def run_task(self, fw_spec):
assert isinstance(self["split"], basestring), self["split"]
assert isinstance(fw_spec[self["split"]], list)
if isinstance(self["task"]["inputs"], list):
assert self["split"] in self["task"]["inputs"]
else:
assert self["split"] == self["task"]["inputs"]
split_field = fw_spec[self["split"]]
lensplit = len(split_field)
assert lensplit != 0, ("input to split is empty:", self["split"])
nchunks = self.get("number of chunks")
if not nchunks:
nchunks = lensplit
chunklen = lensplit // nchunks
if lensplit % nchunks > 0:
chunklen = chunklen + 1
chunks = [
split_field[i:i + chunklen] for i in range(0, lensplit, chunklen)
]
fireworks = []
for index, chunk in enumerate(chunks):
spec = fw_spec.copy()
spec[self["split"]] = chunk
task = load_object(self["task"])
task["chunk_number"] = index
name = f"{self._fw_name} {index}"
fireworks.append(Firework(task, spec=spec, name=name))
return FWAction(detours=fireworks)
def run_task(self, fw_spec):
assert isinstance(self['split'], basestring), self['split']
assert isinstance(fw_spec[self['split']], list)
if isinstance(self['task']['inputs'], list):
assert self['split'] in self['task']['inputs']
else:
assert self['split'] == self['task']['inputs']
split_field = fw_spec[self['split']]
lensplit = len(split_field)
assert lensplit != 0, ('input to split is empty:', self['split'])
nchunks = self.get('number of chunks')
if not nchunks:
nchunks = lensplit
chunklen = lensplit // nchunks
if lensplit % nchunks > 0:
chunklen = chunklen + 1
chunks = [
split_field[i:i + chunklen] for i in range(0, lensplit, chunklen)
]
fireworks = []
for index, chunk in enumerate(chunks):
spec = fw_spec.copy()
spec[self['split']] = chunk
task = load_object(self['task'])
task['chunk_number'] = index
name = self._fw_name + ' ' + str(index)
fireworks.append(Firework(task, spec=spec, name=name))
return FWAction(detours=fireworks)
def run_task(self, fw_spec):
assert isinstance(self['split'], basestring), self['split']
assert isinstance(fw_spec[self['split']], list)
if isinstance(self['task']['inputs'], list):
assert self['split'] in self['task']['inputs']
else:
assert self['split'] == self['task']['inputs']
split_field = fw_spec[self['split']]
lensplit = len(split_field)
assert lensplit != 0, ('input to split is empty:', self['split'])
nchunks = self.get('number of chunks')
if not nchunks:
nchunks = lensplit
chunklen = lensplit // nchunks
if lensplit % nchunks > 0:
chunklen = chunklen + 1
chunks = [split_field[i:i+chunklen] for i in range(0, lensplit, chunklen)]
fireworks = []
for index, chunk in enumerate(chunks):
spec = fw_spec.copy()
spec[self['split']] = chunk
task = load_object(self['task'])
task['chunk_number'] = index
name = self._fw_name + ' ' + str(index)
fireworks.append(Firework(task, spec=spec, name=name))
return FWAction(detours=fireworks)
def exactTasks(self, points):
'''
Build a workflow to excute an exactTask for each point
'''
# De-serialise the exact task from dict
et = load_object(self.exactTask)
tl = [ Firework(ParameterFitting(surrogateModelId=self._id)) ]
dep = {}
e = six.next(six.itervalues(points))
for i in xrange(len(e)):
p = {}
for k in points:
p[k] = points[k][i]
for m in self.substituteModels:
p.update(m.callModel(p))
t = et
t['point'] = p
fw = Firework(t)
tl.append(fw)
dep[fw] = tl[0]
return (tl, dep, tl[0])
def test_modifyincar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file(os.path.join(module_dir, "INCAR"))
# modify and test
ft = ModifyIncar({
"incar_update": {
"ISMEAR": 1000
},
"incar_multiply": {
"ENCUT": 1.5
},
"incar_dictmod": {
"_inc": {
"ISPIN": -1
}
}
})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod['ISMEAR'], 1000)
self.assertEqual(incar_mod['ENCUT'], 780)
self.assertEqual(incar_mod['ISPIN'], 1)
def test_ioset_explicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set=MPRelaxSet(self.struct_si, force_gamma=True))
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_serialization(self):
p = CommonAdapter(
q_type="PBS",
q_name="hello",
template_file=os.path.join(os.path.dirname(__file__), "mypbs.txt"),
hello="world",
queue="random",
)
p_new = load_object(p.to_dict())
# Make sure the original and deserialized version both work properly.
for a in [p, p_new]:
script = a.get_script_str("here")
lines = script.split("\n")
self.assertIn("# world", lines)
self.assertIn("#PBS -q random", lines)
p = CommonAdapter(q_type="PBS",
q_name="hello",
hello="world",
queue="random")
# this uses the default template, which does not have $${hello}
self.assertNotEqual("# world",
p.get_script_str("here").split("\n")[-1])
self.assertNotIn("_fw_template_file", p.to_dict())
def test_ioset_explicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si,
vasp_input_set=MPRelaxSet(self.struct_si, force_gamma=True)))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_pmgobjects(self):
mpvis = MPRelaxSet(self.struct_si, force_gamma=True)
ft = WriteVaspFromPMGObjects(
{"incar": mpvis.incar, "poscar": mpvis.poscar, "kpoints": mpvis.kpoints, "potcar": mpvis.potcar}
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_serialization_details(self):
# This detects a weird bug found in early version of serializers
pbs = CommonAdapter('PBS')
self.assertTrue(isinstance(pbs, CommonAdapter))
self.assertTrue(isinstance(self.get_data(pbs.to_dict()), CommonAdapter))
self.assertTrue(isinstance(load_object(pbs.to_dict()), CommonAdapter))
self.assertTrue(isinstance(self.get_data(pbs.to_dict()), CommonAdapter)) # repeated test on purpose!
def initialisationFw(self):
obj = load_object(self.initialisationStrategy)
return Firework(
Initialisation(
surrogateModelId=self._id,
points=obj.newPoints()
)
)
def test_serialization_details(self):
# This detects a weird bug found in early version of serializers
pbs = CommonAdapter("PBS")
self.assertTrue(isinstance(pbs, CommonAdapter))
self.assertTrue(isinstance(self.get_data(pbs.to_dict()), CommonAdapter))
self.assertTrue(isinstance(load_object(pbs.to_dict()), CommonAdapter))
self.assertTrue(isinstance(self.get_data(pbs.to_dict()), CommonAdapter)) # repeated test on purpose!
def test_potcar_spec(self):
ft = WriteVaspFromIOSet(
structure=self.struct_si,
vasp_input_set="MPRelaxSet",
potcar_spec=True,
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(potcar_spec=True)
def test_pmgobjects(self):
mpvis = MPRelaxSet(self.struct_si, force_gamma=True)
ft = WriteVaspFromPMGObjects({"incar": mpvis.incar,
"poscar": mpvis.poscar,
"kpoints": mpvis.kpoints,
"potcar": mpvis.potcar})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def run_task(self, fw_spec):
assert isinstance(self['split'], (basestring, list)), self['split']
split_list = self['split']
if isinstance(split_list, basestring): split_list = [split_list]
reflen = 0
for split in split_list:
assert isinstance(fw_spec[split], list)
split_field = fw_spec[split]
lensplit = len(split_field)
# update reflen on first iteration
if reflen == 0:
assert lensplit != 0, ('input to split is empty:', split)
reflen = lensplit
nchunks = self.get('number of chunks')
if not nchunks:
nchunks = lensplit
chunklen = lensplit // nchunks
if lensplit % nchunks > 0:
chunklen = chunklen + 1
chunks = [{
split: split_field[i:i + chunklen]
} for i in range(0, lensplit, chunklen)]
else:
assert lensplit == reflen, ('input lists not of equal length:',
split)
for i in range(0, lensplit, chunklen):
chunks[i // chunklen].update(
{split: split_field[i:i + chunklen]})
fireworks = []
chunk_index_spec = self.get('chunk index spec')
# allow for multiple tasks
task_list = self['task']
if not isinstance(task_list, list):
task_list = [task_list]
for index, chunk in enumerate(chunks):
spec = fw_spec.copy()
for split in split_list:
spec[split] = chunk[split]
tasks = []
for task_entry in task_list:
task = load_object(task_entry)
task['chunk_number'] = index
tasks.append(task)
if chunk_index_spec and isinstance(chunk_index_spec, basestring):
spec[chunk_index_spec] = index
name = self._fw_name + ' ' + str(index)
fireworks.append(Firework(tasks, spec=spec, name=name))
return FWAction(detours=fireworks)
def from_dict(cls, m_dict):
"""
Note: The QueueAdapter is loaded based on its fw_name alone
See the docs for to_dict() for more details
"""
qa_dict = {'_fw_name': m_dict['qa_name']}
# load the QueueAdapter object dynamically
qa = load_object(qa_dict)
return QueueParams(qa, m_dict['params'], m_dict['logging_dir'])
def from_dict(cls, m_dict):
"""
Note: The QueueAdapter is loaded based on its fw_name alone
See the docs for to_dict() for more details
"""
qa_dict = {'_fw_name': m_dict['qa_name']}
# load the QueueAdapter object dynamically
qa = load_object(qa_dict)
return QueueParams(qa, m_dict['params'], m_dict['logging_dir'])
def test_implicit_serialization(self):
self.assertEqual(
load_object({
"a": {
"p1": {
"p2": 3
}
},
"_fw_name": "TestSerializer Export Name"
}), self.obj_4, 'Implicit import fails!')
def test_ioset_params(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set="MPRelaxSet",
vasp_input_params={"user_incar_settings": {"ISMEAR": 1000}}))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ISMEAR"], 1000) # make sure override works
incar['ISMEAR'] = -5 # switch back to default
incar.write_file("INCAR")
self._verify_files(skip_kpoints=True)
def run_task(self, fw_spec):
self.run_function(fw_spec)
self.increment_counter(fw_spec)
if not self.eval_condition(fw_spec):
firework = Firework(
tasks=[load_object(task) for task in fw_spec['_tasks']],
spec=fw_spec,
name=self._fw_name)
return FWAction(detours=firework, exit=False)
else:
return FWAction(exit=True)
def test_ioset_params(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set="MPRelaxSet",
vasp_input_params={"user_incar_settings": {"ISMEAR": 1000}}))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar = Incar.from_file("INCAR")
self.assertEqual(incar["ISMEAR"], 1000) # make sure override works
incar['ISMEAR'] = -5 # switch back to default
incar.write_file("INCAR")
self._verify_files(skip_kpoints=True)
def test_modify_kpoints(self):
# create an KPOINTS
kpoints = self.ref_kpoints
kpoints.write_file("KPOINTS")
# modify and test
ft = ModifyKpoints(kpoints_update={"kpts": [[3, 4, 5]]}, )
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
kpoints_mod = Kpoints.from_file("KPOINTS")
self.assertEqual(kpoints_mod.kpts, [[3, 4, 5]])
def test_modify_potcar(self):
Potcar(["Si"]).write_file("POTCAR")
potcar = Potcar.from_file("POTCAR")
self.assertFalse("alt" in potcar[0].header)
# modify/test
ft = ModifyPotcar(potcar_symbols={"Si": "O"})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
new_potcar = Potcar.from_file("POTCAR")
self.assertEqual(len(new_potcar), 1)
self.assertEqual(new_potcar[0].symbol, 'O')
def test_ioset_explicit(self):
for fn in ["POSCAR.gz", "POTCAR.gz", "INCAR.gz"]:
shutil.copy2(os.path.join(self.vasp_dir, fn), ".")
ft = WriteLobsterinputfromIO(
poscar_path="POSCAR.gz",
potcar_path="POTCAR.gz",
incar_path="INCAR.gz",
option="standard",
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self.assertEqual(Lobsterin.from_file("lobsterin"), self.ref_lobsterin)
def test_modify_potcar(self):
Potcar(["Si"]).write_file("POTCAR")
potcar = Potcar.from_file("POTCAR")
self.assertFalse("alt" in potcar[0].header)
# modify/test
ft = ModifyPotcar(potcar_symbols={"Si": "O"})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
new_potcar = Potcar.from_file("POTCAR")
self.assertEqual(len(new_potcar), 1)
self.assertEqual(new_potcar[0].symbol, "O")
def test_ioset_settings(self):
for fn in ["POSCAR.gz", "POTCAR.gz", "INCAR.gz"]:
shutil.copy2(os.path.join(self.vasp_dir, fn), ".")
# user supplied lobsterin inputs
ft = WriteLobsterinputfromIO(
poscar_path="POSCAR.gz",
potcar_path="POTCAR.gz",
incar_path="INCAR.gz",
option="standard",
user_lobsterin_settings={"COHPEndEnergy": 10.0},
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self.assertEqual(Lobsterin.from_file("lobsterin"), self.ref_lobsterin2)
def test_modify_incar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file("INCAR")
# modify and test
ft = ModifyIncar(
{"incar_update": {"ISMEAR": 1000}, "incar_multiply": {"ENCUT": 1.5},
"incar_dictmod": {"_inc": {"ISPIN": -1}}})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod['ISMEAR'], 1000)
self.assertEqual(incar_mod['ENCUT'], 780)
self.assertEqual(incar_mod['ISPIN'], 1)
def test_modify_incar(self):
# create an INCAR
incar = self.ref_incar
incar.write_file("INCAR")
# modify and test
ft = ModifyIncar(
incar_update={"ISMEAR": 1000},
incar_multiply={"ENCUT": 1.5},
incar_dictmod={"_inc": {
"ISPIN": -1
}},
)
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
incar_mod = Incar.from_file("INCAR")
self.assertEqual(incar_mod["ISMEAR"], 1000)
self.assertEqual(incar_mod["ENCUT"], 780)
self.assertEqual(incar_mod["ISPIN"], 1)
def _steal_launches(self, thief_fw):
stolen = False
if thief_fw.state == 'READY' and '_dupefinder' in thief_fw.spec:
m_dupefinder = load_object(thief_fw.spec['_dupefinder'])
# get the query that will limit the number of results to check as duplicates
m_query = m_dupefinder.query(thief_fw.spec)
m_query['launches'] = {'$ne': []}
# iterate through all potential duplicates in the DB
for potential_match in self.fireworks.find(m_query):
spec1 = dict(thief_fw.to_dict()['spec']) # defensive copy
spec2 = dict(potential_match['spec']) # defensive copy
if m_dupefinder.verify(spec1, spec2): # verify the match
# steal the launches
victim_fw = self.get_fw_by_id(potential_match['fw_id'])
thief_launches = [l.launch_id for l in thief_fw.launches]
valuable_launches = [l for l in victim_fw.launches if l.launch_id not in thief_launches]
for launch in valuable_launches:
thief_fw.launches.append(launch)
stolen = True
return stolen
def workflow(self, model):
et = load_object({'_fw_name': '{{modena.Strategy.InitialDataPoints}}'})
points = self.newPoints()
e = six.next(six.itervalues(points))
p = {k: [0] * len(points[k]) for k in points}
for i in xrange(len(e)):
for k in points:
p[k][i] = points[k][i]
t = et
t['point'] = p
t['indices'] = indices
t['modelId'] = self._id
fw = Firework(t)
wf = Workflow2([fw], name='initialising to dataset')
wf.addAfterAll(model.parameterFittingStrategy().workflow(model))
return wf
def workflow(self, model):
et = load_object({'_fw_name': '{{modena.Strategy.InitialDataPoints}}'})
points = self.newPoints()
e = six.next(six.itervalues(points))
p = { k:[0]*len(points[k]) for k in points }
for i in xrange(len(e)):
for k in points:
p[k][i] = points[k][i]
t = et
t['point'] = p
t['indices'] = indices
t['modelId'] = self._id
fw = Firework(t)
wf = Workflow2( [fw], name='initialising to dataset')
wf.addAfterAll(model.parameterFittingStrategy().workflow(model))
return wf
def _steal_launches(self, thief_fw):
stolen = False
if thief_fw.state == 'READY' and '_dupefinder' in thief_fw.spec:
m_dupefinder = load_object(thief_fw.spec['_dupefinder'])
# get the query that will limit the number of results to check as duplicates
m_query = m_dupefinder.query(thief_fw.spec)
m_query['launches'] = {'$ne': []}
# iterate through all potential duplicates in the DB
for potential_match in self.fireworks.find(m_query):
spec1 = dict(thief_fw.to_dict()['spec']) # defensive copy
spec2 = dict(potential_match['spec']) # defensive copy
if m_dupefinder.verify(spec1, spec2): # verify the match
# steal the launches
victim_fw = self.get_fw_by_id(potential_match['fw_id'])
thief_launches = [l.launch_id for l in thief_fw.launches]
valuable_launches = [
l for l in victim_fw.launches
if l.launch_id not in thief_launches
]
for launch in valuable_launches:
thief_fw.launches.append(launch)
stolen = True
return stolen
def test_serialization(self):
p = CommonAdapter(
q_type="PBS",
q_name="hello",
template_file=os.path.join(os.path.dirname(__file__),
"mypbs.txt"),
hello="world", queue="random")
p_new = load_object(p.to_dict())
#Make sure the original and deserialized verison both work properly.
for a in [p, p_new]:
script = a.get_script_str("here")
lines = script.split("\n")
self.assertIn("# world", lines)
self.assertIn("#PBS -q random", lines)
p = CommonAdapter(
q_type="PBS",
q_name="hello",
hello="world", queue="random")
#this uses the default template, which does not have $${hello}
self.assertNotEqual("# world", p.get_script_str("here").split("\n")[
-1])
self.assertNotIn("_fw_template_file", p.to_dict())
def parameterFittingFwAction(self, model, **kwargs):
obj = load_object(self.parameterFittingStrategy)
return obj.newPointsFWAction(model, **kwargs)
def launch_rocket_to_queue(launchpad,
fworker,
qadapter,
launcher_dir='.',
reserve=False,
strm_lvl='INFO'):
"""
Submit a single job to the queue.
:param launchpad: (LaunchPad)
:param fworker: (FWorker)
:param qadapter: (QueueAdapterBase)
:param launcher_dir: (str) The directory where to submit the job
:param reserve: (bool) Whether to queue in reservation mode
:param strm_lvl: (str) level at which to stream log messages
"""
fworker = fworker if fworker else FWorker()
launcher_dir = os.path.abspath(launcher_dir)
l_logger = get_fw_logger('queue.launcher',
l_dir=launchpad.logdir,
stream_level=strm_lvl)
# get the queue adapter
l_logger.debug('getting queue adapter')
qadapter = load_object(qadapter.to_dict(
)) # make a defensive copy, mainly for reservation mode
# make sure launch_dir exists:
if not os.path.exists(launcher_dir):
raise ValueError(
'Desired launch directory {} does not exist!'.format(launcher_dir))
if launchpad.run_exists(fworker):
try:
# move to the launch directory
l_logger.info('moving to launch_dir {}'.format(launcher_dir))
os.chdir(launcher_dir)
oldlaunch_dir = None
if '--offline' in qadapter['rocket_launch'] and not reserve:
raise ValueError(
"Must use reservation mode (-r option) of qlaunch when using offline mode (--offline option) of rlaunch!!"
)
elif reserve:
l_logger.debug('finding a FW to reserve...')
fw, launch_id = launchpad._reserve_fw(fworker, launcher_dir)
if not fw:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!'
)
return False
l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))
# set job name to the FW name
job_name = get_slug(fw.name)
job_name = job_name[0:20] if len(job_name) > 20 else job_name
qadapter.update({'job_name':
job_name}) # set the job name to FW name
if '_queueadapter' in fw.spec:
l_logger.debug(
'updating queue params using FireWork spec..')
qadapter.update(fw.spec['_queueadapter'])
# update the exe to include the FW_id
if 'singleshot' not in qadapter.get('rocket_launch', ''):
raise ValueError(
'Reservation mode of queue launcher only works for singleshot Rocket Launcher!'
)
qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)
if '--offline' in qadapter['rocket_launch']:
# handle _launch_dir parameter early...
if '_launch_dir' in fw.spec:
os.chdir(fw.spec['_launch_dir'])
oldlaunch_dir = launcher_dir
launcher_dir = os.path.abspath(os.getcwd())
launchpad._change_launch_dir(launch_id, launcher_dir)
# write FW.json
fw.to_file("FW.json")
# write Launchid
with open('FW_offline.json', 'w') as f:
f.write('{"launch_id":%s}' % launch_id)
launchpad.add_offline_run(launch_id, fw.fw_id, fw.name)
# write and submit the queue script using the queue adapter
l_logger.debug('writing queue script')
with open(SUBMIT_SCRIPT_NAME, 'w') as f:
queue_script = qadapter.get_script_str(launcher_dir)
f.write(queue_script)
l_logger.info('submitting queue script')
reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
if not reservation_id:
raise RuntimeError(
'queue script could not be submitted, check queue adapter and queue server status!'
)
elif reserve:
launchpad.set_reservation_id(launch_id, reservation_id)
return reservation_id
except:
log_exception(l_logger, 'Error writing/submitting queue script!')
return False
finally:
if oldlaunch_dir:
os.chdir(
oldlaunch_dir
) # this only matters in --offline mode with _launch_dir!
else:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!')
return False
def test_ioset_implicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si, vasp_input_set="MPRelaxSet"))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(skip_kpoints=True)
def launch_rocket_to_queue(launchpad, fworker, qadapter, launcher_dir='.', reserve=False, strm_lvl='INFO'):
"""
Submit a single job to the queue.
:param launchpad: (LaunchPad)
:param fworker: (FWorker)
:param qadapter: (QueueAdapterBase)
:param launcher_dir: (str) The directory where to submit the job
:param reserve: (bool) Whether to queue in reservation mode
:param strm_lvl: (str) level at which to stream log messages
"""
fworker = fworker if fworker else FWorker()
launcher_dir = os.path.abspath(launcher_dir)
l_logger = get_fw_logger('queue.launcher', l_dir=launchpad.logdir, stream_level=strm_lvl)
l_logger.debug('getting queue adapter')
qadapter = load_object(qadapter.to_dict()) # make a defensive copy, mainly for reservation mode
fw, launch_id = None, None # only needed in reservation mode
oldlaunch_dir = None # only needed in --offline mode with _launch_dir option
if not os.path.exists(launcher_dir):
raise ValueError('Desired launch directory {} does not exist!'.format(launcher_dir))
if '--offline' in qadapter['rocket_launch'] and not reserve:
raise ValueError("Must use reservation mode (-r option) of qlaunch when using offline option of rlaunch!!")
if reserve and 'singleshot' not in qadapter.get('rocket_launch', ''):
raise ValueError('Reservation mode of queue launcher only works for singleshot Rocket Launcher!')
if launchpad.run_exists(fworker):
try:
# move to the launch directory
l_logger.info('moving to launch_dir {}'.format(launcher_dir))
with cd(launcher_dir):
if reserve:
l_logger.debug('finding a FW to reserve...')
fw, launch_id = launchpad.reserve_fw(fworker, launcher_dir)
if not fw:
l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
return False
l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))
# update qadapter job_name based on FW name
job_name = get_slug(fw.name)[0:20]
qadapter.update({'job_name': job_name})
if '_queueadapter' in fw.spec:
l_logger.debug('updating queue params using Firework spec..')
qadapter.update(fw.spec['_queueadapter'])
# reservation mode includes --fw_id in rocket launch
qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)
if '--offline' in qadapter['rocket_launch']:
# handle _launch_dir parameter now b/c we can't call
# launchpad.change_launch_dir() later on in offline mode
if '_launch_dir' in fw.spec:
os.chdir(fw.spec['_launch_dir'])
oldlaunch_dir = launcher_dir
launcher_dir = os.path.abspath(os.getcwd())
launchpad.change_launch_dir(launch_id, launcher_dir)
setup_offline_job(launchpad, fw, launch_id)
l_logger.debug('writing queue script')
with open(SUBMIT_SCRIPT_NAME, 'w') as f:
queue_script = qadapter.get_script_str(launcher_dir)
f.write(queue_script)
l_logger.info('submitting queue script')
reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
if not reservation_id:
if reserve:
l_logger.info('Un-reserving FW with fw_id, launch_id: {}, {}'.format(fw.fw_id, launch_id))
launchpad.cancel_reservation(launch_id)
raise RuntimeError('queue script could not be submitted, check queue script/queue adapter/queue server status!')
elif reserve:
launchpad.set_reservation_id(launch_id, reservation_id)
return reservation_id
except:
log_exception(l_logger, 'Error writing/submitting queue script!')
return False
finally:
if oldlaunch_dir:
os.chdir(oldlaunch_dir) # this only matters in --offline mode with _launch_dir!
else:
l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
return False
def outOfBoundsFwAction(self, model, caller, **kwargs):
obj = load_object(self.outOfBoundsStrategy)
return obj.newPointsFWAction(model, caller, **kwargs)
def test_ioset_implicit(self):
ft = WriteVaspFromIOSet(dict(structure=self.struct_si, vasp_input_set="MPRelaxSet"))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files(skip_kpoints=True)
def launch_rocket_to_queue(launchpad,
fworker,
qadapter,
launcher_dir='.',
reserve=False,
strm_lvl='INFO',
create_launcher_dir=False):
"""
Submit a single job to the queue.
:param launchpad: (LaunchPad)
:param fworker: (FWorker)
:param qadapter: (QueueAdapterBase)
:param launcher_dir: (str) The directory where to submit the job
:param reserve: (bool) Whether to queue in reservation mode
:param strm_lvl: (str) level at which to stream log messages
:param create_launcher_dir: (bool) Whether to create a subfolder launcher+timestamp, if needed
"""
fworker = fworker if fworker else FWorker()
launcher_dir = os.path.abspath(launcher_dir)
l_logger = get_fw_logger('queue.launcher',
l_dir=launchpad.logdir,
stream_level=strm_lvl)
l_logger.debug('getting queue adapter')
qadapter = load_object(qadapter.to_dict(
)) # make a defensive copy, mainly for reservation mode
fw, launch_id = None, None # only needed in reservation mode
if not os.path.exists(launcher_dir):
raise ValueError(
'Desired launch directory {} does not exist!'.format(launcher_dir))
if '--offline' in qadapter['rocket_launch'] and not reserve:
raise ValueError(
"Must use reservation mode (-r option) of qlaunch when using offline option of rlaunch!!"
)
if reserve and 'singleshot' not in qadapter.get('rocket_launch', ''):
raise ValueError(
'Reservation mode of queue launcher only works for singleshot Rocket Launcher!'
)
if launchpad.run_exists(fworker):
try:
if reserve:
l_logger.debug('finding a FW to reserve...')
fw, launch_id = launchpad.reserve_fw(fworker, launcher_dir)
if not fw:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!'
)
return False
l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))
# update qadapter job_name based on FW name
job_name = get_slug(fw.name)[0:QUEUE_JOBNAME_MAXLEN]
qadapter.update({'job_name': job_name})
if '_queueadapter' in fw.spec:
l_logger.debug(
'updating queue params using Firework spec..')
qadapter.update(fw.spec['_queueadapter'])
# reservation mode includes --fw_id in rocket launch
qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)
# update launcher_dir if _launch_dir is selected in reserved fw
if '_launch_dir' in fw.spec:
fw_launch_dir = os.path.expandvars(fw.spec['_launch_dir'])
if not os.path.isabs(fw_launch_dir):
fw_launch_dir = os.path.join(launcher_dir,
fw_launch_dir)
launcher_dir = fw_launch_dir
try:
os.makedirs(launcher_dir)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir,
l_logger,
prefix='launcher_')
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir,
l_logger,
prefix='launcher_')
# move to the launch directory
l_logger.info('moving to launch_dir {}'.format(launcher_dir))
with cd(launcher_dir):
if '--offline' in qadapter['rocket_launch']:
setup_offline_job(launchpad, fw, launch_id)
l_logger.debug('writing queue script')
with open(SUBMIT_SCRIPT_NAME, 'w') as f:
queue_script = qadapter.get_script_str(launcher_dir)
f.write(queue_script)
l_logger.info('submitting queue script')
reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
if not reservation_id:
if reserve:
l_logger.info(
'Un-reserving FW with fw_id, launch_id: {}, {}'.
format(fw.fw_id, launch_id))
launchpad.cancel_reservation(launch_id)
raise RuntimeError(
'queue script could not be submitted, check queue script/queue adapter/queue server status!'
)
elif reserve:
launchpad.set_reservation_id(launch_id, reservation_id)
return reservation_id
except:
log_exception(l_logger, 'Error writing/submitting queue script!')
return False
else:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!')
return False
def launch_rocket_to_queue(launchpad,
fworker,
qadapter,
launcher_dir='.',
reserve=False,
strm_lvl='INFO',
create_launcher_dir=False,
fill_mode=False,
fw_id=None):
"""
Submit a single job to the queue.
Args:
launchpad (LaunchPad)
fworker (FWorker)
qadapter (QueueAdapterBase)
launcher_dir (str): The directory where to submit the job
reserve (bool): Whether to queue in reservation mode
strm_lvl (str): level at which to stream log messages
create_launcher_dir (bool): Whether to create a subfolder launcher+timestamp, if needed
fill_mode (bool): whether to submit jobs even when there is nothing to run
(only in non-reservation mode)
fw_id (int): specific fw_id to reserve (reservation mode only)
"""
fworker = fworker if fworker else FWorker()
launcher_dir = os.path.abspath(launcher_dir)
l_logger = get_fw_logger('queue.launcher',
l_dir=launchpad.logdir,
stream_level=strm_lvl)
l_logger.debug('getting queue adapter')
qadapter = load_object(qadapter.to_dict(
)) # make a defensive copy, mainly for reservation mode
fw, launch_id = None, None # only needed in reservation mode
if not os.path.exists(launcher_dir):
raise ValueError(
'Desired launch directory {} does not exist!'.format(launcher_dir))
if '--offline' in qadapter['rocket_launch'] and not reserve:
raise ValueError("Must use reservation mode (-r option) of qlaunch "
"when using offline option of rlaunch!!")
if reserve and 'singleshot' not in qadapter.get('rocket_launch', ''):
raise ValueError(
'Reservation mode of queue launcher only works for singleshot Rocket Launcher!'
)
if fill_mode and reserve:
raise ValueError(
"Fill_mode cannot be used in conjunction with reserve mode!")
if fw_id and not reserve:
raise ValueError(
"qlaunch for specific fireworks may only be used in reservation mode."
)
if fill_mode or launchpad.run_exists(fworker):
launch_id = None
try:
if reserve:
if fw_id:
l_logger.debug('finding a FW to reserve...')
fw, launch_id = launchpad.reserve_fw(fworker,
launcher_dir,
fw_id=fw_id)
if not fw:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!'
)
return False
l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))
# update qadapter job_name based on FW name
job_name = get_slug(fw.name)[0:QUEUE_JOBNAME_MAXLEN]
qadapter.update({'job_name': job_name})
if '_queueadapter' in fw.spec:
l_logger.debug(
'updating queue params using Firework spec..')
qadapter.update(fw.spec['_queueadapter'])
# reservation mode includes --fw_id in rocket launch
qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)
# update launcher_dir if _launch_dir is selected in reserved fw
if '_launch_dir' in fw.spec:
fw_launch_dir = os.path.expandvars(fw.spec['_launch_dir'])
if not os.path.isabs(fw_launch_dir):
fw_launch_dir = os.path.join(launcher_dir,
fw_launch_dir)
launcher_dir = fw_launch_dir
makedirs_p(launcher_dir)
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir,
l_logger,
prefix='launcher_')
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir,
l_logger,
prefix='launcher_')
# move to the launch directory
l_logger.info('moving to launch_dir {}'.format(launcher_dir))
with cd(launcher_dir):
if '--offline' in qadapter['rocket_launch']:
setup_offline_job(launchpad, fw, launch_id)
l_logger.debug('writing queue script')
with open(SUBMIT_SCRIPT_NAME, 'w') as f:
queue_script = qadapter.get_script_str(launcher_dir)
f.write(queue_script)
l_logger.info('submitting queue script')
reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
if not reservation_id:
raise RuntimeError(
'queue script could not be submitted, check queue '
'script/queue adapter/queue server status!')
elif reserve:
launchpad.set_reservation_id(launch_id, reservation_id)
return reservation_id
except:
log_exception(l_logger, 'Error writing/submitting queue script!')
if reserve and launch_id is not None:
try:
l_logger.info(
'Un-reserving FW with fw_id, launch_id: {}, {}'.format(
fw.fw_id, launch_id))
launchpad.cancel_reservation(launch_id)
launchpad.forget_offline(launch_id)
except:
log_exception(
l_logger,
'Error unreserving FW with fw_id {}'.format(fw.fw_id))
return False
else:
l_logger.info(
'No jobs exist in the LaunchPad for submission to queue!')
return None # note: this is a hack (rather than False) to indicate a soft failure to rapidfire()
def test_explicit_serialization(self):
self.assertEqual(load_object(self.s_dict), self.s_obj)
def launch_rocket_to_queue(launchpad, fworker, qadapter, launcher_dir='.', reserve=False,
strm_lvl='INFO', create_launcher_dir=False, fill_mode=False,
fw_id=None):
"""
Submit a single job to the queue.
Args:
launchpad (LaunchPad)
fworker (FWorker)
qadapter (QueueAdapterBase)
launcher_dir (str): The directory where to submit the job
reserve (bool): Whether to queue in reservation mode
strm_lvl (str): level at which to stream log messages
create_launcher_dir (bool): Whether to create a subfolder launcher+timestamp, if needed
fill_mode (bool): whether to submit jobs even when there is nothing to run
(only in non-reservation mode)
fw_id (int): specific fw_id to reserve (reservation mode only)
"""
fworker = fworker if fworker else FWorker()
launcher_dir = os.path.abspath(launcher_dir)
l_logger = get_fw_logger('queue.launcher', l_dir=launchpad.logdir, stream_level=strm_lvl)
l_logger.debug('getting queue adapter')
qadapter = load_object(qadapter.to_dict()) # make a defensive copy, mainly for reservation mode
fw, launch_id = None, None # only needed in reservation mode
if not os.path.exists(launcher_dir):
raise ValueError('Desired launch directory {} does not exist!'.format(launcher_dir))
if '--offline' in qadapter['rocket_launch'] and not reserve:
raise ValueError("Must use reservation mode (-r option) of qlaunch "
"when using offline option of rlaunch!!")
if reserve and 'singleshot' not in qadapter.get('rocket_launch', ''):
raise ValueError('Reservation mode of queue launcher only works for singleshot Rocket Launcher!')
if fill_mode and reserve:
raise ValueError("Fill_mode cannot be used in conjunction with reserve mode!")
if fw_id and not reserve:
raise ValueError("qlaunch for specific fireworks may only be used in reservation mode.")
if fill_mode or launchpad.run_exists(fworker):
launch_id = None
try:
if reserve:
if fw_id:
l_logger.debug('finding a FW to reserve...')
fw, launch_id = launchpad.reserve_fw(fworker, launcher_dir, fw_id=fw_id)
if not fw:
l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
return False
l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))
# update qadapter job_name based on FW name
job_name = get_slug(fw.name)[0:QUEUE_JOBNAME_MAXLEN]
qadapter.update({'job_name': job_name})
if '_queueadapter' in fw.spec:
l_logger.debug('updating queue params using Firework spec..')
qadapter.update(fw.spec['_queueadapter'])
# reservation mode includes --fw_id in rocket launch
qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)
# update launcher_dir if _launch_dir is selected in reserved fw
if '_launch_dir' in fw.spec:
fw_launch_dir = os.path.expandvars(fw.spec['_launch_dir'])
if not os.path.isabs(fw_launch_dir):
fw_launch_dir = os.path.join(launcher_dir, fw_launch_dir)
launcher_dir = fw_launch_dir
makedirs_p(launcher_dir)
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir, l_logger, prefix='launcher_')
launchpad.change_launch_dir(launch_id, launcher_dir)
elif create_launcher_dir:
# create launcher_dir
launcher_dir = create_datestamp_dir(launcher_dir, l_logger, prefix='launcher_')
# move to the launch directory
l_logger.info('moving to launch_dir {}'.format(launcher_dir))
with cd(launcher_dir):
if '--offline' in qadapter['rocket_launch']:
setup_offline_job(launchpad, fw, launch_id)
l_logger.debug('writing queue script')
with open(SUBMIT_SCRIPT_NAME, 'w') as f:
queue_script = qadapter.get_script_str(launcher_dir)
f.write(queue_script)
l_logger.info('submitting queue script')
reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
if not reservation_id:
raise RuntimeError('queue script could not be submitted, check queue '
'script/queue adapter/queue server status!')
elif reserve:
launchpad.set_reservation_id(launch_id, reservation_id)
return reservation_id
except:
log_exception(l_logger, 'Error writing/submitting queue script!')
if reserve and launch_id is not None:
try:
l_logger.info('Un-reserving FW with fw_id, launch_id: {}, {}'.format(
fw.fw_id, launch_id))
launchpad.cancel_reservation(launch_id)
launchpad.forget_offline(launch_id)
except:
log_exception(l_logger, 'Error unreserving FW with fw_id {}'.format(fw.fw_id))
return False
else:
l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
return None # note: this is a hack (rather than False) to indicate a soft failure to rapidfire()
def test_explicit_serialization(self):
self.assertEqual(load_object(self.s_dict), self.s_obj)
def test_implicit_serialization(self):
self.assertEqual(load_object({"a": {"p1": {"p2": 3}}, "_fw_name": "TestSerializer Export Name"}), self.obj_4,
'Implicit import fails!')