Stderr output

<core_client_version>7.4.25</core_client_version>
<![CDATA[
<stderr_txt>
00:56:32 (26193): wrapper (7.7.26015): starting
00:56:32 (26193): wrapper: running run_atlas (--nthreads 1)
2019-08-17 00:56:32,462: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 00:56:32,462: sys.argv = ['run_atlas', '--nthreads', '1']
2019-08-17 00:56:32,463: THREADS=1

2019-08-17 00:56:32,464: Checking for CVMFS
2019-08-17 00:56:33,398: CVMFS is installed
2019-08-17 00:56:33,404: OS:cat: /etc/redhat-release: No such file or directory
2019-08-17 00:56:33,404: This is not SLC6, need to run with Singularity....
2019-08-17 00:56:33,404: Checking Singularity...
2019-08-17 00:56:33,412: Singularity is installed, version 2.6.1-dist
2019-08-17 00:56:33,412: Testing the function of Singularity...
2019-08-17 00:56:33,412: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-17 00:56:33,528: Singularity Works...
2019-08-17 00:56:33,528: copy /home/m/BOINC/slots/3/shared/ATLAS.root_0
2019-08-17 00:56:33,942: copy /home/m/BOINC/slots/3/shared/start_atlas.sh
2019-08-17 00:56:33,942: copy /home/m/BOINC/slots/3/shared/RTE.tar.gz
2019-08-17 00:56:33,943: copy /home/m/BOINC/slots/3/shared/input.tar.gz
2019-08-17 00:56:33,973: start atlas job with PandaID=4448565872
2019-08-17 00:56:33,973: cmd = singularity exec --pwd /home/m/BOINC/slots/3 -B /cvmfs,/home /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-08-18 20:06:28,336: running cmd return value is 0
2019-08-18 20:06:28,338: Moving ./HITS.18722326._011414.pool.root.1 to shared/HITS.pool.root.1
2019-08-18 20:06:28,343: *****************The last 100 lines of the pilot log******************
2019-08-18 20:06:28,347: 2019-08-18 19:06:07,473 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-18 19:06:07,473 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4448565872
2019-08-18 19:06:07,473 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722326
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 152802 s
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 8711
2019-08-18 19:06:07,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 8711
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4448565872 has completed
2019-08-18 19:06:07,475 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-18 19:06:07,476 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/m/BOINC/slots/3/PanDA_Pilot-4448565872
2019-08-18 19:06:08,480 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [8711]
2019-08-18 19:06:08,480 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 8711
2019-08-18 19:06:08,480 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-18 19:06:09,482 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-18 19:06:09,483 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=8711
2019-08-18 19:06:09,526 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [8711] (in reverse order)
2019-08-18 19:06:09,560 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-18 19:06:09,561 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-18 19:06:09,561 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-18 19:06:09,561 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-18 19:06:10,069 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-18 19:06:20,119 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-18 19:06:20,120 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/m/BOINC/slots/3
2019-08-18 19:06:20,146 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (441702154240 B)
2019-08-18 19:06:20,147 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-18 19:06:20,147 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-18 19:06:20,182 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-18 19:06:20,188 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-18 19:06:20,189 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-18 19:06:20,328 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-18 19:06:20,366 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-18 19:06:20,367 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-18 19:06:20,416 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-18 19:06:20,417 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(job, started 140080430085888)>, <ExcThread(validate_post, started 140079863416576)>, <ExcThread(payload, started 140080396515072)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(execute_payloads, started 140079351723776)>, <ExcThread(copytool_out, started 140080404907776)>, <ExcThread(copytool_in, started 140079846631168)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(validate_pre, started 140079880201984)>, <ExcThread(queue_monitoring, started 140080379729664)>, <ExcThread(failed_post, started 140079838238464)>, <ExcThread(validate, started 140080413300480)>]
2019-08-18 19:06:20,560 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-18 19:06:20,610 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-18 19:06:20,718 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-18 19:06:20,718 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(job, started 140080430085888)>, <ExcThread(payload, started 140080396515072)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(copytool_out, started 140080404907776)>, <ExcThread(copytool_in, started 140079846631168)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(validate_pre, started 140079880201984)>, <ExcThread(queue_monitoring, started 140080379729664)>, <ExcThread(failed_post, started 140079838238464)>, <ExcThread(validate, started 140080413300480)>]
2019-08-18 19:06:20,728 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-18 19:06:20,728 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-18 19:06:20,919 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-18 19:06:20,920 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(payload, started 140080396515072)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(copytool_out, started 140080404907776)>, <ExcThread(copytool_in, started 140079846631168)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(validate_pre, started 140079880201984)>, <ExcThread(queue_monitoring, started 140080379729664)>, <ExcThread(failed_post, started 140079838238464)>, <ExcThread(validate, started 140080413300480)>]
2019-08-18 19:06:21,056 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-18 19:06:21,057 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-18 19:06:21,121 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-18 19:06:21,121 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(payload, started 140080396515072)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(copytool_out, started 140080404907776)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(validate_pre, started 140079880201984)>, <ExcThread(queue_monitoring, started 140080379729664)>, <ExcThread(failed_post, started 140079838238464)>]
2019-08-18 19:06:21,134 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-18 19:06:21,134 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-18 19:06:21,188 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-18 19:06:21,222 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-18 19:06:21,222 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(validate_pre, started 140079880201984)>, <ExcThread(queue_monitoring, started 140080379729664)>, <ExcThread(failed_post, started 140079838238464)>]
2019-08-18 19:06:21,534 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-18 19:06:21,559 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-18 19:06:21,625 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-18 19:06:21,625 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(queue_monitor, started 140079855023872)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(queue_monitoring, started 140080379729664)>]
2019-08-18 19:06:21,989 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-18 19:06:21,989 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-18 19:06:22,028 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-18 19:06:22,028 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(job_monitor, started 140079871809280)>, <ExcThread(queue_monitoring, started 140080379729664)>]
2019-08-18 19:06:23,183 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-18 19:06:23,236 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-18 19:06:23,236 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080646358784)>, <ExcThread(job_monitor, started 140079871809280)>]
2019-08-18 19:06:27,965 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-18 19:06:27,966 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-18 19:06:28,066 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-18 19:06:28,067 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-18 19:06:28,067 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-18 19:06:28 UTC [wrapper] ==== pilot stdout END ====
2019-08-18 19:06:28 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-18 19:06:28 UTC [wrapper] Pilot exit status: 0
2019-08-18 19:06:28 UTC [wrapper] STATUSCODE: 0
2019-08-18 19:06:28 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------  1 m m 11357 Jul 25 15:38 LICENSE
drwx------ 14 m m  4096 Aug 17 00:57 pilot
-rwx------  1 m m 20463 Jul 25 15:38 pilot.py
-rw-------  1 m m     8 Aug  7 12:02 PILOTVERSION
-rw-------  1 m m  2251 Jul 25 15:38 README.md
-rw-------  1 m m   221 Jul 25 15:38 TODO.md

2019-08-18 19:06:28 UTC [wrapper] Test setup, not cleaning
2019-08-18 19:06:28 UTC [wrapper] ==== wrapper stdout END ====
2019-08-18 19:06:28 UTC [wrapper] ==== wrapper stderr END ====
2019-08-18 19:06:28 UTC [wrapper] wrapper wrapperexiting ec=0, duration=155394
2019-08-18 19:06:28 UTC [wrapper] apfmon messages muted
2019-08-18 20:06:28,349: ***************diag file************
2019-08-18 20:06:28,349: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=155393.95s
KernelTime=1935.74s
UserTime=152378.14s
CPUUsage=99%
MaxResidentMemory=1951520kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=2406275
MinorPageFaults=77942628
Swaps=0
ForcedSwitches=40503039
WaitSwitches=75931572
Inputs=571492928
Outputs=667768
SocketReceived=0
SocketSent=0
Signals=0

nodename=m@TeeC16
exitcode=0
2019-08-18 20:06:28,353: ******************************WorkDir***********************
2019-08-18 20:06:28,353: total 293132
drwxrwx--x 6 m m      4096 Aug 18 20:06 .
drwxrwx--x 6 m m      4096 Aug 17 00:56 ..
-rw------- 1 m m   7411700 Aug 17 00:57 agis_ddmendpoints.json
-rw------- 1 m m   4399526 Aug 17 00:57 agis_schedconf.cvmfs.json
drwx------ 2 m m      4096 Aug 17 00:56 .alrb
drwxr-xr-x 3 m m      4096 Aug 17 00:56 APPS
-rw------- 1 m m       541 Aug 17 00:56 .asetup
-rw------- 1 m m       826 Aug 17 00:58 .asetup.save
-rw-rw-r-- 1 m m         0 Aug 17 00:56 boinc_lockfile
-rw-rw-r-- 1 m m      8192 Aug 18 20:06 boinc_mmap_file
-rw-rw-r-- 1 m m       539 Aug 18 20:04 boinc_task_state.xml
-rw-rw-r-- 1 m m 280356958 Aug 17 00:56 EVNT.18605758._000386.pool.root.1
-rw------- 1 m m     83458 Aug 18 20:06 heartbeat.json
-rw-rw-r-- 1 m m      5681 Aug 18 19:59 init_data.xml
-rw-rw-r-- 1 m m    261621 Aug 17 00:56 input.tar.gz
-rw------- 1 m m       499 Aug 18 20:06 irhNDmuHzIvnShfckohDCDFpABFKDmABFKDmRMlKDmABFKDmfVrxdn.diag
-rw-rw-r-- 1 m m       112 Aug 17 00:56 job.xml
-rw------- 1 m m   6606061 Aug 18 20:06 log.18722326._011414.job.log.1
-rw------- 1 m m    593464 Aug 18 20:05 log.18722326._011414.job.log.tgz.1
-rw------- 1 m m       391 Aug 18 20:06 output.list
-rw------- 1 m m      2915 Aug 16 22:50 pandaJobData.out
drwx------ 3 m m      4096 Aug  7 12:02 pilot2
-rw-r--r-- 1 m m    253018 Aug 16 22:27 pilot2.tar.gz
-rw------- 1 m m     10393 Aug 18 20:06 pilotlog.txt
-rw-r--r-- 1 m m      4468 Aug 16 22:50 queuedata.json
-rw-rw-r-- 1 m m       815 Aug 17 00:56 RTE.tar.gz
-rwxr-xr-x 1 m m      8466 Aug 17 00:56 run_atlas
-rwx------ 1 m m     12641 Aug 16 22:50 runpilot2-wrapper.sh
-rw-rw-r-- 1 m m       692 Aug 18 20:06 runtime_log
-rw-rw-r-- 1 m m      7801 Aug 18 20:06 runtime_log.err
-rw------- 1 m m       248 Aug 17 00:56 setup.sh.local
drwxrwx--x 2 m m      4096 Aug 18 20:06 shared
-rw-rw-r-- 1 m m      8659 Aug 17 00:56 start_atlas.sh
-rw-rw-r-- 1 m m     18753 Aug 18 20:06 stderr.txt
-rw-rw-r-- 1 m m       107 Aug 17 00:56 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r-- 1 m m        30 Aug 18 20:06 wrapper_checkpoint.txt

2019-08-18 20:06:28,353: running start_atlas return value is 0
2019-08-18 20:06:28,353: Parent exit 0
2019-08-18 20:06:28,353: child process exit 0
20:06:29 (26193): run_atlas exited; CPU time 152378.395233
20:06:29 (26193): called boinc_finish(0)

</stderr_txt>
]]>

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