def submit(self, previous_job=None):
from xfel.command_line.striping import Script
from xfel.command_line.cxi_mpi_submit import get_submission_id
from libtbx import easy_run
configs_dir = os.path.join(settings_dir, "cfgs")
identifier_string = self.get_identifier_string()
target_phil_path = os.path.join(configs_dir,
identifier_string + "_params.phil")
with open(target_phil_path, 'w') as f:
f.write(self.task.parameters)
path = get_run_path(self.app.params.output_folder, self.trial,
self.rungroup, self.run, self.task)
os.mkdir(path)
arguments = """
mp.queue={}
mp.nproc={}
mp.method={}
{}
mp.use_mpi=False
striping.results_dir={}
striping.trial={}
striping.rungroup={}
striping.run={}
{}
striping.chunk_size=3000
striping.stripe=False
striping.dry_run=True
striping.output_folder={}
""".format(
self.app.params.mp.queue
if len(self.app.params.mp.queue) > 0 else None,
self.app.params.mp.nproc,
self.app.params.mp.method,
'\n'.join([
'mp.env_script={}'.format(p)
for p in self.app.params.mp.env_script
]),
self.app.params.output_folder,
self.trial.trial,
self.rungroup.id,
self.run.run,
target_phil_path,
path,
).split()
commands = Script(arguments).run()
submission_ids = []
for command in commands:
try:
result = easy_run.fully_buffered(command=command)
result.raise_if_errors()
except Exception as e:
if not "Warning: job being submitted without an AFS token." in str(
e):
raise e
submission_ids.append(
get_submission_id(result, self.app.params.mp.method))
return ",".join(submission_ids)
def submit(self, previous_job = None):
from xfel.command_line.striping import Script
from xfel.command_line.cxi_mpi_submit import get_submission_id
from libtbx import easy_run
configs_dir = os.path.join(settings_dir, "cfgs")
identifier_string = self.get_identifier_string()
target_phil_path = os.path.join(configs_dir, identifier_string + "_params.phil")
with open(target_phil_path, 'w') as f:
if self.task.parameters:
f.write(self.task.parameters)
path = get_run_path(self.app.params.output_folder, self.trial, self.rungroup, self.run, self.task)
os.mkdir(path)
arguments = """
mp.queue={}
mp.nnodes={}
mp.nproc_per_node={}
mp.method={}
{}
{}
mp.use_mpi=False
mp.mpi_command={}
{}
striping.results_dir={}
striping.trial={}
striping.rungroup={}
striping.run={}
{}
striping.chunk_size=200
striping.stripe=False
striping.dry_run=True
striping.output_folder={}
reintegration.integration.lookup.mask={}
mp.local.include_mp_in_command=False
""".format(self.app.params.mp.queue if len(self.app.params.mp.queue) > 0 else None,
1,#self.app.params.mp.nproc,
self.app.params.mp.nproc_per_node,
self.app.params.mp.method,
'\n'.join(['mp.env_script={}'.format(p) for p in self.app.params.mp.env_script if p]),
'\n'.join(['mp.phenix_script={}'.format(p) for p in self.app.params.mp.phenix_script if p]),
self.app.params.mp.mpi_command,
"\n".join(["extra_options={}".format(opt) for opt in self.app.params.mp.extra_options]),
self.app.params.output_folder,
self.trial.trial,
self.rungroup.id,
self.run.run,
target_phil_path,
path,
self.rungroup.untrusted_pixel_mask_path,
).split()
try:
commands = Script(arguments).run()
except Exception as e:
if 'no DIALS integration results found' in str(e):
print("No DIALS integration results found")
self.status = "EXIT"
return
else: raise
submission_ids = []
if self.app.params.mp.method == 'local':
self.status = "RUNNING"
for command in commands:
try:
result = easy_run.fully_buffered(command=command)
result.raise_if_errors()
except Exception as e:
if not "Warning: job being submitted without an AFS token." in str(e):
raise e
submission_ids.append(get_submission_id(result, self.app.params.mp.method))
if self.app.params.mp.method == 'local':
self.status = "DONE"
else:
return ",".join(submission_ids)