def make_firework(atoms, fw_name, vasp_settings):
'''
This function makes a FireWorks rocket to perform a VASP relaxation
Args:
atoms `ase.Atoms` object to relax
fw_name Dictionary of tags/etc to use as the FireWorks name
vasp_settings Dictionary of VASP settings to pass to Vasp()
Returns:
firework An instance of a `fireworks.Firework` object that is set up
to perform a VASP relaxation
'''
# Warn the user if they're submitting a big one
if len(atoms) > 80:
warnings.warn(
'You are making a firework with %i atoms in it. This may '
'take awhile.' % len(atoms), RuntimeWarning)
# Take the `vasp_functions` submodule in GASpy and then pass it out to each
# FireWork rocket to use.
vasp_filename = vasp_functions.__file__
if vasp_filename.split(
'.')[-1] == 'pyc': # Make sure we use the source file
vasp_filename = vasp_filename[:-3] + 'py'
with open(vasp_filename) as file_handle:
vasp_functions_contents = file_handle.read()
pass_vasp_functions = FileWriteTask(
files_to_write=[{
'filename': 'vasp_functions.py',
'contents': vasp_functions_contents
}])
# Convert the atoms object to a string so that we can pass it through
# FireWorks, and then tell the FireWork rocket to use our `vasp_functions`
# submodule to unpack the string
atom_trajhex = encode_atoms_to_trajhex(atoms)
read_atoms_file = PyTask(func='vasp_functions.hex_to_file',
args=['slab_in.traj', atom_trajhex])
# Tell the FireWork rocket to perform the relaxation
relax = PyTask(func='vasp_functions.runVasp',
args=['slab_in.traj', 'slab_relaxed.traj', vasp_settings],
stored_data_varname='opt_results')
fw_name['user'] = getpass.getuser()
firework = Firework([pass_vasp_functions, read_atoms_file, relax],
name=fw_name)
return firework
def add_namefile(original_wf, use_slug=True):
"""
Every FireWork begins by writing an empty file with the name
"FW--<fw.name>". This makes it easy to figure out what jobs are in what
launcher directories, e.g. "ls -l launch*/FW--*" from within a "block" dir.
Args:
original_wf (Workflow)
use_slug (bool): whether to replace whitespace-type chars with a slug
Returns:
Workflow
"""
for idx, fw in enumerate(original_wf.fws):
fname = "FW--{}".format(fw.name)
if use_slug:
fname = get_slug(fname)
original_wf.fws[idx].tasks.insert(0, FileWriteTask(
files_to_write=[{"filename": fname, "contents": ""}]))
return original_wf
def addRunSteps(self, inpSim, userID, cores):
#builds the following workflow for running simulations
#creates directory for simulation using the sim name and uuid
#writes gkyl input file to the directory
#runs file in the directory
#if run is successful, prints 'Done', if not, prints 'Failed
#plots task
#userid --> for folder location
self.fws = []
print(inpSim)
self.last = len(self.launchpad.get_fw_ids())
# for fwork in self.launchpad.get_fw_ids():
# self.launchpad.delete_fws([fwork])
sim = Sim(inpSim)
# path = '/home/adaniel99/gkylsoft/sims/'+str(userID)+'/'+inpSim+'/'
path = '/home/dalex_99/gkylsoft/sims/' + str(
userID) + '/' + inpSim + '/'
n = 0
# for f in os.listdir('/home/adaniel99/gkylsoft/sims/'):
for f in os.listdir('/home/dalex_99/gkylsoft/sims/'):
if f == str(userID):
# for f in os.listdir('/home/adaniel99/gkylsoft/sims/'+str(userID)+'/'):
for f in os.listdir('/home/dalex_99/gkylsoft/sims/' +
str(userID) + '/'):
if f == inpSim:
n = n + 1
self.rerun = True
if n == 0:
desttask = ScriptTask.from_str('mkdir ' + path)
writetask = FileWriteTask({
'files_to_write': ([{
'filename': sim.name(),
'contents': sim.inpFile()
}]),
'dest':
path
})
runtask = ScriptTask.from_str(
'redis-cli PUBLISH ' + User(userID).name() +
'2 "Running Simulation"; mpiexec -n ' + cores + 'gkyl ' +
path + sim.name())
runFlag = ScriptTask.from_str('redis-cli PUBLISH ' +
User(userID).name() + '2' + ' Done')
deleteFail = ScriptTask.from_str('lpad defuse_fws -i ' +
str(6 + self.last))
flagFail = ScriptTask.from_str('redis-cli PUBLISH ' +
User(userID).name() + '2' +
' Failed')
self.ids.clear()
dest = Firework(desttask, name='Make Folder', fw_id=1 + self.last)
self.ids.append(1 + self.last)
write = Firework(writetask, name='Write', fw_id=2 + self.last)
self.ids.append(2 + self.last)
run = Firework(runtask, name='Run', fw_id=3 + self.last)
self.ids.append(3 + self.last)
flag1 = Firework(runFlag, name='done?', fw_id=4 + self.last)
self.ids.append(4 + self.last)
delfail = Firework(deleteFail,
name='remove fail flag',
fw_id=5 + self.last)
self.ids.append(5 + self.last)
failflag = Firework(flagFail,
name='fail flag',
fw_id=6 + self.last)
self.ids.append(6 + self.last)
self.fws.append(dest)
self.fws.append(write)
self.fws.append(run)
self.fws.append(flag1)
self.fws.append(delfail)
self.fws.append(failflag)
wf = Workflow(self.fws, {
dest: [write],
write: [run],
run: [flag1],
flag1: [delfail]
},
name='Running ' + sim.name())
self.launchpad.add_wf(wf)
if n == 1:
writetask = FileWriteTask({
'files_to_write': ([{
'filename': sim.name(),
'contents': sim.inpFile()
}]),
'dest':
path
})
runtask = ScriptTask.from_str(
'redis-cli PUBLISH ' + User(userID).name() +
'2 "Running Simulation"; mpiexec -n ' + cores + 'gkyl ' +
path + sim.name())
runFlag = ScriptTask.from_str('redis-cli PUBLISH ' +
User(userID).name() + '2' + ' Done')
deleteFail = ScriptTask.from_str('lpad defuse_fws -i ' +
str(5 + self.last))
flagFail = ScriptTask.from_str('redis-cli PUBLISH ' +
User(userID).name() + '2' +
' Failed')
self.ids.clear()
write = Firework(writetask, name='Write', fw_id=1 + self.last)
self.ids.append(1 + self.last)
run = Firework(runtask, name='Run', fw_id=2 + self.last)
self.ids.append(2 + self.last)
flag1 = Firework(runFlag, name='done?', fw_id=3 + self.last)
self.ids.append(3 + self.last)
delfail = Firework(deleteFail,
name='remove fail flag',
fw_id=4 + self.last)
self.ids.append(4 + self.last)
failflag = Firework(flagFail,
name='fail flag',
fw_id=5 + self.last)
self.ids.append(5 + self.last)
wf = Workflow([write, run, flag1, delfail, failflag], {
write: [run],
run: [flag1],
flag1: [delfail]
},
name='Running ' + sim.name())
self.launchpad.add_wf(wf)