(
FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']),
fw_id=-1))
connections[-2] = -1
wf = Workflow(fws, connections)
return FWAction(detours=wf)
# not successful and not due to convergence problem - FIZZLE
raise ValueError("DB insertion successful, but don't know how to fix this FireWork! Can't continue with workflow...")
