def check_htcondor_max_runtime(specification):
"""Check if the field htcondor_max_runtime has a valid input.
:param reana_specification: reana specification of workflow.
"""
check_pass = True
steps_with_max_runtime = (step for step in specification["steps"]
if step.get("htcondor_max_runtime", False))
for i, step in enumerate(steps_with_max_runtime):
htcondor_max_runtime = step["htcondor_max_runtime"]
if (not str.isdigit(htcondor_max_runtime)
and htcondor_max_runtime not in HTCONDOR_JOB_FLAVOURS):
check_pass = False
click.secho(
"In step {0}:\n'{1}' is not a valid input for htcondor_max_runtime. Inputs must be a digit in the form of a string, or one of the following job flavours: '{2}'."
.format(
step.get("name", i),
htcondor_max_runtime,
"' '".join([
k for k, v in sorted(HTCONDOR_JOB_FLAVOURS.items(),
key=lambda key: key[1])
]),
),
fg="red",
)
return check_pass
def execute(self):
"""Execute / submit a job with HTCondor."""
os.chdir(self.workflow_workspace)
job_ad = classad.ClassAd()
job_ad["JobDescription"] = (
self.workflow.get_full_workflow_name() + "_" + self.job_name
)
job_ad["JobMaxRetries"] = 3
job_ad["LeaveJobInQueue"] = classad.ExprTree(
"(JobStatus == 4) && ((StageOutFinish =?= UNDEFINED) || "
"(StageOutFinish == 0))"
)
job_ad["Cmd"] = (
"./job_wrapper.sh"
if not self.unpacked_img
else "./job_singularity_wrapper.sh"
)
if not self.unpacked_img:
job_ad["Arguments"] = self._format_arguments()
job_ad["DockerImage"] = self.docker_img
job_ad["WantDocker"] = True
job_ad["Environment"] = self._format_env_vars()
job_ad["Out"] = classad.ExprTree(
'strcat("reana_job.", ClusterId, ".", ProcId, ".out")'
)
job_ad["Err"] = classad.ExprTree(
'strcat("reana_job.", ClusterId, ".", ProcId, ".err")'
)
job_ad["log"] = classad.ExprTree('strcat("reana_job.", ClusterId, ".err")')
job_ad["ShouldTransferFiles"] = "YES"
job_ad["WhenToTransferOutput"] = "ON_EXIT"
job_ad["TransferInput"] = self._get_input_files()
job_ad["TransferOutput"] = "."
job_ad["PeriodicRelease"] = classad.ExprTree("(HoldReasonCode == 35)")
if self.htcondor_max_runtime in HTCONDOR_JOB_FLAVOURS.keys():
job_ad["JobFlavour"] = self.htcondor_max_runtime
elif str.isdigit(self.htcondor_max_runtime):
job_ad["MaxRunTime"] = int(self.htcondor_max_runtime)
else:
job_ad["MaxRunTime"] = 3600
if self.htcondor_accounting_group:
job_ad["AccountingGroup"] = self.htcondor_accounting_group
future = current_app.htcondor_executor.submit(self._submit, job_ad)
clusterid = future.result()
return clusterid