Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
05:05:58 (4884): wrapper (7.7.26015): starting
05:05:58 (4884): wrapper: running run_atlas (--nthreads 4)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '4']
THREADS=4
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.6.1810 (Core) 

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is not installed, using version from CVMFS
Testing the function of Singularity...
Checking singularity with cmd:/cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
Singularity Works...

copy /home/grid/slots/0/shared/ATLAS.root_0
copy /home/grid/slots/0/shared/input.tar.gz
copy /home/grid/slots/0/shared/RTE.tar.gz
copy /home/grid/slots/0/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=4;start atlas job with PandaID=4438039947
cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /home/grid/slots/0 -B /cvmfs,/home /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
running cmd return value is 0
Moving ./HITS.18722298._008300.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4438039947
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 07:19:39,523 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 58372 s
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 11573
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 11573
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 07:19:39,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 07:19:39,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 07:19:39,525 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4438039947 has completed
2019-08-13 07:19:39,525 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 07:19:39,536 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4438039947
2019-08-13 07:19:40,537 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11573]
2019-08-13 07:19:40,537 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11573
2019-08-13 07:19:40,537 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 07:19:41,542 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 07:19:41,543 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11573
2019-08-13 07:19:41,593 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11573] (in reverse order)
2019-08-13 07:19:41,633 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 07:19:41,633 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 07:19:41,633 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 07:19:41,633 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 07:19:41,643 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 07:19:51,677 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 07:19:51,677 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 07:19:51,725 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35961962496 B)
2019-08-13 07:19:51,725 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 07:19:51,725 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 07:19:51,750 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 07:19:51,750 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 07:19:51,764 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 07:19:51,764 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 07:19:51,906 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-13 07:19:51,907 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(job, started 139991608661760)>, <ExcThread(failed_post, started 139990742845184)>, <ExcThread(execute_payloads, started 139990734452480)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(validate_post, started 139990751237888)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(create_data_payload, started 139991583483648)>, <ExcThread(data, started 139991591876352)>, <ExcThread(validate_pre, started 139991338432256)>, <ExcThread(validate, started 139991600269056)>, <ExcThread(copytool_in, started 139990759630592)>, <ExcThread(monitor, started 139991330039552)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:51,945 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 07:19:51,947 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 07:19:52,014 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 07:19:52,014 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 07:19:52,108 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-13 07:19:52,108 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(job, started 139991608661760)>, <ExcThread(failed_post, started 139990742845184)>, <ExcThread(execute_payloads, started 139990734452480)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(validate_post, started 139990751237888)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(validate_pre, started 139991338432256)>, <ExcThread(validate, started 139991600269056)>, <ExcThread(copytool_in, started 139990759630592)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:52,110 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 07:19:52,131 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 07:19:52,310 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 07:19:52,310 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(job, started 139991608661760)>, <ExcThread(failed_post, started 139990742845184)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(validate_post, started 139990751237888)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(validate, started 139991600269056)>, <ExcThread(copytool_in, started 139990759630592)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:52,332 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 07:19:52,407 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 07:19:52,407 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | will abort 
2019-08-13 07:19:52,415 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 07:19:52,415 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 07:19:52,418 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 07:19:52,419 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(failed_post, started 139990742845184)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(validate_post, started 139990751237888)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(validate, started 139991600269056)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:52,424 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 07:19:52,520 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-13 07:19:52,520 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(failed_post, started 139990742845184)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(validate, started 139991600269056)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:52,571 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 07:19:52,581 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 07:19:52,621 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 07:19:52,621 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(copytool_out, started 139991363610368)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:53,408 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | aborting
2019-08-13 07:19:53,408 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 07:19:53,427 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 07:19:53,427 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(job_monitor, started 139991346824960)>, <ExcThread(queue_monitoring, started 139991321646848)>]
2019-08-13 07:19:54,609 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 07:19:57,610 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 07:19:57,657 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 07:19:57,657 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139991822812928)>, <ExcThread(job_monitor, started 139991346824960)>]
2019-08-13 07:20:03,963 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 07:20:03,963 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 07:20:04,002 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 07:20:04,003 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 07:20:04,003 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 07:20:04 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 07:20:04 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 07:20:04 UTC [wrapper] Pilot exit status: 0
2019-08-13 07:20:04 UTC [wrapper] STATUSCODE: 0
2019-08-13 07:20:04 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 44
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 13 05:06 pilot
-rwx------.  1 grid grid 20463 Jul 25 16:38 pilot.py
-rw-------.  1 grid grid     8 Jul 31 19:00 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-13 07:20:04 UTC [wrapper] Test setup, not cleaning
2019-08-13 07:20:04 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 07:20:04 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15242.92s
KernelTime=457.94s
UserTime=58129.15s
CPUUsage=384%
MaxResidentMemory=1920364kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=452690
MinorPageFaults=18697491
Swaps=0
ForcedSwitches=7087585
WaitSwitches=10967338
Inputs=109286272
Outputs=943328
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 284548
drwxrwx--x. 7 grid grid      4096 Aug 13 09:20 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409065 Aug 13 05:06 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517698 Aug 13 05:06 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 05:06 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 05:06 APPS
drwxr-xr-x. 2 grid grid         6 Aug 13 05:06 .arc
-rw-------. 1 grid grid       538 Aug 13 05:06 .asetup
-rw-------. 1 grid grid       826 Aug 13 05:06 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 05:05 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 09:20 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 13 09:14 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 277066882 Aug 13 05:06 EVNT.18605754._000161.pool.root.1
-rw-------. 1 grid grid     95064 Aug 13 09:19 heartbeat.json
-rw-rw-r--. 1 grid grid      5863 Aug 13 05:05 init_data.xml
-rw-rw-r--. 1 grid grid    261808 Aug 13 05:06 input.tar.gz
-rw-------. 1 grid grid       519 Aug 13 09:20 JgsLDmEQbEvnShfckohDCDFpABFKDmABFKDmft4TDmABFKDmuozqym.diag
-rw-rw-r--. 1 grid grid       112 Aug 13 05:05 job.xml
-rw-------. 1 grid grid    756350 Aug 13 09:20 log.18722298._008300.job.log.1
-rw-------. 1 grid grid    849600 Aug 13 09:19 log.18722298._008300.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 13 09:20 output.list
-rw-------. 1 grid grid      2914 Aug  4 21:32 pandaJobData.out
drwx------. 3 grid grid       174 Jul 31 19:00 pilot2
-rw-r--r--. 1 grid grid    252463 Aug  1 05:54 pilot2.tar.gz
-rw-------. 1 grid grid     10599 Aug 13 09:20 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  4 21:32 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 05:06 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 05:05 run_atlas
-rwx------. 1 grid grid     15232 Aug  4 21:32 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 09:20 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 09:20 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 09:20 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 05:06 start_atlas.sh
-rw-rw-r--. 1 grid grid     18445 Aug 13 09:20 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 05:05 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 13 09:20 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
09:20:04 (4884): run_atlas exited; CPU time 58129.540634
09:20:04 (4884): called boinc_finish(0)

</stderr_txt>
]]>

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