Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
05:25:19 (12224): wrapper (7.7.26015): starting
05:25:19 (12224): 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=4445519267
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.18722495._008579.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-15 07:50:27,657 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-15 07:50:27,657 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 61064 s
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 18916
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 18916
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 07:50:27,658 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-15 07:50:27,659 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4445519267 has completed
2019-08-15 07:50:27,659 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-15 07:50:27,667 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4445519267
2019-08-15 07:50:28,673 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [18916]
2019-08-15 07:50:28,673 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 18916
2019-08-15 07:50:28,673 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-15 07:50:29,678 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-15 07:50:29,678 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=18916
2019-08-15 07:50:29,737 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [18916] (in reverse order)
2019-08-15 07:50:29,778 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-15 07:50:29,778 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-15 07:50:29,778 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-15 07:50:29,778 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-15 07:50:30,288 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-15 07:50:31,856 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-15 07:50:40,346 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-15 07:50:40,347 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-15 07:50:40,381 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36367761408 B)
2019-08-15 07:50:40,381 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-15 07:50:40,382 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-15 07:50:40,383 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-15 07:50:40,384 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-15 07:50:40,397 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-15 07:50:40,397 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(job, started 139821653124864)>, <ExcThread(validate_pre, started 139821091636992)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(failed_post, started 139820579944192)>, <ExcThread(copytool_in, started 139821074851584)>, <ExcThread(execute_payloads, started 139820571551488)>, <ExcThread(monitor, started 139821100029696)>, <ExcThread(validate, started 139821644732160)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>, <ExcThread(copytool_out, started 139821602768640)>, <ExcThread(payload, started 139821611161344)>]
2019-08-15 07:50:40,409 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-15 07:50:40,432 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-15 07:50:40,699 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-15 07:50:40,699 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(job, started 139821653124864)>, <ExcThread(validate_pre, started 139821091636992)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(failed_post, started 139820579944192)>, <ExcThread(copytool_in, started 139821074851584)>, <ExcThread(execute_payloads, started 139820571551488)>, <ExcThread(validate, started 139821644732160)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>, <ExcThread(copytool_out, started 139821602768640)>, <ExcThread(payload, started 139821611161344)>]
2019-08-15 07:50:40,747 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-15 07:50:40,795 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-15 07:50:40,954 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-15 07:50:40,996 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-15 07:50:40,996 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-15 07:50:41,001 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-15 07:50:41,001 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(failed_post, started 139820579944192)>, <ExcThread(validate, started 139821644732160)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>, <ExcThread(copytool_out, started 139821602768640)>, <ExcThread(payload, started 139821611161344)>]
2019-08-15 07:50:41,402 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-15 07:50:41,403 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-15 07:50:41,404 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(failed_post, started 139820579944192)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>, <ExcThread(copytool_out, started 139821602768640)>, <ExcThread(payload, started 139821611161344)>]
2019-08-15 07:50:41,430 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-15 07:50:41,431 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-15 07:50:41,432 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-15 07:50:41,505 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-15 07:50:41,505 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(failed_post, started 139820579944192)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:50:41,676 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-15 07:50:41,706 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-15 07:50:41,706 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(validate_post, started 139821066458880)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:50:41,801 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-15 07:50:41,807 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-15 07:50:41,807 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(create_data_payload, started 139821627946752)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:50:41,859 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-15 07:50:41,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-15 07:50:41,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(queue_monitor, started 139821083244288)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:50:42,125 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-15 07:50:42,125 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-15 07:50:42,152 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-15 07:50:42,211 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-15 07:50:42,211 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(queue_monitoring, started 139821108422400)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:50:45,153 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-15 07:50:45,232 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-15 07:50:45,233 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821869397760)>, <ExcThread(job_monitor, started 139821116815104)>]
2019-08-15 07:51:33,458 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-15 07:51:33,459 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-15 07:51:33,464 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-15 07:51:33,464 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-15 07:51:33,464 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-15 07:51:33 UTC [wrapper] ==== pilot stdout END ====
2019-08-15 07:51:33 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-15 07:51:33 UTC [wrapper] Pilot exit status: 0
2019-08-15 07:51:33 UTC [wrapper] STATUSCODE: 0
2019-08-15 07:51:33 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 15 05:25 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

2019-08-15 07:51:33 UTC [wrapper] Test setup, not cleaning
2019-08-15 07:51:33 UTC [wrapper] ==== wrapper stdout END ====
2019-08-15 07:51:33 UTC [wrapper] ==== wrapper stderr END ====
2019-08-15 07:51:33 UTC [wrapper] wrapper wrapperexiting ec=0, duration=15972
2019-08-15 07:51:33 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15972.34s
KernelTime=417.28s
UserTime=60838.75s
CPUUsage=383%
MaxResidentMemory=1945128kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=463977
MinorPageFaults=19124927
Swaps=0
ForcedSwitches=7023156
WaitSwitches=9769797
Inputs=112218688
Outputs=973832
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 246188
drwxrwx--x. 6 grid grid      4096 Aug 15 09:51 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409162 Aug 15 05:25 agis_ddmendpoints.json
-rw-------. 1 grid grid   4448398 Aug 15 05:25 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 05:25 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 05:25 APPS
-rw-------. 1 grid grid       538 Aug 15 05:25 .asetup
-rw-------. 1 grid grid       826 Aug 15 05:26 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 05:25 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 15 09:51 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 15 09:44 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 237860642 Aug 15 05:25 EVNT.18605790._000163.pool.root.1
-rw-------. 1 grid grid     81246 Aug 15 09:50 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 05:25 init_data.xml
-rw-rw-r--. 1 grid grid    261607 Aug 15 05:25 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 05:25 job.xml
-rw-------. 1 grid grid    764811 Aug 15 09:51 log.18722495._008579.job.log.1
-rw-------. 1 grid grid    850597 Aug 15 09:50 log.18722495._008579.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 15 09:51 output.list
-rw-------. 1 grid grid      2949 Aug 14 12:32 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 14 12:32 pilot2.tar.gz
-rw-------. 1 grid grid     12141 Aug 15 09:51 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 14 12:32 queuedata.json
-rw-------. 1 grid grid       518 Aug 15 09:51 rH7MDmxk5HvnShfckohDCDFpABFKDmABFKDmdXvaDmABFKDmanJnzm.diag
-rw-rw-r--. 1 grid grid       815 Aug 15 05:25 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 05:25 run_atlas
-rwx------. 1 grid grid     12641 Aug 14 12:32 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 15 09:51 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 15 09:51 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 15 09:51 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 05:25 start_atlas.sh
-rw-rw-r--. 1 grid grid     19374 Aug 15 09:51 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 05:25 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 15 09:51 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
09:51:34 (12224): run_atlas exited; CPU time 60839.141143
09:51:34 (12224): called boinc_finish(0)

</stderr_txt>
]]>

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