| Name | tJPODmqECJvnShfckohDCDFpABFKDmABFKDmpf6KDmABFKDmtBqfln_1 |
| Workunit | 1918349 |
| Created | 17 Aug 2019, 14:17:48 UTC |
| Sent | 17 Aug 2019, 15:53:02 UTC |
| Report deadline | 24 Aug 2019, 15:53:02 UTC |
| Received | 17 Aug 2019, 16:04:37 UTC |
| Server state | Over |
| Outcome | Validate error |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 3848 |
| Run time | 9 min 53 sec |
| CPU time | 3 min 14 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 9.34 GFLOPS |
| Application version | ATLAS Simulation v0.72 (native_mt) x86_64-pc-linux-gnu |
| Peak working set size | 153.21 MB |
| Peak swap size | 4.11 GB |
| Peak disk usage | 473.17 MB |
Stderr output
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
17:54:35 (4634): wrapper (7.7.26015): starting
17:54:35 (4634): wrapper: running run_atlas (--nthreads 3)
2019-08-17 17:54:35,907: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 17:54:35,907: sys.argv = ['run_atlas', '--nthreads', '3']
2019-08-17 17:54:35,908: THREADS=3
2019-08-17 17:54:35,914: Checking for CVMFS
2019-08-17 17:55:26,181: CVMFS is installed
2019-08-17 17:55:26,221: OS:CentOS Linux release 7.4.1708 (Core)
2019-08-17 17:55:26,221: This is not SLC6, need to run with Singularity....
2019-08-17 17:55:26,221: Checking Singularity...
2019-08-17 17:55:26,281: Singularity is installed, version 2.6.1-dist
2019-08-17 17:55:26,281: Testing the function of Singularity...
2019-08-17 17:55:26,281: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-17 17:55:34,492: Singularity Works...
2019-08-17 17:55:34,492: copy /root/slots/5/shared/ATLAS.root_0
2019-08-17 17:55:35,300: copy /root/slots/5/shared/input.tar.gz
2019-08-17 17:55:35,300: copy /root/slots/5/shared/RTE.tar.gz
2019-08-17 17:55:35,309: copy /root/slots/5/shared/start_atlas.sh
2019-08-17 17:55:35,310: export ATHENA_PROC_NUMBER=3;
2019-08-17 17:55:35,495: start atlas job with PandaID=4449868768
2019-08-17 17:55:35,495: cmd = singularity exec --pwd /root/slots/5 -B /cvmfs,/root /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-08-17 18:04:26,172: running cmd return value is 0
2019-08-17 18:04:26,173: *****************The last 100 lines of the pilot log******************
2019-08-17 18:04:26,206: 2019-08-17 16:03:22,299 | INFO | retrieve | pilot.util.auxiliary | make_job_report | event service: False
2019-08-17 16:03:22,299 | INFO | retrieve | pilot.util.auxiliary | make_job_report | --------------------------------------------------
2019-08-17 16:03:22,299 | INFO | retrieve | pilot.util.auxiliary | make_job_report |
2019-08-17 16:03:22,299 | INFO | retrieve | pilot.control.job | has_job_completed | job 4449868768 has completed
2019-08-17 16:03:22,299 | INFO | retrieve | pilot.util.processes | cleanup | overall cleanup function is called
2019-08-17 16:03:22,301 | DEBUG | retrieve | pilot.util.processes | cleanup | work directory was removed: /root/slots/5/PanDA_Pilot-4449868768
2019-08-17 16:03:23,310 | INFO | retrieve | pilot.info.jobdata | collect_zombies | --- collectZombieJob: --- 10, [None]
2019-08-17 16:03:23,314 | INFO | retrieve | pilot.info.jobdata | collect_zombies | zombie collector trying to kill pid None
File "/root/slots/5/pilot2/pilot/common/exception.py", line 413, in run
self._Thread__target(**self._Thread__kwargs)
File "/root/slots/5/pilot2/pilot/control/job.py", line 1351, in retrieve
if has_job_completed(queues):
File "/root/slots/5/pilot2/pilot/control/job.py", line 1431, in has_job_completed
cleanup(job)
File "/root/slots/5/pilot2/pilot/util/processes.py", line 565, in cleanup
job.collect_zombies(tn=10)
File "/root/slots/5/pilot2/pilot/info/jobdata.py", line 776, in collect_zombies
_id, rc = os.waitpid(x, os.WNOHANG)
exception caught by thread run() function: (<type 'exceptions.TypeError'>, TypeError('an integer is required',), <traceback object at 0x27181b8>)
Traceback (most recent call last):
File "/root/slots/5/pilot2/pilot/common/exception.py", line 413, in run
self._Thread__target(**self._Thread__kwargs)
File "/root/slots/5/pilot2/pilot/control/job.py", line 1351, in retrieve
if has_job_completed(queues):
File "/root/slots/5/pilot2/pilot/control/job.py", line 1431, in has_job_completed
cleanup(job)
File "/root/slots/5/pilot2/pilot/util/processes.py", line 565, in cleanup
job.collect_zombies(tn=10)
File "/root/slots/5/pilot2/pilot/info/jobdata.py", line 776, in collect_zombies
_id, rc = os.waitpid(x, os.WNOHANG)
TypeError: an integer is required
None
exception has been put in bucket queue belonging to thread 'retrieve'
setting graceful stop in 10 s since there is no point in continuing
2019-08-17 16:03:24,789 | WARNING | job | pilot.control.job | control | thread 'retrieve' received an exception from bucket: an integer is required
2019-08-17 16:03:33,433 | WARNING | queue_monitor | pilot.util.common | should_abort | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 16:03:33,434 | WARNING | queue_monitor | pilot.control.job | pause_queue_monitor | since job:queue_monitor is responsible for sending job updates, we sleep for 20 s
2019-08-17 16:03:33,437 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 16 threads
2019-08-17 16:03:33,438 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job, started 140622695565056)>, <ExcThread(copytool_in, started 140622103037696)>, <ExcThread(validate_post, started 140622564407040)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(validate, started 140622687172352)>, <ExcThread(validate_pre, started 140622572799744)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(payload, started 140622581192448)>, <ExcThread(copytool_out, started 140622589585152)>, <ExcThread(create_data_payload, started 140622597977856)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(failed_post, started 140622119823104)>, <ExcThread(monitor, started 140622547621632)>, <ExcThread(execute_payloads, started 140622111430400)>, <ExcThread(data, started 140622678779648)>]
2019-08-17 16:03:33,458 | WARNING | copytool_out | pilot.util.common | should_abort | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 16:03:33,600 | INFO | monitor | pilot.control.monitor | control | [monitor] control thread has ended
2019-08-17 16:03:33,719 | DEBUG | data | pilot.control.data | control | data control ending since graceful_stop has been set
2019-08-17 16:03:33,719 | DEBUG | data | pilot.control.data | control | [data] control thread has finished
2019-08-17 16:03:33,825 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 14 threads
2019-08-17 16:03:33,825 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job, started 140622695565056)>, <ExcThread(copytool_in, started 140622103037696)>, <ExcThread(validate_post, started 140622564407040)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(validate, started 140622687172352)>, <ExcThread(validate_pre, started 140622572799744)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(payload, started 140622581192448)>, <ExcThread(copytool_out, started 140622589585152)>, <ExcThread(create_data_payload, started 140622597977856)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(failed_post, started 140622119823104)>, <ExcThread(execute_payloads, started 140622111430400)>]
2019-08-17 16:03:33,914 | DEBUG | job | pilot.control.job | control | job control ending since graceful_stop has been set
2019-08-17 16:03:33,914 | DEBUG | job | pilot.control.job | control | [job] control thread has finished
2019-08-17 16:03:33,915 | INFO | validate_pre | pilot.control.payload | validate_pre | [payload] validate_pre thread has finished
2019-08-17 16:03:33,968 | DEBUG | create_data_payload | pilot.control.job | create_data_payload | [job] create_data_payload thread has finished
2019-08-17 16:03:34,027 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 11 threads
2019-08-17 16:03:34,028 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(copytool_in, started 140622103037696)>, <ExcThread(validate_post, started 140622564407040)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(validate, started 140622687172352)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(payload, started 140622581192448)>, <ExcThread(copytool_out, started 140622589585152)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(failed_post, started 140622119823104)>, <ExcThread(execute_payloads, started 140622111430400)>]
2019-08-17 16:03:34,098 | DEBUG | validate | pilot.control.job | validate | [job] validate thread has finished
2019-08-17 16:03:34,231 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 10 threads
2019-08-17 16:03:34,231 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(copytool_in, started 140622103037696)>, <ExcThread(validate_post, started 140622564407040)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(payload, started 140622581192448)>, <ExcThread(copytool_out, started 140622589585152)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(failed_post, started 140622119823104)>, <ExcThread(execute_payloads, started 140622111430400)>]
2019-08-17 16:03:34,444 | DEBUG | payload | pilot.control.payload | control | payload control ending since graceful_stop has been set
2019-08-17 16:03:34,444 | DEBUG | payload | pilot.control.payload | control | [payload] control thread has finished
2019-08-17 16:03:34,463 | DEBUG | copytool_out | pilot.control.data | copytool_out | [data] copytool_out thread has finished
2019-08-17 16:03:34,496 | INFO | validate_post | pilot.control.payload | validate_post | [payload] validate_post thread has finished
2019-08-17 16:03:34,518 | INFO | failed_post | pilot.control.payload | failed_post | [payload] failed_post thread has finished
2019-08-17 16:03:34,587 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 6 threads
2019-08-17 16:03:34,587 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(copytool_in, started 140622103037696)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(execute_payloads, started 140622111430400)>]
2019-08-17 16:03:34,591 | WARNING | queue_monitoring | pilot.util.common | should_abort | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 16:03:34,708 | DEBUG | copytool_in | pilot.control.data | copytool_in | [data] copytool_in thread has finished
2019-08-17 16:03:34,813 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 5 threads
2019-08-17 16:03:34,815 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(queue_monitoring, started 140622556014336)>, <ExcThread(execute_payloads, started 140622111430400)>]
2019-08-17 16:03:34,859 | INFO | execute_payloads | pilot.control.payload | execute_payloads | [payload] execute_payloads thread has finished
2019-08-17 16:03:34,928 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 4 threads
2019-08-17 16:03:34,928 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(queue_monitor, started 140622086252288)>, <ExcThread(queue_monitoring, started 140622556014336)>]
2019-08-17 16:03:37,597 | DEBUG | queue_monitoring | pilot.control.data | queue_monitoring | [data] queue_monitor thread has finished
2019-08-17 16:03:37,598 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 3 threads
2019-08-17 16:03:37,598 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job_monitor, started 140622094644992)>, <ExcThread(queue_monitor, started 140622086252288)>]
2019-08-17 16:03:55,559 | DEBUG | queue_monitor | pilot.control.job | queue_monitor | [job] queue monitor thread has finished
2019-08-17 16:03:55,583 | DEBUG | MainThread | pilot.workflow.generic | run | thread count now at 2 threads
2019-08-17 16:03:55,583 | DEBUG | MainThread | pilot.workflow.generic | run | enumerate: [<_MainThread(MainThread, started 140622916114176)>, <ExcThread(job_monitor, started 140622094644992)>]
2019-08-17 16:04:20,454 | WARNING | job_monitor | pilot.control.job | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-17 16:04:20,458 | DEBUG | job_monitor | pilot.control.job | job_monitor | [job] job monitor thread has finished
2019-08-17 16:04:20,547 | INFO | MainThread | pilot.workflow.generic | run | end of generic workflow (traces error code: 1186)
2019-08-17 16:04:20,548 | INFO | MainThread | root | wrap_up | traces error code: 1186
2019-08-17 16:04:20,548 | INFO | MainThread | root | wrap_up | an exit code was already set: 1186 (will be converted to a standard shell code)
2019-08-17 16:04:20,548 | INFO | MainThread | root | wrap_up | pilot has finished
2019-08-17 16:04:21 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 16:04:22 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 16:04:22 UTC [wrapper] Pilot exit status: 73
2019-08-17 16:04:22 UTC [wrapper] STATUSCODE: 73
2019-08-17 16:04:22 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
insgesamt 44
-rw-rw-r--. 1 320 320 11357 25. Jul 16:38 LICENSE
drwxrwxr-x. 14 320 320 216 17. Aug 18:00 pilot
-rwxrwxr-x. 1 320 320 20463 25. Jul 16:38 pilot.py
-rw-r--r--. 1 320 320 8 7. Aug 13:02 PILOTVERSION
-rw-rw-r--. 1 320 320 2251 25. Jul 16:38 README.md
-rw-rw-r--. 1 320 320 221 25. Jul 16:38 TODO.md
2019-08-17 16:04:24 UTC [wrapper] Test setup, not cleaning
2019-08-17 16:04:24 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 16:04:24 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 16:04:24 UTC [wrapper] wrapper wrapperexiting ec=0, duration=521
2019-08-17 16:04:25 UTC [wrapper] apfmon messages muted
2019-08-17 18:04:26,224: ***************diag file************
2019-08-17 18:04:26,225: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=522.11s
KernelTime=193.65s
UserTime=98.25s
CPUUsage=55%
MaxResidentMemory=158024kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=26079
MinorPageFaults=979811
Swaps=0
ForcedSwitches=7918
WaitSwitches=264928
Inputs=6328384
Outputs=15656
SocketReceived=0
SocketSent=0
Signals=0
nodename=maeax@ryzcos7
exitcode=0
2019-08-17 18:04:26,266: ******************************WorkDir***********************
2019-08-17 18:04:26,267: insgesamt 244508
drwxrwx--x. 6 root root 4096 17. Aug 18:04 .
drwxrwx--x. 14 root root 116 17. Aug 15:22 ..
-rw-------. 1 root root 5302438 17. Aug 18:01 agis_ddmendpoints.agis.ALL.json
-rw-------. 1 root root 0 17. Aug 18:02 agis_ddmendpoints.json
-rw-------. 1 root root 8700 17. Aug 18:00 agis_schedconf.agis.BOINC_MCORE.json
-rw-------. 1 root root 0 17. Aug 18:01 agis_schedconf.cvmfs.json
drwx------. 2 root root 6 17. Aug 17:55 .alrb
drwxr-xr-x. 3 root root 17 17. Aug 17:55 APPS
-rw-------. 1 root root 533 17. Aug 17:56 .asetup
-rw-r--r--. 1 root root 0 17. Aug 17:54 boinc_lockfile
-rw-r--r--. 1 root root 8192 17. Aug 18:04 boinc_mmap_file
-rw-r--r--. 1 root root 532 17. Aug 18:04 boinc_task_state.xml
-rw-r--r--. 1 root root 244152862 17. Aug 17:55 EVNT.18605745._000399.pool.root.1
-rw-------. 1 root root 1956 17. Aug 18:03 heartbeat.json
-rw-r--r--. 1 root root 5888 17. Aug 17:54 init_data.xml
-rw-r--r--. 1 root root 261618 17. Aug 17:55 input.tar.gz
-rw-r--r--. 1 root root 112 17. Aug 17:54 job.xml
-rw-------. 1 root root 103522 17. Aug 18:04 log.18722183._018977.job.log.1
-rw-------. 1 root root 8045 17. Aug 18:02 log.18722183._018977.job.log.tgz.1
-rw-------. 1 root root 205 17. Aug 18:04 output.list
-rw-------. 1 4871 1028 2921 17. Aug 13:39 pandaJobData.out
drwxr-xr-x. 3 320 320 174 7. Aug 13:02 pilot2
-rw-r--r--. 1 root root 253018 17. Aug 13:39 pilot2.tar.gz
-rw-------. 1 root root 84239 17. Aug 18:04 pilotlog.txt
-rw-r--r--. 1 root root 4468 17. Aug 13:39 queuedata.json
-rw-r--r--. 1 root root 815 17. Aug 17:55 RTE.tar.gz
-rwxr-xr-x. 1 root root 8466 17. Aug 17:54 run_atlas
-rwx------. 1 4871 1028 12641 17. Aug 13:39 runpilot2-wrapper.sh
-rw-r--r--. 1 root root 692 17. Aug 18:04 runtime_log
-rw-r--r--. 1 root root 6549 17. Aug 18:04 runtime_log.err
drwxrwx--x. 2 root root 107 17. Aug 18:04 shared
-rw-r--r--. 1 root root 8688 17. Aug 17:55 start_atlas.sh
-rw-r--r--. 1 root root 16996 17. Aug 18:04 stderr.txt
-rw-------. 1 root root 482 17. Aug 18:04 tJPODmqECJvnShfckohDCDFpABFKDmABFKDmpf6KDmABFKDmtBqfln.diag
-rw-r--r--. 1 root root 107 17. Aug 17:54 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 root root 24 17. Aug 18:04 wrapper_checkpoint.txt
2019-08-17 18:04:26,267: running start_atlas return value is 0
2019-08-17 18:04:26,267: Parent exit 0
2019-08-17 18:04:26,267: child process exit 0
18:04:27 (4634): run_atlas exited; CPU time 100.633638
18:04:27 (4634): called boinc_finish(0)
</stderr_txt>
]]>
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