def execute(self, name):
try:
self.state.saveState('READY')
lp = LaunchPad(**self.db)
lp.reset('', require_password=False)
tasks = []
for idx, command in enumerate(self.commands):
if idx > 0:
tasks.append(
Firework(ScriptTask.from_str(command),
name=f'task_{idx}',
fw_id=idx,
parents=[tasks[idx - 1]]))
else:
tasks.append(
Firework(ScriptTask.from_str(command),
name=f'task_{idx}',
fw_id=idx))
self.state.saveState('RUNNING')
wf = Workflow(tasks, name=name)
lp.add_wf(wf)
rapidfire(lp)
self.state.saveState('FINISHED')
except Exception as e:
print(e)
self.state.saveState('ERROR')
def run_workflows():
TESTDB_NAME = 'rsled'
launchpad = LaunchPad(name=TESTDB_NAME)
# clean up tw database if necessary
launchpad.reset(password=None, require_password=False)
launchpad.add_wf(wf_creator([1, 1, 2, "red"]))
rapidfire(launchpad, nlaunches=23, sleep_time=0)
def lp(request):
lp = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
lp.reset(password=None, require_password=False)
def fin():
lp.connection.drop_database(TESTDB_NAME)
request.addfinalizer(fin)
return lp
def lp(request):
lp = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
lp.reset(password=None, require_password=False)
def fin():
lp.connection.drop_database(TESTDB_NAME)
# request.addfinalizer(fin)
return lp
def main(algorithms, supports, datasets, working_directory, reset,
launchpad_args):
launchpad = LaunchPad(**launchpad_args)
if reset:
launchpad.reset("", require_password=False)
working_directory = os.path.expandvars(
os.path.expanduser(working_directory))
for dataset in datasets:
for algorithm in algorithms:
tasks = []
links = {}
spec = {}
spec["directory"] = os.path.join(working_directory, algorithm)
spec["local_files"] = [os.path.abspath(dataset)]
spec["_priority"] = 1000
try:
short_working_directory = spec["directory"].replace(
os.path.expanduser('~'), '~', 1)
except ValueError:
short_working_directory = spec["directory"]
setup_firework_name = "setup {0}".format(short_working_directory)
setup_firework = Firework(SetupWorkingDirectory(),
spec=spec,
name=setup_firework_name)
tasks.append(setup_firework)
for support in supports:
spec = {}
spec["database_filename"] = os.path.basename(dataset)
spec["algorithm"] = algorithm
spec["support"] = support
spec["timings_filename"] = "{0}.{1}.{2}.timing".format(
os.path.basename(dataset), algorithm,
str(support).zfill(3))
spec["patterns_filename"] = "{0}.{1}.{2}.patterns.gz".format(
os.path.basename(dataset), algorithm,
str(support).zfill(3))
spec["_priority"] = support
support_firework_name = "{0} {1}".format(algorithm, support)
support_firework = Firework(SPMFTask(),
spec=spec,
name=support_firework_name)
tasks.append(support_firework)
links.setdefault(setup_firework, []).append(support_firework)
workflow_name = "{0} {1}".format(os.path.basename(dataset),
algorithm)
workflow = Workflow(tasks, links, name=workflow_name)
launchpad.add_wf(workflow)
def lpad(database, debug_mode):
from fireworks import LaunchPad
lpad = LaunchPad(name=database)
lpad.reset("", require_password=False)
yield lpad
if not debug_mode:
lpad.reset("", require_password=False)
for coll in lpad.db.list_collection_names():
lpad.db[coll].drop()
def run_workflows():
TESTDB_NAME = 'rsled'
launchpad = LaunchPad(name=TESTDB_NAME)
# clean up tw database if necessary
launchpad.reset(password=None, require_password=False)
# load 10 batch workflows onto the launchpad
for _ in range(10):
launchpad.add_wf(wf_creator(random_guess(X_dim)))
rapidfire(launchpad, nlaunches=10, sleep_time=0)
def run_workflows():
TESTDB_NAME = 'rsled'
# clean up tw database if necessary
launchpad = LaunchPad(name=TESTDB_NAME)
launchpad.reset(password=None, require_password=False)
launchpad.add_wf(wf_creator([1, 1, 2, "red"], launchpad, 3, my_kwarg=1))
# if n_launches > 24 for this particular example, the search space will be
# exhausted and OptTask will throw an exception
rapidfire(launchpad, nlaunches=24, sleep_time=0)
def main(reset, launchpad_args, rocket_args):
if rocket_args["m_dir"]:
try:
os.makedirs(rocket_args["m_dir"])
except OSError:
pass
launchpad = LaunchPad(**launchpad_args)
if reset:
launchpad.reset("", require_password=False)
rapidfire(launchpad=launchpad, **rocket_args)
def setUp(self):
lpad = LaunchPad(name="test_emmet")
lpad.reset('', require_password=False)
self.lpad = lpad
self.nofilter = PropertyWorkflowBuilder(
self.elasticity, self.materials, wf_elastic_constant,
material_filter=None, lpad=self.lpad)
self.nofilter.connect()
self.filter = PropertyWorkflowBuilder(
self.elasticity, self.materials, wf_elastic_constant,
material_filter={"task_id": {"$lt": 3}}, lpad=self.lpad)
self.filter.connect()
def main():
# set up the LaunchPad and reset it
launchpad = LaunchPad()
launchpad.reset('', require_password=False)
# Build the flow
nflows = 2
for i in range(nflows):
flow = build_flow("flow_" + str(i))
flow.build_and_pickle_dump()
# create the Firework consisting of a single task
firework = Firework(FireTaskWithFlow(flow=flow))
# store workflow
launchpad.add_wf(firework)
#launch it locally
#launch_rocket(launchpad)
return 0
def main():
# set up the LaunchPad and reset it
launchpad = LaunchPad()
launchpad.reset('', require_password=False)
# Build the flow
nflows = 2
for i in range(nflows):
flow = build_flow("flow_" + str(i))
flow.build_and_pickle_dump()
# create the Firework consisting of a single task
firework = Firework(FireTaskWithFlow(flow=flow))
# store workflow
launchpad.add_wf(firework)
#launch it locally
#launch_rocket(launchpad)
return 0
n_cands = 20
n_runs = 20
filename = 'perovskites_{}_{}_{}cands_{}runs.p'.format(
predictor, TESTDB_NAME, n_cands, n_runs)
Y = []
for i in range(n_runs):
rundb = TESTDB_NAME + "_{}".format(i)
conn = MongoClient('localhost', 27017)
db = getattr(conn, rundb)
collection = db.test_perovskites
filedir = os.path.dirname(os.path.realpath(__file__))
launchpad = LaunchPad(name=rundb)
launchpad.reset(password=None, require_password=False)
launchpad.add_wf(
wf_creator(random.choice(space_noex),
predictor,
get_z,
launchpad,
filedir + '/space_gs_cat_included.p',
chemical_rules=True))
y = []
cands = 0
while cands != n_cands:
launch_rocket(launchpad)
cands = collection.find({'yi': 30.0}).count()
y.append(cands)
"EDIFF": 1E-7,
"EDIFFG": -1E-3,
"PREC": "Accurate",
"NPAR": 2}
custom_settings_dfpt = {"SYSTEM": "Si",
"ENCUT": 600,
"ISTART": 0,
"ICHARG": 2,
"ISMEAR": -5,
"SIGMA": 0.02,
"IBRION": 8,
"IALGO": 38,
"EDIFF": 1E-7,
"EDIFFG": 1E-6,
"PREC": "Accurate",
"LCHARG": ".FALSE.",
"LWAVE": ".FALSE.",
"LREAL": ".FALSE.",
"ADDGRID": ".TRUE."}
KPOINT = Generate_kpoints(struct, 0.03)
# set up the LaunchPad and reset it
launchpad = LaunchPad(host=<your database url>, name="test")
launchpad.reset('', require_password=False)
workflow = wf_phonon_conductivity(struct, vasp_input_set_relax=custom_settings_relax, vasp_input_set_fixvol_relax=custom_settings_fixvol_relax, vasp_input_set_dfpt=custom_settings_dfpt, vasp_kpoint_set=KPOINT, vasp_cmd=">>vasp_cmd<<", db_file=">>db_file<<", Temp=[300], ifscale=True, supercell=[2,2,2])
# store workflow and launch it locally
launchpad.add_wf(workflow)
def run_workflows():
TESTDB_NAME = 'rsled'
launchpad = LaunchPad(name=TESTDB_NAME)
launchpad.reset(password=None, require_password=False)
launchpad.add_wf(wf_creator([5, 5, 2]))
rapidfire(launchpad, nlaunches=10, sleep_time=0)
class automatic:
def __init__(self, wfname, fxyz, fprot, reset=False):
self.launchpad = LaunchPad()
if reset:
self.launchpad.reset('', require_password=False)
self.wfname = wfname
self.fxyz = fxyz
self.fprot = fprot
self.ftxyz = wfname + '.txyz'
self.fkey = wfname + '.key'
self.fref = wfname + '.hdf5'
return
def copy2cmcc(self):
# copy to CMCC
copy1 = FileTransferTask({
'files': ['../' + self.fxyz, '../' + self.fprot],
'dest':
'ffgen/fireworks',
'mode':
'rtransfer',
'server':
'cmcc'
})
copy = Firework([copy1],
name='copy to cmcc',
spec={
"pass_job_info": True,
})
return copy
def TMsetup(self, parent):
# setup TM
setup0 = FileTransferTask({
'files': ['../' + self.fxyz, '../' + self.fprot],
'dest':
'.',
'mode':
'copy'
})
setup1 = ScriptTask.from_str(x2t(self.fxyz)) # x2t
setup2 = ScriptTask.from_str(define(self.fprot)) # define
setup3 = ScriptTask.from_str(info(self.wfname, 'TM_setup'))
setup = Firework([setup0, setup1, setup2, setup3],
name='TM_setup',
spec={
"_pass_job_info": True,
'_fworker': 'cmcc_front'
},
parents=[parent])
return setup
def opt(self, parent):
#optimization
opt1 = JobexTask(wf_name=self.wfname)
opt = Firework([opt1],
name='opt',
parents=[parent],
spec={
"_pass_job_info": True,
'_fworker': 'cmcc_queue'
})
return opt
def hessian(self, parent):
# aoforce
force1 = AoforceTask(wf_name=self.wfname)
force = Firework([force1],
name='hessian',
parents=[parent],
spec={
"_pass_job_info": True,
'_fworker': 'cmcc_queue'
})
return force
def extract(self, parent):
# extract infos
extract1 = ExtractTask(fxyz=self.fxyz, fref=self.wfname)
extract2 = ScriptTask.from_str(info(self.wfname, 'extract'))
extract = Firework([extract1, extract2],
name='extract',
parents=[parent],
spec={
"_pass_job_info": True,
'_fworker': 'cmcc_front'
})
return extract
def FFsetup(self, parent):
# setup FF
FF1 = CopyTask()
FF2 = ScriptTask.from_str(info(self.wfname, 'FF_setup'))
FF3 = ScriptTask.from_str(
'xyz2txyz -i final.xyz -o %s > /dev/null 2> xyz2txyz.err' %
self.ftxyz)
FF4 = ScriptTask.from_str(
'atomtyper -c %s -o %s > /dev/null 2> atomtyper.err' %
(self.ftxyz, self.ftxyz))
FF5 = ScriptTask.from_str(
'create_key -i %s -o %s -r %s > key.out 2> key.err' %
(self.ftxyz, self.fkey, self.wfname))
FF = Firework([FF1, FF2, FF3, FF4, FF5],
name='FF_setup',
parents=[parent],
spec={
"_pass_job_info": True,
'_fworker': 'cmcc_front'
})
return FF
def FFfit(self, parent):
# fit FF
fit0 = ScriptTask.from_str(info(self.wfname, 'FF_fit'))
fit1 = RemoteCopyTask(server='cmcc',
files=[self.fkey, self.ftxyz, self.fref])
fit2 = ScriptTask.from_str('fit-cma -c %s -k %s -r %s > fit.out \
2> fit.err' % (self.ftxyz, self.fkey, self.wfname))
fit3 = ScriptTask.from_str('compare-freqs -c %s -k %s/opt.key -r %s > \
/dev/null 2> compare-freqs.err' %
(self.ftxyz, self.wfname, self.wfname))
fit = Firework([fit0, fit1, fit2, fit3],
name='FF_fit',
parents=[parent],
spec={
"_pass_job_info": True,
'_fworker': 'merry'
})
return fit
def __call__(self):
copy = self.copy2cmcc()
setup = self.TMsetup(copy)
opt = self.opt(setup)
force = self.hessian(opt)
extract = self.extract(force)
FF = self.FFsetup(extract)
fit = self.FFfit(FF)
workflow = Workflow([copy, setup, opt, force, extract, FF, fit],
name=self.wfname)
# store workflow and launch it locally
#launchpad.add_wf(setup)
self.launchpad.add_wf(workflow)
rapidfire(self.launchpad, FWorker())
return
from fireworks import Firework, Workflow, LaunchPad, ScriptTask
from fireworks.core.rocket_launcher import rapidfire
# set up the LaunchPad and reset it
launchpad = LaunchPad()
launchpad.reset('', require_password=False)
# create the individual FireWorks and Workflow
fw1 = Firework(ScriptTask.from_str('echo "hello"'), name="hello")
fw2 = Firework(ScriptTask.from_str('echo "goodbye"'), name="goodbye", parents=[fw1,])
wf = Workflow([fw1, fw2], name="test workflow")
# store workflow and launch it locally
launchpad.add_wf(wf)
rapidfire(launchpad)
def run_workflows():
TESTDB_NAME = 'rsled'
launchpad = LaunchPad(name=TESTDB_NAME)
launchpad.reset(password=None, require_password=False)
launchpad.add_wf(wf_creator([60, 45.0, "industry standard"]))
rapidfire(launchpad, nlaunches=500, sleep_time=0)
Returns:
(Workflow): A workflow containing one FireWork (two FireTasks) which
is automatically set up to run the optimization loop.
"""
spec = {'_x': x}
# ObjectiveFuncTask writes _y field to the spec internally.
firework1 = Firework([ObjectiveFuncTask(), OptTask(**db_info)], spec=spec)
return Workflow([firework1])
if __name__ == "__main__":
# Make a MissionControl object
mc = MissionControl(**db_info)
# Reset the launchpad and optimization db for this example
launchpad.reset(password=None, require_password=False)
mc.reset(hard=True)
# Configure the optimization db with MissionControl
mc.configure(wf_creator=wf_creator, dimensions=x_dim)
# Run the optimization loop 10 times.
launchpad.add_wf(wf_creator([5, 5, 2]))
rapidfire(launchpad, nlaunches=10, sleep_time=0)
# Examine results
plt = mc.plot()
plt.show()
