sbatch_report

gistfile1.txt

###example_sbatch.err
slurmstepd-midway2-0002: error: task/cgroup: unable to add task[pid=14585] to memory cg '(null)'
slurmstepd-midway2-0002: error: Job 50098285 exceeded memory limit (1062800 > 327680), being killed
slurmstepd-midway2-0002: error: Exceeded job memory limit
slurmstepd-midway2-0002: error: *** JOB 50098285 ON midway2-0002 CANCELLED AT 2018-09-25T13:20:08 ***


###example_sbatch.out
[2018-09-25 18:19:47,44] [info] Running with database db.url = jdbc:hsqldb:mem:47a741e8-0324-4c29-a170-f4dd54d61b24;shutdown=false;hsqldb.tx=mvcc
[2018-09-25 18:19:55,46] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-09-25 18:19:55,47] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-09-25 18:19:55,56] [info] Running with database db.url = jdbc:hsqldb:mem:124b08c3-9730-416e-a798-3cf91acbf493;shutdown=false;hsqldb.tx=mvcc
[2018-09-25 18:19:55,88] [warn] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory for PAPI v2
[2018-09-25 18:19:55,92] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-09-25 18:19:55,92] [info] Using noop to send events.
[2018-09-25 18:19:56,19] [info] Slf4jLogger started
[2018-09-25 18:19:56,37] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-a9ac2b1",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2018-09-25 18:19:56,40] [info] Metadata summary refreshing every 2 seconds.
[2018-09-25 18:19:56,43] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-09-25 18:19:56,43] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-09-25 18:19:56,43] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-09-25 18:19:57,18] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-09-25 18:19:57,20] [info] SingleWorkflowRunnerActor: Version 34
[2018-09-25 18:19:57,20] [info] JES batch polling interval is 33333 milliseconds
[2018-09-25 18:19:57,20] [info] JES batch polling interval is 33333 milliseconds
[2018-09-25 18:19:57,20] [info] JES batch polling interval is 33333 milliseconds
[2018-09-25 18:19:57,20] [info] PAPIQueryManager Running with 3 workers
[2018-09-25 18:19:57,21] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-09-25 18:19:57,25] [info] Unspecified type (Unspecified version) workflow 40567000-f7d2-491b-b255-44cdcec9a54b submitted
[2018-09-25 18:19:57,30] [info] SingleWorkflowRunnerActor: Workflow submitted 40567000-f7d2-491b-b255-44cdcec9a54b
[2018-09-25 18:19:57,31] [info] 1 new workflows fetched
[2018-09-25 18:19:57,31] [info] WorkflowManagerActor Starting workflow 40567000-f7d2-491b-b255-44cdcec9a54b
[2018-09-25 18:19:57,31] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-09-25 18:19:57,31] [info] WorkflowManagerActor Successfully started WorkflowActor-40567000-f7d2-491b-b255-44cdcec9a54b
[2018-09-25 18:19:57,32] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-09-25 18:19:57,32] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-09-25 18:19:57,37] [info] MaterializeWorkflowDescriptorActor [40567000]: Parsing workflow as WDL draft-2