Stderr output

<core_client_version>7.4.25</core_client_version>
<![CDATA[
<stderr_txt>
00:56:12 (22463): wrapper (7.7.26015): starting
00:56:12 (22463): wrapper: running run_atlas (--nthreads 1)
2019-08-17 00:56:12,807: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 00:56:12,807: sys.argv = ['run_atlas', '--nthreads', '1']
2019-08-17 00:56:12,808: THREADS=1

2019-08-17 00:56:12,808: Checking for CVMFS
2019-08-17 00:56:13,377: CVMFS is installed
2019-08-17 00:56:13,380: OS:cat: /etc/redhat-release: No such file or directory
2019-08-17 00:56:13,380: This is not SLC6, need to run with Singularity....
2019-08-17 00:56:13,380: Checking Singularity...
2019-08-17 00:56:13,392: Singularity is installed, version 2.6.1-dist
2019-08-17 00:56:13,392: Testing the function of Singularity...
2019-08-17 00:56:13,392: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-17 00:56:13,492: Singularity Works...
2019-08-17 00:56:13,492: copy /home/m/BOINC/slots/2/shared/ATLAS.root_0
2019-08-17 00:56:13,832: copy /home/m/BOINC/slots/2/shared/start_atlas.sh
2019-08-17 00:56:13,832: copy /home/m/BOINC/slots/2/shared/RTE.tar.gz
2019-08-17 00:56:13,832: copy /home/m/BOINC/slots/2/shared/input.tar.gz
2019-08-17 00:56:13,847: start atlas job with PandaID=4444737870
2019-08-17 00:56:13,847: cmd = singularity exec --pwd /home/m/BOINC/slots/2 -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 19:38:33,208: running cmd return value is 0
2019-08-18 19:38:33,208: Moving ./HITS.18722552._007039.pool.root.1 to shared/HITS.pool.root.1
2019-08-18 19:38:33,209: *****************The last 100 lines of the pilot log******************
2019-08-18 19:38:33,210: 2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4444737870
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722552
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-18 18:37:21,123 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 151049 s
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 32725
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 32725
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4444737870 has completed
2019-08-18 18:37:21,124 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-18 18:37:21,126 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/m/BOINC/slots/2/PanDA_Pilot-4444737870
2019-08-18 18:37:22,130 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [32725]
2019-08-18 18:37:22,130 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 32725
2019-08-18 18:37:22,130 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-18 18:37:23,134 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-18 18:37:23,135 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=32725
2019-08-18 18:37:23,185 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [32725] (in reverse order)
2019-08-18 18:37:23,213 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-18 18:37:23,213 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-18 18:37:23,213 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-18 18:37:23,213 | 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 18:37:23,720 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-18 18:37:31,299 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-18 18:37:33,767 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-18 18:37:33,767 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/m/BOINC/slots/2
2019-08-18 18:37:33,783 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (440681889792 B)
2019-08-18 18:37:33,783 | 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 18:37:33,784 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-18 18:37:33,847 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-18 18:37:33,899 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-18 18:37:34,061 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-18 18:37:34,061 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(job, started 140478294836992)>, <ExcThread(failed_post, started 140477357610752)>, <ExcThread(validate_post, started 140477860910848)>, <ExcThread(data, started 140478286444288)>, <ExcThread(validate_pre, started 140477894481664)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(copytool_out, started 140477902874368)>, <ExcThread(execute_payloads, started 140477349218048)>, <ExcThread(create_data_payload, started 140478261266176)>, <ExcThread(copytool_in, started 140477374396160)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(payload, started 140478269658880)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:34,246 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-18 18:37:34,263 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-18 18:37:34,278 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-18 18:37:34,278 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-18 18:37:34,336 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-18 18:37:34,364 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-18 18:37:34,393 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-18 18:37:34,394 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(job, started 140478294836992)>, <ExcThread(validate_pre, started 140477894481664)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(copytool_out, started 140477902874368)>, <ExcThread(execute_payloads, started 140477349218048)>, <ExcThread(copytool_in, started 140477374396160)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(payload, started 140478269658880)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:34,401 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-18 18:37:34,465 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-18 18:37:34,465 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-18 18:37:34,569 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-18 18:37:34,569 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-18 18:37:34,595 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-18 18:37:34,595 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(validate_pre, started 140477894481664)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(copytool_out, started 140477902874368)>, <ExcThread(execute_payloads, started 140477349218048)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:34,874 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-18 18:37:34,897 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-18 18:37:34,897 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(copytool_out, started 140477902874368)>, <ExcThread(execute_payloads, started 140477349218048)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:34,909 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-18 18:37:34,997 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-18 18:37:34,998 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(copytool_out, started 140477902874368)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:35,336 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-18 18:37:35,372 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-18 18:37:35,400 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-18 18:37:35,400 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(queue_monitor, started 140477366003456)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:35,597 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-18 18:37:35,598 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-18 18:37:35,602 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-18 18:37:35,602 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(queue_monitoring, started 140477877696256)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:37:38,373 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-18 18:37:38,417 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-18 18:37:38,417 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140478511109888)>, <ExcThread(job_monitor, started 140477869303552)>]
2019-08-18 18:38:32,901 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-18 18:38:32,902 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-18 18:38:32,929 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-18 18:38:32,930 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-18 18:38:32,930 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-18 18:38:33 UTC [wrapper] ==== pilot stdout END ====
2019-08-18 18:38:33 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-18 18:38:33 UTC [wrapper] Pilot exit status: 0
2019-08-18 18:38:33 UTC [wrapper] STATUSCODE: 0
2019-08-18 18:38:33 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 00:56 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 18:38:33 UTC [wrapper] Test setup, not cleaning
2019-08-18 18:38:33 UTC [wrapper] ==== wrapper stdout END ====
2019-08-18 18:38:33 UTC [wrapper] ==== wrapper stderr END ====
2019-08-18 18:38:33 UTC [wrapper] wrapper wrapperexiting ec=0, duration=153739
2019-08-18 18:38:33 UTC [wrapper] apfmon messages muted
2019-08-18 19:38:33,212: ***************diag file************
2019-08-18 19:38:33,212: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=153739.11s
KernelTime=1920.29s
UserTime=150620.28s
CPUUsage=99%
MaxResidentMemory=1940404kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=2405291
MinorPageFaults=77099675
Swaps=0
ForcedSwitches=40218172
WaitSwitches=75031461
Inputs=571910000
Outputs=659584
SocketReceived=0
SocketSent=0
Signals=0

nodename=m@TeeC16
exitcode=0
2019-08-18 19:38:33,215: ******************************WorkDir***********************
2019-08-18 19:38:33,215: total 251652
drwxrwx--x 6 m m      4096 Aug 18 19:38 .
drwxrwx--x 6 m m      4096 Aug 17 00:56 ..
-rw------- 1 m m       499 Aug 18 19:38 9lAMDmSFoHvnShfckohDCDFpABFKDmABFKDmLmTaDmABFKDmRDkVtm.diag
-rw------- 1 m m   7411700 Aug 17 00:56 agis_ddmendpoints.json
-rw------- 1 m m   4399526 Aug 17 00:56 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 00:57 .asetup.save
-rw-rw-r-- 1 m m         0 Aug 17 00:56 boinc_lockfile
-rw-rw-r-- 1 m m      8192 Aug 18 19:38 boinc_mmap_file
-rw-rw-r-- 1 m m       539 Aug 18 19:35 boinc_task_state.xml
-rw-rw-r-- 1 m m 237938582 Aug 17 00:56 EVNT.18605796._000123.pool.root.1
-rw------- 1 m m     83820 Aug 18 19:37 heartbeat.json
-rw-rw-r-- 1 m m      5679 Aug 17 20:45 init_data.xml
-rw-rw-r-- 1 m m    261631 Aug 17 00:56 input.tar.gz
-rw-rw-r-- 1 m m       112 Aug 17 00:56 job.xml
-rw------- 1 m m   6549865 Aug 18 19:38 log.18722552._007039.job.log.1
-rw------- 1 m m    589199 Aug 18 19:37 log.18722552._007039.job.log.tgz.1
-rw------- 1 m m       391 Aug 18 19:38 output.list
-rw------- 1 m m      2949 Aug 13 16:50 pandaJobData.out
drwx------ 3 m m      4096 Aug  7 12:02 pilot2
-rw-r--r-- 1 m m    253018 Aug 13 16:30 pilot2.tar.gz
-rw------- 1 m m     10300 Aug 18 19:38 pilotlog.txt
-rw-r--r-- 1 m m      4468 Aug 13 16:50 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 13 16:50 runpilot2-wrapper.sh
-rw-rw-r-- 1 m m       692 Aug 18 19:38 runtime_log
-rw-rw-r-- 1 m m      7774 Aug 18 19:38 runtime_log.err
-rw------- 1 m m       248 Aug 17 00:56 setup.sh.local
drwxrwx--x 2 m m      4096 Aug 18 19:38 shared
-rw-rw-r-- 1 m m      8659 Aug 17 00:56 start_atlas.sh
-rw-rw-r-- 1 m m     18493 Aug 18 19:38 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 19:38 wrapper_checkpoint.txt

2019-08-18 19:38:33,215: running start_atlas return value is 0
2019-08-18 19:38:33,215: Parent exit 0
2019-08-18 19:38:33,216: child process exit 0
19:38:33 (22463): run_atlas exited; CPU time 150620.547104
19:38:33 (22463): called boinc_finish(0)

</stderr_txt>
]]>

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