Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
20:36:34 (336): wrapper (7.7.26015): starting
20:36:34 (336): wrapper: running run_atlas (--nthreads 4)
2019-08-21 20:36:34,876: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-21 20:36:34,876: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-21 20:36:34,877: THREADS=4

2019-08-21 20:36:34,879: Checking for CVMFS
2019-08-21 20:36:36,503: CVMFS is installed
2019-08-21 20:36:36,507: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-21 20:36:36,507: This is not SLC6, need to run with Singularity....
2019-08-21 20:36:36,508: Checking Singularity...
2019-08-21 20:36:36,511: Singularity is not installed, using version from CVMFS
2019-08-21 20:36:36,511: Testing the function of Singularity...
2019-08-21 20:36:36,511: 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
2019-08-21 20:36:36,734: Singularity Works...
2019-08-21 20:36:36,735: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-21 20:36:37,241: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-21 20:36:37,242: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-21 20:36:37,242: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-21 20:36:37,243: export ATHENA_PROC_NUMBER=4;
2019-08-21 20:36:37,264: start atlas job with PandaID=4456789259
2019-08-21 20:36:37,264: 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
2019-08-22 00:55:56,161: running cmd return value is 0
2019-08-22 00:55:56,166: Moving ./HITS.18722298._026993.pool.root.1 to shared/HITS.pool.root.1
2019-08-22 00:55:56,167: *****************The last 100 lines of the pilot log******************
2019-08-22 00:55:56,175: 2019-08-21 22:55:04,909 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 58879 s
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7199
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7199
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 22:55:04,910 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 22:55:04,911 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4456789259 has completed
2019-08-21 22:55:04,911 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-21 22:55:04,921 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4456789259
2019-08-21 22:55:05,924 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7199]
2019-08-21 22:55:05,924 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7199
2019-08-21 22:55:05,924 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-21 22:55:06,929 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-21 22:55:06,929 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7199
2019-08-21 22:55:06,991 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7199] (in reverse order)
2019-08-21 22:55:07,040 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-21 22:55:07,040 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-21 22:55:07,041 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-21 22:55:07,041 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-21 22:55:07,554 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-21 22:55:16,436 | INFO     | monitor             | pilot.control.monitor            | control                   | 15504 s have passed since pilot start
2019-08-21 22:55:17,581 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-21 22:55:17,581 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-21 22:55:17,624 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35967205376 B)
2019-08-21 22:55:17,624 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-21 22:55:17,624 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-21 22:55:17,658 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-21 22:55:17,667 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-21 22:55:17,851 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-21 22:55:17,851 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-21 22:55:17,852 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-21 22:55:17,852 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(job, started 139902360753920)>, <ExcThread(execute_payloads, started 139901420947200)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(copytool_in, started 139901446125312)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(data, started 139902343968512)>, <ExcThread(failed_post, started 139901429339904)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(create_data_payload, started 139901982996224)>, <ExcThread(validate, started 139902352361216)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:17,918 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-21 22:55:17,994 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-21 22:55:17,994 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-21 22:55:17,995 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-21 22:55:18,053 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-21 22:55:18,053 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(job, started 139902360753920)>, <ExcThread(execute_payloads, started 139901420947200)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(copytool_in, started 139901446125312)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(failed_post, started 139901429339904)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:18,082 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-21 22:55:18,082 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-21 22:55:18,154 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-21 22:55:18,154 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(execute_payloads, started 139901420947200)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(copytool_in, started 139901446125312)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(failed_post, started 139901429339904)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:18,421 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-21 22:55:18,457 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-21 22:55:18,457 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(copytool_in, started 139901446125312)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(failed_post, started 139901429339904)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:18,720 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-21 22:55:18,759 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-21 22:55:18,759 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(failed_post, started 139901429339904)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:18,934 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-21 22:55:18,961 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-21 22:55:18,961 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>, <ExcThread(validate_pre, started 139901966210816)>]
2019-08-21 22:55:19,048 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-21 22:55:19,050 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-21 22:55:19,062 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-21 22:55:19,062 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(job_monitor, started 139901941032704)>, <ExcThread(queue_monitor, started 139901437732608)>]
2019-08-21 22:55:19,393 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-21 22:55:19,399 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-21 22:55:19,400 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-21 22:55:19,465 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-21 22:55:19,465 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(copytool_out, started 139902327183104)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(job_monitor, started 139901941032704)>]
2019-08-21 22:55:20,049 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-21 22:55:20,069 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-21 22:55:20,069 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(queue_monitoring, started 139901957818112)>, <ExcThread(job_monitor, started 139901941032704)>]
2019-08-21 22:55:22,394 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-21 22:55:22,486 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-21 22:55:22,487 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139902577026816)>, <ExcThread(job_monitor, started 139901941032704)>]
2019-08-21 22:55:55,663 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-21 22:55:55,663 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-21 22:55:55,714 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-21 22:55:55,714 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-21 22:55:55,715 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-21 22:55:55 UTC [wrapper] ==== pilot stdout END ====
2019-08-21 22:55:55 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-21 22:55:55 UTC [wrapper] Pilot exit status: 0
2019-08-21 22:55:55 UTC [wrapper] STATUSCODE: 0
2019-08-21 22:55:55 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 21 20:36 pilot
-rwx------.  1 grid grid 20628 Aug 19 14:00 pilot.py
-rw-------.  1 grid grid     9 Aug 19 14:00 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-21 22:55:56 UTC [wrapper] Test setup, not cleaning
2019-08-21 22:55:56 UTC [wrapper] ==== wrapper stdout END ====
2019-08-21 22:55:56 UTC [wrapper] ==== wrapper stderr END ====
2019-08-21 22:55:56 UTC [wrapper] wrapper wrapperexiting ec=0, duration=15559
2019-08-21 22:55:56 UTC [wrapper] apfmon messages muted
2019-08-22 00:55:56,179: ***************diag file************
2019-08-22 00:55:56,179: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15558.50s
KernelTime=428.34s
UserTime=58635.17s
CPUUsage=379%
MaxResidentMemory=1945196kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=458354
MinorPageFaults=18835134
Swaps=0
ForcedSwitches=6765036
WaitSwitches=9465148
Inputs=110501208
Outputs=953552
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-22 00:55:56,189: ******************************WorkDir***********************
2019-08-22 00:55:56,189: total 286568
drwxrwx--x. 6 grid grid      4096 Aug 22 00:55 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7469803 Aug 21 20:36 agis_ddmendpoints.json
-rw-------. 1 grid grid   4337015 Aug 21 20:36 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 21 20:36 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 21 20:36 APPS
-rw-------. 1 grid grid       538 Aug 21 20:36 .asetup
-rw-------. 1 grid grid       826 Aug 21 20:37 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 21 20:36 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 22 00:55 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 22 00:45 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 279285811 Aug 21 20:36 EVNT.18605754._000296.pool.root.1
-rw-------. 1 grid grid     78337 Aug 22 00:55 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 21 20:36 init_data.xml
-rw-rw-r--. 1 grid grid    263681 Aug 21 20:36 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 21 20:36 job.xml
-rw-------. 1 grid grid       518 Aug 22 00:55 kYqLDmMydKvnShfckohDCDFpABFKDmABFKDmoeUNDmABFKDmleyRhm.diag
-rw-------. 1 grid grid    729731 Aug 22 00:55 log.18722298._026993.job.log.1
-rw-------. 1 grid grid    847962 Aug 22 00:54 log.18722298._026993.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 22 00:55 output.list
-rw-------. 1 grid grid      2915 Aug 21 13:28 pandaJobData.out
drwx------. 3 grid grid       174 Aug 19 14:00 pilot2
-rw-r--r--. 1 grid grid    255033 Aug 21 13:28 pilot2.tar.gz
-rw-------. 1 grid grid     11680 Aug 22 00:55 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 21 13:28 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 21 20:36 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 21 20:36 run_atlas
-rwx------. 1 grid grid     12641 Aug 21 13:28 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 22 00:55 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 22 00:55 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 22 00:55 shared
-rw-rw-r--. 1 grid grid      8688 Aug 21 20:36 start_atlas.sh
-rw-rw-r--. 1 grid grid     19529 Aug 22 00:55 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 21 20:36 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 22 00:55 wrapper_checkpoint.txt

2019-08-22 00:55:56,190: running start_atlas return value is 0
2019-08-22 00:55:56,190: Parent exit 0
2019-08-22 00:55:56,192: child process exit 0
00:55:56 (336): run_atlas exited; CPU time 58635.576635
00:55:56 (336): called boinc_finish(0)

</stderr_txt>
]]>

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