Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
00:46:00 (3210): wrapper (7.7.26015): starting
00:46:00 (3210): 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=4443081504
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._018287.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4443081504
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 03:04:53,159 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 59193 s
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 9907
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 9907
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443081504 has completed
2019-08-13 03:04:53,160 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 03:04:53,169 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443081504
2019-08-13 03:04:54,174 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [9907]
2019-08-13 03:04:54,175 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 9907
2019-08-13 03:04:54,175 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 03:04:55,179 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 03:04:55,179 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=9907
2019-08-13 03:04:55,222 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [9907] (in reverse order)
2019-08-13 03:04:55,261 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 03:04:55,261 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 03:04:55,261 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 03:04:55,261 | 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 03:04:55,769 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 03:05:05,815 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 03:05:05,815 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 03:05:05,854 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36236689408 B)
2019-08-13 03:05:05,855 | 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 03:05:05,855 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 03:05:05,857 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 03:05:05,995 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 03:05:06,080 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 03:05:06,170 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-13 03:05:06,170 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job, started 139840419137280)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(validate_pre, started 139840041514752)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(payload, started 139840385566464)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(data, started 139840402351872)>, <ExcThread(create_data_payload, started 139840016336640)>, <ExcThread(copytool_in, started 139839999551232)>, <ExcThread(validate_post, started 139840007943936)>, <ExcThread(failed_post, started 139839991158528)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:06,199 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 03:05:06,203 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 03:05:06,203 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 03:05:06,309 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 03:05:06,427 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 03:05:06,462 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 03:05:06,463 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 03:05:06,472 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-13 03:05:06,473 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(validate_pre, started 139840041514752)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(payload, started 139840385566464)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(create_data_payload, started 139840016336640)>, <ExcThread(copytool_in, started 139839999551232)>, <ExcThread(validate_post, started 139840007943936)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:06,512 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 03:05:06,598 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 03:05:06,598 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 03:05:06,605 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 03:05:06,606 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(validate_pre, started 139840041514752)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(create_data_payload, started 139840016336640)>, <ExcThread(validate_post, started 139840007943936)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:06,807 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 03:05:06,808 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 03:05:06,809 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(create_data_payload, started 139840016336640)>, <ExcThread(validate_post, started 139840007943936)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:06,974 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 03:05:07,010 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-13 03:05:07,011 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(validate_post, started 139840007943936)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:07,033 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 03:05:07,112 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 03:05:07,112 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(queue_monitoring, started 139840033122048)>, <ExcThread(copytool_out, started 139840393959168)>]
2019-08-13 03:05:07,310 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 03:05:07,313 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 03:05:07,314 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(queue_monitor, started 139839479465728)>, <ExcThread(queue_monitoring, started 139840033122048)>]
2019-08-13 03:05:07,641 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 03:05:07,641 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 03:05:07,716 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 03:05:07,717 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>, <ExcThread(queue_monitoring, started 139840033122048)>]
2019-08-13 03:05:09,200 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 03:05:09,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 03:05:09,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139840635410176)>, <ExcThread(job_monitor, started 139839487858432)>]
2019-08-13 03:05:53,667 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 03:05:53,668 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 03:05:53,768 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 03:05:53,769 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 03:05:53,769 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 03:05:54 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 03:05:54 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 03:05:54 UTC [wrapper] Pilot exit status: 0
2019-08-13 03:05:54 UTC [wrapper] STATUSCODE: 0
2019-08-13 03:05:54 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 00:46 pilot
-rwx------.  1 grid grid 20463 Jul 25 16:38 pilot.py
-rw-------.  1 grid grid     8 Aug  7 13:02 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 03:05:54 UTC [wrapper] Test setup, not cleaning
2019-08-13 03:05:54 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 03:05:54 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15590.43s
KernelTime=439.47s
UserTime=58957.77s
CPUUsage=380%
MaxResidentMemory=1944652kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=454118
MinorPageFaults=18761406
Swaps=0
ForcedSwitches=6927783
WaitSwitches=9529726
Inputs=109580592
Outputs=973192
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 285040
drwxrwx--x. 7 grid grid      4096 Aug 13 05:05 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409065 Aug 13 00:46 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517921 Aug 13 00:46 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 00:46 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 00:46 APPS
drwxr-xr-x. 2 grid grid         6 Aug 13 00:46 .arc
-rw-------. 1 grid grid       538 Aug 13 00:46 .asetup
-rw-------. 1 grid grid       826 Aug 13 00:46 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 00:46 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 05:05 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 13 04:56 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 277593482 Aug 13 00:46 EVNT.18605754._000355.pool.root.1
-rw-------. 1 grid grid     78352 Aug 13 05:04 heartbeat.json
-rw-rw-r--. 1 grid grid      5863 Aug 13 00:46 init_data.xml
-rw-rw-r--. 1 grid grid    262346 Aug 13 00:46 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 13 00:45 job.xml
-rw-------. 1 grid grid    744714 Aug 13 05:05 log.18722298._018287.job.log.1
-rw-------. 1 grid grid    850487 Aug 13 05:04 log.18722298._018287.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 13 05:05 output.list
-rw-------. 1 grid grid      2915 Aug 11 19:36 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 19:22 pilot2.tar.gz
-rw-------. 1 grid grid     10786 Aug 13 05:05 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 19:36 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 00:46 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 00:45 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 19:36 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 05:05 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 05:05 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 05:05 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 00:46 start_atlas.sh
-rw-rw-r--. 1 grid grid     18625 Aug 13 05:05 stderr.txt
-rw-------. 1 grid grid       518 Aug 13 05:05 WPSNDmyw6GvnShfckohDCDFpABFKDmABFKDmTwKZDmABFKDm5GNSVm.diag
-rw-rw-r--. 1 grid grid       107 Aug 13 00:45 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 13 05:05 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
05:05:54 (3210): run_atlas exited; CPU time 58958.151340
05:05:54 (3210): called boinc_finish(0)

</stderr_txt>
]]>

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