def basic_wf_ex():
print '--- BASIC WORKFLOW EXAMPLE ---'
# setup
launchpad = setup()
# add FireWorks
task1 = ScriptTask.from_str('echo "Ingrid is the CEO."')
task2 = ScriptTask.from_str('echo "Jill is a manager."')
task3 = ScriptTask.from_str('echo "Jack is a manager."')
task4 = ScriptTask.from_str('echo "Kip is an intern."')
fw1 = FireWork(task1, fw_id=-1)
fw2 = FireWork(task2, fw_id=-2)
fw3 = FireWork(task3, fw_id=-3)
fw4 = FireWork(task4, fw_id=-4)
# make workflow
workflow = Workflow([fw1, fw2, fw3, fw4], {
-1: [-2, -3],
-2: [-4],
-3: [-4]
})
launchpad.add_wf(workflow)
# launch Rocket
rapidfire(launchpad)
def add_work(self, parameters):
from fireworks.core.firework import FireWork
tasks = []
job = parameters['job']
print('adding job ' + job + ' to the workslist as ', self.fw_id)
if job == 'prep':
launch_spec = {
'task_type': 'Preparation job',
'_category': 'cluster',
'_queueadapter': 'qadapterdict'
}
task = VaspGWInputTask(parameters)
tasks.append(task)
task = VaspGWExecuteTask(parameters)
tasks.append(task)
task = VaspGWToDiagTask(parameters)
tasks.append(task)
task = VaspGWExecuteTask(parameters)
tasks.append(task)
fw = FireWork(tasks,
spec=launch_spec,
name=job,
created_on=now(),
fw_id=self.fw_id)
self.connections[self.fw_id] = []
self.prep_id = self.fw_id
self.fw_id += 1
print(self.connections)
elif job in ['G0W0', 'GW0', 'scGW0']:
launch_spec = {
'task_type': 'GW job',
'_category': 'cluster',
'_queueadapter': 'qadapterdict'
}
task = VaspGWInputTask(parameters)
tasks.append(task)
task = VaspGWGetPrepResTask(parameters)
tasks.append(task)
task = VaspGWExecuteTask(parameters)
tasks.append(task)
if parameters['spec']['converge']:
task = VaspGWWriteConDatTask(parameters)
tasks.append(task)
task = VaspGWTestConTask(parameters)
tasks.append(task)
fw = FireWork(tasks,
spec=launch_spec,
name=job,
created_on=now(),
fw_id=self.fw_id)
self.connections[self.fw_id] = []
self.connections[self.prep_id].append(self.fw_id)
self.fw_id += 1
else:
fw = []
print('unspecified job, this should have been captured before !!')
exit()
self.work_list.append(fw)
def snl_to_wf_phonon(snl, parameters=None):
fws = []
connections = {}
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition.from_formula(snl.structure.composition.reduced_formula).alphabetical_formula
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {'task_type': 'Add to SNL database', 'snl': snl.to_dict, '_queueadapter': QA_DB, '_priority': snl_priority}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.to_dict
spec['force_snlgroup_id'] = parameters['snlgroup_id']
del spec['snl']
fws.append(FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=0))
connections[0] = [1]
# run GGA structure optimization for force convergence
spec = snl_to_wf._snl_to_spec(snl, parameters=parameters)
spec = update_spec_force_convergence(spec)
spec['run_tags'].append("origin")
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
spec['task_type'] = "Vasp force convergence"
tasks = [VaspWriterTask(), get_custodian_task(spec)]
fws.append(FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), fw_id=1))
# insert into DB - GGA structure optimization
spec = {'task_type': 'VASP db insertion', '_priority': priority,
'_allow_fizzled_parents': True, '_queueadapter': QA_DB}
fws.append(
FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']), fw_id=2))
connections[1] = [2]
spec = {'task_type': 'Setup Deformed Struct Task', '_priority': priority,
'_queueadapter': QA_CONTROL}
fws.append(
FireWork([SetupDeformedStructTask()], spec, name=get_slug(f + '--' + spec['task_type']),
fw_id=3))
connections[2] = [3]
wf_meta = get_meta_from_structure(snl.structure)
wf_meta['run_version'] = 'May 2013 (1)'
if '_materialsproject' in snl.data and 'submission_id' in snl.data['_materialsproject']:
wf_meta['submission_id'] = snl.data['_materialsproject']['submission_id']
return Workflow(fws, connections, name=Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula, metadata=wf_meta)
def test_org_wf(self):
test1 = ScriptTask.from_str("python -c 'print(\"test1\")'",
{'store_stdout': True})
test2 = ScriptTask.from_str("python -c 'print(\"test2\")'",
{'store_stdout': True})
fw1 = FireWork(test1, fw_id=-1)
fw2 = FireWork(test2, fw_id=-2)
wf = Workflow([fw1, fw2], {-1: -2})
self.lp.add_wf(wf)
launch_rocket(self.lp, self.fworker)
self.assertEqual(self.lp.get_launch_by_id(1).action.stored_data['stdout'],
str(six.b('test1\n')))
launch_rocket(self.lp, self.fworker)
self.assertEqual(self.lp.get_launch_by_id(2).action.stored_data['stdout'],
str(six.b('test2\n')))
def submit_new_workflow(self):
# finds a submitted job, creates a workflow, and submits it to FireWorks
job = self.jobs.find_and_modify({'state': 'SUBMITTED'},
{'$set': {
'state': 'WAITING'
}})
if job:
submission_id = job['submission_id']
try:
firework = FireWork(
[StructurePredictionTask()],
spec={
'species': job['species'],
'threshold': job['threshold'],
'submission_id': submission_id
})
wf = Workflow([firework],
metadata={'submission_id': submission_id})
self.launchpad.add_wf(wf)
print 'ADDED WORKFLOW FOR {}'.format(job['species'])
except:
self.jobs.find_and_modify({'submission_id': submission_id},
{'$set': {
'state': 'ERROR'
}})
traceback.print_exc()
return submission_id
def test_basic_fw(self):
test1 = ScriptTask.from_str("python -c 'print(\"test1\")'",
{'store_stdout': True})
fw = FireWork(test1)
self.lp.add_wf(fw)
launch_rocket(self.lp, self.fworker)
self.assertEqual(self.lp.get_launch_by_id(1).action.stored_data[
'stdout'], str(six.b('test1\n')))
def test_add_fw(self):
fw = FireWork(AdditionTask(), {'input_array': [5, 7]})
self.lp.add_wf(fw)
rapidfire(self.lp,
m_dir=MODULE_DIR,
nlaunches=1,
sleep_time=5,
max_loops=60)
self.assertEqual(
self.lp.get_launch_by_id(1).action.stored_data['sum'], 12)
def test_basic_fw(self):
test1 = ScriptTask.from_str("python -c 'print \"test1\"'",
{'store_stdout': True})
fw = FireWork(test1)
self.lp.add_wf(fw)
launch_rocket(self.lp)
time.sleep(3)
self.assertEqual(
self.lp.get_launch_by_id(1).action.stored_data['stdout'],
'test1\n')
def test_fibadder(self):
fib = FibonacciAdderTask()
fw = FireWork(fib, {'smaller': 0, 'larger': 1, 'stop_point': 3})
self.lp.add_wf(fw)
rapidfire(self.lp, self.fworker, m_dir=MODULE_DIR)
self.assertEqual(self.lp.get_launch_by_id(1).action.stored_data['next_fibnum'], 1)
self.assertEqual(self.lp.get_launch_by_id(2).action.stored_data['next_fibnum'], 2)
self.assertEqual(self.lp.get_launch_by_id(3).action.stored_data, {})
self.assertFalse(self.lp.run_exists())
def rapid_fire_ex():
print('--- RAPIDFIRE EXAMPLE ---')
# setup
launchpad = setup()
# add FireWorks
firetask = ScriptTask.from_str(
'echo "howdy, your job launched successfully!"')
fw1 = FireWork(firetask)
launchpad.add_wf(fw1)
# re-add multiple times
fw2 = FireWork(firetask)
launchpad.add_wf(fw2)
fw3 = FireWork(firetask)
launchpad.add_wf(fw3)
# launch Rocket
rapidfire(launchpad, FWorker())
def from_tarfile(cls, tar_filename):
t = tarfile.open(tar_filename, 'r')
links = None
fws = []
for f_name in t.getnames():
m_file = t.extractfile(f_name)
m_format = m_file.name.split('.')[-1]
m_contents = m_file.read()
if 'links' in f_name:
links = Workflow.Links.from_format(m_contents, m_format)
else:
fws.append(FireWork.from_format(m_contents, m_format))
return Workflow(fws, dict(links))
def from_tarfile(cls, tar_filename):
t = tarfile.open(tar_filename, 'r')
links = None
fws = []
for f_name in t.getnames():
m_file = t.extractfile(f_name)
m_format = m_file.name.split('.')[-1]
m_contents = m_file.read()
if 'links' in f_name:
links = Workflow.Links.from_format(m_contents, m_format)
else:
fws.append(FireWork.from_format(m_contents, m_format))
return Workflow(fws, dict(links))
def basic_fw_ex():
print('--- BASIC FIREWORK EXAMPLE ---')
# setup
launchpad = setup()
# add FireWork
firetask = ScriptTask.from_str(
'echo "howdy, your job launched successfully!"')
firework = FireWork(firetask)
launchpad.add_wf(firework)
# launch Rocket
launch_rocket(launchpad, FWorker())
def run_task(self, fw_spec):
smaller = fw_spec['smaller']
larger = fw_spec['larger']
stop_point = fw_spec['stop_point']
m_sum = smaller + larger
if m_sum < stop_point:
print 'The next Fibonacci number is: {}'.format(m_sum)
# create a new Fibonacci Adder to add to the workflow
new_fw = FireWork(FibonacciAdderTask(), {'smaller': larger, 'larger': m_sum, 'stop_point': stop_point})
return FWAction('CREATE', {'next_fibnum': m_sum}, {'create_fw': new_fw})
else:
print 'We have now exceeded our limit; (the next Fibonacci number would have been: {})'.format(m_sum)
return FWAction('CONTINUE')
def multiple_tasks_ex():
print('--- MULTIPLE FIRETASKS EXAMPLE ---')
# setup
launchpad = setup()
# add FireWorks
firetask1 = ScriptTask.from_str('echo "This is TASK #1"')
firetask2 = ScriptTask.from_str('echo "This is TASK #2"')
firetask3 = ScriptTask.from_str('echo "This is TASK #3"')
fw = FireWork([firetask1, firetask2, firetask3])
launchpad.add_wf(fw)
# launch Rocket
rapidfire(launchpad, FWorker())
def task_dict_to_wf(task_dict, launchpad):
fw_id = launchpad.get_new_fw_id()
l_id = launchpad.get_new_launch_id()
spec = {'task_type': task_dict['task_type'], 'run_tags': task_dict['run_tags'],
'vaspinputset_name': None, 'vasp': None, 'mpsnl': task_dict['snl'],
'snlgroup_id': task_dict['snlgroup_id']}
tasks = [DummyLegacyTask()]
launch_dir = task_dict['dir_name_full']
stored_data = {'error_list': []}
update_spec = {'prev_vasp_dir': task_dict['dir_name'],
'prev_task_type': spec['task_type'],
'mpsnl': spec['mpsnl'], 'snlgroup_id': spec['snlgroup_id'],
'run_tags': spec['run_tags']}
fwaction = FWAction(stored_data=stored_data, update_spec=update_spec)
if task_dict['completed_at']:
complete_date = datetime.datetime.strptime(task_dict['completed_at'], "%Y-%m-%d %H:%M:%S")
state_history = [{"created_on": complete_date, 'state': 'COMPLETED'}]
else:
state_history = []
launches = [Launch('COMPLETED', launch_dir, fworker=None, host=None, ip=None, action=fwaction,
state_history=state_history, launch_id=l_id, fw_id=fw_id)]
f = Composition.from_formula(task_dict['pretty_formula']).alphabetical_formula
fw = FireWork(tasks, spec, name=get_slug(f + '--' + spec['task_type']), launches=launches, state='COMPLETED', created_on=None,
fw_id=fw_id)
wf_meta = get_meta_from_structure(Structure.from_dict(task_dict['snl']))
wf_meta['run_version'] = 'preproduction (0)'
wf = Workflow.from_FireWork(fw, name=f, metadata=wf_meta)
launchpad.add_wf(wf, reassign_all=False)
launchpad._upsert_launch(launches[0])
print 'ADDED', fw_id
# return fw_id
return fw_id
def test_backgroundtask(self):
dest1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'hello.txt')
self._teardown([dest1])
try:
test1 = ScriptTask.from_str("python -c 'print(\"testing background...\")'",
{'store_stdout': True})
bg_task1 = BackgroundTask(FileWriteTask({'files_to_write': [{'filename': dest1, 'contents': 'hello'}]}), num_launches=1, run_on_finish=True)
fw = FireWork(test1, spec={'_background_tasks': [bg_task1]})
self.lp.add_wf(fw)
launch_rocket(self.lp, self.fworker)
with open(dest1) as f:
self.assertEqual(f.read(), 'hello')
finally:
self._teardown([dest1])
def add_scripts(args):
lp = get_lp(args)
args.names = args.names if args.names else [None] * len(args.scripts)
args.wf_name = args.wf_name if args.wf_name else args.names[0]
fws = []
links = {}
for idx, s in enumerate(args.scripts):
fws.append(
FireWork(ScriptTask({
'script': s,
'use_shell': True
}),
name=args.names[idx],
fw_id=idx))
if idx != 0:
links[idx - 1] = idx
lp.add_wf(Workflow(fws, links, args.wf_name))
def get_fw_by_id(self, fw_id):
"""
Given a FireWork id, give back a FireWork object
:param fw_id: FireWork id (int)
:return: FireWork object
"""
fw_dict = self.fireworks.find_one({'fw_id': fw_id})
if not fw_dict:
raise ValueError('No FireWork exists with id: {}'.format(fw_id))
# recreate launches from the launch collection
launches = []
for launch_id in fw_dict['launches']:
launches.append(self.get_launch_by_id(launch_id).to_dict())
fw_dict['launches'] = launches
return FireWork.from_dict(fw_dict)
def get_fw_by_id(self, fw_id):
"""
Given a FireWork id, give back a FireWork object
:param fw_id: FireWork id (int)
:return: FireWork object
"""
fw_dict = self.fireworks.find_one({'fw_id': fw_id})
if not fw_dict:
raise ValueError('No FireWork exists with id: {}'.format(fw_id))
# recreate launches from the launch collection
launches = []
for launch_id in fw_dict['launches']:
launches.append(self.get_launch_by_id(launch_id).to_dict())
fw_dict['launches'] = launches
return FireWork.from_dict(fw_dict)
def get_fw_by_id(self, fw_id):
"""
Given a FireWork id, give back a FireWork object
:param fw_id: FireWork id (int)
:return: FireWork object
"""
fw_dict = self.fireworks.find_one({'fw_id': fw_id})
if not fw_dict:
raise ValueError('No FireWork exists with id: {}'.format(fw_id))
# recreate launches from the launch collection
fw_dict['launches'] = list(self.launches.find(
{'launch_id': {"$in": fw_dict['launches']}}))
fw_dict['archived_launches'] = list(self.launches.find(
{'launch_id': {"$in": fw_dict['archived_launches']}}))
return FireWork.from_dict(fw_dict)
def get_fw_by_id(self, fw_id):
"""
Given a FireWork id, give back a FireWork object
:param fw_id: FireWork id (int)
:return: FireWork object
"""
fw_dict = self.fireworks.find_one({'fw_id': fw_id})
if not fw_dict:
raise ValueError('No FireWork exists with id: {}'.format(fw_id))
# recreate launches from the launch collection
fw_dict['launches'] = list(self.launches.find(
{'launch_id': {"$in": fw_dict['launches']}}))
fw_dict['archived_launches'] = list(self.launches.find(
{'launch_id': {"$in": fw_dict['archived_launches']}}))
return FireWork.from_dict(fw_dict)
def test_multi_fw_complex(self):
dest1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'inputs.txt')
dest2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp_file.txt')
self._teardown([dest1, dest2])
try:
# create the FireWork consisting of multiple tasks
firetask1 = TemplateWriterTask({'context': {'opt1': 5.0, 'opt2': 'fast method'}, 'template_file': 'simple_template.txt', 'output_file': dest1})
firetask2 = FileTransferTask({'files': [{'src': dest1, 'dest': dest2}], 'mode': 'copy'})
fw = FireWork([firetask1, firetask2])
# store workflow and launch it locally, single shot
self.lp.add_wf(fw)
launch_rocket(self.lp, FWorker())
# read inputs.txt, words.txt, dest
for d in [dest1, dest2]:
with open(d) as f:
self.assertEqual(f.read(), 'option1 = 5.0\noption2 = fast method')
finally:
self._teardown([dest1, dest2])
def test_fibadder(self):
fib = FibonacciAdderTask()
fw = FireWork(fib, {'smaller': 0, 'larger': 1, 'stop_point': 3})
self.lp.add_wf(fw)
rapidfire(self.lp,
m_dir=MODULE_DIR,
nlaunches=3,
sleep_time=5,
max_loops=30)
time.sleep(5)
self.assertEqual(
self.lp.get_launch_by_id(1).action.stored_data['next_fibnum'], 1)
self.assertEqual(
self.lp.get_launch_by_id(2).action.stored_data['next_fibnum'], 2)
try:
self.assertEqual(
self.lp.get_launch_by_id(3).action.stored_data, {})
except:
time.sleep(30) # TODO: this is really ugly! but needed ... ugh
self.assertEqual(
self.lp.get_launch_by_id(3).action.stored_data, {})
self.assertFalse(self.lp.run_exists())
def test_init(self):
fws = []
for i in range(5):
fw = FireWork([PyTask(func="print", args=[i])], fw_id=i)
fws.append(fw)
wf = Workflow(fws, links_dict={0: [1, 2, 3], 1: [4], 2: [4]})
self.assertIsInstance(wf, Workflow)
self.assertRaises(ValueError,
Workflow,
fws,
links_dict={
0: [1, 2, 3],
1: [4],
100: [4]
})
self.assertRaises(ValueError,
Workflow,
fws,
links_dict={
0: [1, 2, 3],
1: [4],
2: [100]
})
def structure_to_wf(structure):
"""
This method starts with a Structure object and creates a Workflow object
The workflow has two steps - a structure relaxation and a static run
:param structure:
:return:
"""
fws = [] # list of FireWorks to run
connections = defaultdict(list) # dependencies between FireWorks
# generate VASP input objects for 1st VASP run - this is put in the FW spec
mpvis = MPGGAVaspInputSet(user_incar_settings={'NPAR': 2})
incar = mpvis.get_incar(structure)
poscar = mpvis.get_poscar(structure)
kpoints = mpvis.get_kpoints(structure)
potcar = mpvis.get_potcar(structure)
# serialize the VASP input objects to the FW spec
spec = {}
spec['vasp'] = {}
spec['vasp']['incar'] = incar.to_dict
spec['vasp']['poscar'] = poscar.to_dict
spec['vasp']['kpoints'] = kpoints.to_dict
spec['vasp']['potcar'] = potcar.to_dict
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA optimize structure (2x) example'
# set up the custodian that we want to run
jobs = VaspJob.double_relaxation_run('', gzipped=False)
for j in jobs: # turn off auto npar, it doesn't work for >1 node
j.auto_npar = False
handlers = [VaspErrorHandler(), FrozenJobErrorHandler(), MeshSymmetryErrorHandler(),
NonConvergingErrorHandler()]
c_params = {'jobs': [j.to_dict for j in jobs], 'handlers': [h.to_dict for h in handlers], 'max_errors': 5}
custodiantask = VaspCustodianTaskEx(c_params)
# 1st FireWork - run GGA optimize structure
# VaspWriterTask - write input files (INCAR, POSCAR, KPOINTS, POSCAR) based on spec
# CustodianTaskEx - run VASP within a custodian
tasks = [VaspWriterTask(), custodiantask]
fws.append(FireWork(tasks, spec, name=get_name(structure, spec['task_type']), fw_id=1))
# 2nd FireWork - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
FireWork([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=2))
connections[1] = [2]
# 3rd FireWork - static run.
# VaspCopyTask - copy output from previous run to this directory
# SetupStaticRunTask - override old parameters for static run
# CustodianTaskEx - run VASP within a custodian
spec = {'task_type': 'GGA static example'}
copytask = VaspCopyTask({'use_CONTCAR': True, 'skip_CHGCAR': True})
setuptask = SetupStaticRunTask()
custodiantask = VaspCustodianTaskEx({'jobs': [VaspJob('', auto_npar=False).to_dict], 'handlers': [h.to_dict for h in handlers], 'max_errors': 5})
fws.append(FireWork([copytask, setuptask, custodiantask], spec, name=get_name(structure, spec['task_type']), fw_id=3))
connections[2] = [3]
# 4th FireWork - insert previous run into DB
spec = {'task_type': 'VASP db insertion example'}
fws.append(
FireWork([VaspToDBTaskEx()], spec, name=get_name(structure, spec['task_type']), fw_id=4))
connections[3] = [4]
return Workflow(fws, connections, name=get_slug(structure.formula))
def from_dict(cls, m_dict):
return Workflow([FireWork.from_dict(f) for f in m_dict['fws']], Workflow.Links.from_dict(m_dict['links']))
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..."
)
def run_task(self, fw_spec):
print 'sleeping 10s for Mongo'
time.sleep(10)
print 'done sleeping'
print 'the gap is {}, the cutoff is {}'.format(
fw_spec['analysis']['bandgap'], self.gap_cutoff)
if fw_spec['analysis']['bandgap'] >= self.gap_cutoff:
print 'Adding more runs...'
type_name = 'GGA+U' if 'GGA+U' in fw_spec[
'prev_task_type'] else 'GGA'
snl = StructureNL.from_dict(fw_spec['mpsnl'])
f = Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula
fws = []
connections = {}
priority = fw_spec['_priority']
trackers = [
Tracker('FW_job.out'),
Tracker('FW_job.error'),
Tracker('vasp.out'),
Tracker('OUTCAR'),
Tracker('OSZICAR')
]
trackers_db = [Tracker('FW_job.out'), Tracker('FW_job.error')]
# run GGA static
spec = fw_spec # pass all the items from the current spec to the new
spec.update({
'task_type': '{} static v2'.format(type_name),
'_queueadapter': QA_VASP_SMALL,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
})
fws.append(
FireWork([
VaspCopyTask({
'use_CONTCAR': True,
'skip_CHGCAR': True
}),
SetupStaticRunTask(),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-10))
# insert into DB - GGA static
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-9))
connections[-10] = -9
# run GGA Uniform
spec = {
'task_type': '{} Uniform v2'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
}
fws.append(
FireWork([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({'mode': 'uniform'}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-8))
connections[-9] = -8
# insert into DB - GGA Uniform
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
FireWork([VaspToDBTask({'parse_uniform': True})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-7))
connections[-8] = -7
# run GGA Band structure
spec = {
'task_type': '{} band structure v2'.format(type_name),
'_queueadapter': QA_VASP,
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': priority,
'_trackers': trackers
}
fws.append(
FireWork([
VaspCopyTask({'use_CONTCAR': False}),
SetupNonSCFTask({'mode': 'line'}),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-6))
connections[-7] = [-6]
# insert into DB - GGA Band structure
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority * 2,
"_dupefinder": DupeFinderDB().to_dict(),
'_trackers': trackers_db
}
fws.append(
FireWork([VaspToDBTask({})],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-5))
connections[-6] = -5
if fw_spec.get('parameters') and fw_spec['parameters'].get(
'boltztrap'):
# run Boltztrap
spec = {
'task_type': '{} Boltztrap'.format(type_name),
'_queueadapter': QA_DB,
'_dupefinder': DupeFinderDB().to_dict(),
'_priority': priority
}
fws.append(
FireWork([BoltztrapRunTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-4))
connections[-7].append(-4)
wf = Workflow(fws, connections)
print 'Done adding more runs...'
return FWAction(additions=wf)
return FWAction()
def snl_to_wf(snl, parameters=None):
fws = []
connections = {}
parameters = parameters if parameters else {}
snl_priority = parameters.get('priority', 1)
priority = snl_priority * 2 # once we start a job, keep going!
f = Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula
# add the SNL to the SNL DB and figure out duplicate group
tasks = [AddSNLTask()]
spec = {
'task_type': 'Add to SNL database',
'snl': snl.to_dict,
'_queueadapter': QA_DB,
'_priority': snl_priority
}
if 'snlgroup_id' in parameters and isinstance(snl, MPStructureNL):
spec['force_mpsnl'] = snl.to_dict
spec['force_snlgroup_id'] = parameters['snlgroup_id']
del spec['snl']
fws.append(
FireWork(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=0))
connections[0] = [1]
# run GGA structure optimization
spec = _snl_to_spec(snl, enforce_gga=True)
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
tasks = [VaspWriterTask(), get_custodian_task(spec)]
fws.append(
FireWork(tasks,
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=1))
# insert into DB - GGA structure optimization
spec = {
'task_type': 'VASP db insertion',
'_priority': priority,
'_allow_fizzled_parents': True,
'_queueadapter': QA_DB
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=2))
connections[1] = [2]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
FireWork([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=3))
connections[2] = [3]
# determine if GGA+U FW is needed
incar = MPVaspInputSet().get_incar(snl.structure).to_dict
if 'LDAU' in incar and incar['LDAU']:
spec = _snl_to_spec(snl, enforce_gga=False)
del spec[
'vasp'] # we are stealing all VASP params and such from previous run
spec['_priority'] = priority
spec['_queueadapter'] = QA_VASP
fws.append(
FireWork(
[VaspCopyTask(),
SetupGGAUTask(),
get_custodian_task(spec)],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=10))
connections[2].append(10)
spec = {
'task_type': 'VASP db insertion',
'_queueadapter': QA_DB,
'_allow_fizzled_parents': True,
'_priority': priority
}
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=11))
connections[10] = [11]
if not parameters.get('skip_bandstructure', False):
spec = {
'task_type': 'Controller: add Electronic Structure v2',
'_priority': priority,
'_queueadapter': QA_CONTROL
}
fws.append(
FireWork([AddEStructureTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=12))
connections[11] = [12]
wf_meta = get_meta_from_structure(snl.structure)
wf_meta['run_version'] = 'May 2013 (1)'
if '_materialsproject' in snl.data and 'submission_id' in snl.data[
'_materialsproject']:
wf_meta['submission_id'] = snl.data['_materialsproject'][
'submission_id']
return Workflow(
fws,
connections,
name=Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula,
metadata=wf_meta)
lp.reset(args.password)
elif args.command == 'detect_fizzled':
# TODO: report when fixed
print lp.detect_fizzled(args.time, args.fix)
elif args.command == 'detect_unreserved':
# TODO: report when fixed
print lp.detect_unreserved(args.time, args.fix)
elif args.command == 'add':
# TODO: make this cleaner, e.g. make TAR option explicit
# fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
# lp.add_wf(fwf)
try:
fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
lp.add_wf(fwf)
except:
try:
if '.tar' in args.wf_file:
fwf = Workflow.from_tarfile(args.wf_file)
else:
fwf = Workflow.from_file(args.wf_file)
lp.add_wf(fwf)
except:
print 'Error reading FireWork/Workflow file.'
traceback.print_exc()
elif args.command == 'get_fw':
fw = lp.get_fw_by_id(args.fw_id)
fw_dict = fw.to_dict()
def run(self):
"""
Run the rocket (check out a job from the database and execute it)
"""
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())
# 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
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['started_on'] = datetime.utcnow().isoformat()
f.seek(0)
f.write(json.dumps(d))
f.truncate()
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
if '_launch_dir' in m_fw.spec:
prev_dir = launch_dir
os.chdir(m_fw.spec['_launch_dir'])
launch_dir = os.path.abspath(os.getcwd())
if lp:
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
# 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')
try:
my_spec = dict(
m_fw.spec) # make a copy of spec, don't override original
# set up heartbeat (pinging the server that we're still alive)
ping_stop = start_ping_launch(lp, launch_id)
# start background tasks
btask_stops = []
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 my_task in m_fw.tasks:
m_action = my_task.run_task(my_spec)
# 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 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
if lp:
lp.complete_launch(launch_id, m_action, 'COMPLETED')
else:
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'COMPLETED'
d['completed_on'] = datetime.utcnow().isoformat()
f.seek(0)
f.write(json.dumps(d))
f.truncate()
return True
except:
stop_backgrounds(ping_stop, btask_stops)
traceback.print_exc()
try:
m_action = FWAction(stored_data={
'_message': 'runtime error during task',
'_task': my_task.to_dict(),
'_exception': traceback.format_exc()
},
exit=True)
except:
m_action = FWAction(stored_data={
'_message': 'runtime error during task',
'_task': None,
'_exception': traceback.format_exc()
},
exit=True)
if lp:
lp.complete_launch(launch_id, m_action, 'FIZZLED')
else:
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
f.seek(0)
f.write(json.dumps(d))
f.truncate()
return True
lp.reset(args.password)
elif args.command == 'detect_fizzled':
# TODO: report when fixed
print lp.detect_fizzled(args.time, args.fix)
elif args.command == 'detect_unreserved':
# TODO: report when fixed
print lp.detect_unreserved(args.time, args.fix)
elif args.command == 'add':
# TODO: make this cleaner, e.g. make TAR option explicit
# fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
# lp.add_wf(fwf)
try:
fwf = Workflow.from_FireWork(FireWork.from_file(args.wf_file))
lp.add_wf(fwf)
except:
try:
if '.tar' in args.wf_file:
fwf = Workflow.from_tarfile(args.wf_file)
else:
fwf = Workflow.from_file(args.wf_file)
lp.add_wf(fwf)
except:
print 'Error reading FireWork/Workflow file.'
traceback.print_exc()
elif args.command == 'get_fw':
fw = lp.get_fw_by_id(args.fw_id)
fw_dict = fw.to_dict()
def from_dict(cls, m_dict):
return Workflow([FireWork.from_dict(f) for f in m_dict['fws']],
Workflow.Links.from_dict(m_dict['links']))
def run(self):
"""
Run the rocket (check out a job from the database and execute it)
"""
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())
# 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
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['started_on'] = datetime.utcnow().isoformat()
f.seek(0)
f.write(json.dumps(d))
f.truncate()
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
if '_launch_dir' in m_fw.spec:
prev_dir = launch_dir
os.chdir(m_fw.spec['_launch_dir'])
launch_dir = os.path.abspath(os.getcwd())
if lp:
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
if lp:
message = 'RUNNING fw_id: {} in directory: {}'.\
format(m_fw.fw_id, os.getcwd())
lp.log_message(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')
try:
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
btask_stops = []
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 my_task in m_fw.tasks:
m_action = my_task.run_task(my_spec)
# 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 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
if lp:
lp.complete_launch(launch_id, m_action, 'COMPLETED')
else:
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'COMPLETED'
d['completed_on'] = datetime.utcnow().isoformat()
f.seek(0)
f.write(json.dumps(d))
f.truncate()
return True
except:
stop_backgrounds(ping_stop, btask_stops)
traceback.print_exc()
try:
m_action = FWAction(stored_data={'_message': 'runtime error during task', '_task': my_task.to_dict(),
'_exception': traceback.format_exc()}, exit=True)
except:
m_action = FWAction(stored_data={'_message': 'runtime error during task', '_task': None,
'_exception': traceback.format_exc()}, exit=True)
if lp:
lp.complete_launch(launch_id, m_action, 'FIZZLED')
else:
with open('FW_offline.json', 'r+') as f:
d = json.loads(f.read())
d['fwaction'] = m_action.to_dict()
d['state'] = 'FIZZLED'
f.seek(0)
f.write(json.dumps(d))
f.truncate()
return True
def test_add_fw(self):
fw = FireWork(AdditionTask(), {'input_array': [5, 7]})
self.lp.add_wf(fw)
rapidfire(self.lp, self.fworker, m_dir=MODULE_DIR)
self.assertEqual(self.lp.get_launch_by_id(1).action.stored_data['sum'], 12)
