Stderr output

<core_client_version>7.4.25</core_client_version>
<![CDATA[
<stderr_txt>
01:36:50 (31379): wrapper (7.7.26015): starting
01:36:50 (31379): wrapper: running run_atlas (--nthreads 1)
2019-08-17 01:36:50,060: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 01:36:50,060: sys.argv = ['run_atlas', '--nthreads', '1']
2019-08-17 01:36:50,062: THREADS=1

2019-08-17 01:36:50,063: Checking for CVMFS
2019-08-17 01:36:51,135: CVMFS is installed
2019-08-17 01:36:51,143: OS:cat: /etc/redhat-release: No such file or directory
2019-08-17 01:36:51,144: This is not SLC6, need to run with Singularity....
2019-08-17 01:36:51,144: Checking Singularity...
2019-08-17 01:36:51,161: Singularity is installed, version 2.6.1-dist
2019-08-17 01:36:51,161: Testing the function of Singularity...
2019-08-17 01:36:51,161: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-17 01:36:51,280: Singularity Works...
2019-08-17 01:36:51,280: copy /home/m/BOINC/slots/0/shared/ATLAS.root_0
2019-08-17 01:36:51,650: copy /home/m/BOINC/slots/0/shared/start_atlas.sh
2019-08-17 01:36:51,650: copy /home/m/BOINC/slots/0/shared/RTE.tar.gz
2019-08-17 01:36:51,650: copy /home/m/BOINC/slots/0/shared/input.tar.gz
2019-08-17 01:36:51,684: start atlas job with PandaID=4448457033
2019-08-17 01:36:51,684: cmd = singularity exec --pwd /home/m/BOINC/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
2019-08-17 20:25:10,620: running cmd return value is 0
2019-08-17 20:25:10,656: Moving ./HITS.18722183._016981.pool.root.1 to shared/HITS.pool.root.1
2019-08-17 20:25:10,656: *****************The last 100 lines of the pilot log******************
2019-08-17 20:25:10,734: 2019-08-17 19:24:30,048 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722183
2019-08-17 19:24:30,048 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-17 19:24:30,048 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-17 19:24:30,048 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 19:24:30,048 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 65948 s
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 19:24:30,049 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 5972
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 5972
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4448457033 has completed
2019-08-17 19:24:30,050 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 19:24:30,055 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/m/BOINC/slots/0/PanDA_Pilot-4448457033
2019-08-17 19:24:31,059 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [5972]
2019-08-17 19:24:31,059 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 5972
2019-08-17 19:24:31,060 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 19:24:32,065 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 19:24:32,065 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=5972
2019-08-17 19:24:32,150 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [5972] (in reverse order)
2019-08-17 19:24:32,282 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 19:24:32,282 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 19:24:32,282 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 19:24:32,282 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-17 19:24:32,790 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 19:24:42,839 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 19:24:42,840 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/m/BOINC/slots/0
2019-08-17 19:24:42,882 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (440851759104 B)
2019-08-17 19:24:42,882 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-17 19:24:42,882 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 19:24:42,889 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 19:24:42,891 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 19:24:42,898 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-17 19:24:42,898 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(job, started 139922559645440)>, <ExcThread(validate_post, started 139922283411200)>, <ExcThread(create_data_payload, started 139922534467328)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(validate, started 139922551252736)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(copytool_out, started 139922316982016)>, <ExcThread(execute_payloads, started 139922266625792)>, <ExcThread(failed_post, started 139922275018496)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(data, started 139922542860032)>, <ExcThread(queue_monitor, started 139921746540288)>, <ExcThread(payload, started 139922308589312)>]
2019-08-17 19:24:42,919 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 19:24:43,039 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 19:24:43,039 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 19:24:43,109 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 19:24:43,116 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 19:24:43,267 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-17 19:24:43,268 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(create_data_payload, started 139922534467328)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(validate, started 139922551252736)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(copytool_out, started 139922316982016)>, <ExcThread(execute_payloads, started 139922266625792)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(data, started 139922542860032)>, <ExcThread(queue_monitor, started 139921746540288)>, <ExcThread(payload, started 139922308589312)>]
2019-08-17 19:24:43,351 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 19:24:43,371 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 19:24:43,417 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 19:24:43,569 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-17 19:24:43,569 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(copytool_out, started 139922316982016)>, <ExcThread(execute_payloads, started 139922266625792)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(data, started 139922542860032)>, <ExcThread(queue_monitor, started 139921746540288)>, <ExcThread(payload, started 139922308589312)>]
2019-08-17 19:24:43,608 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 19:24:43,608 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 19:24:43,771 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-17 19:24:43,772 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(copytool_out, started 139922316982016)>, <ExcThread(execute_payloads, started 139922266625792)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(queue_monitor, started 139921746540288)>, <ExcThread(payload, started 139922308589312)>]
2019-08-17 19:24:43,847 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 19:24:43,856 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 19:24:43,857 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 19:24:43,872 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-17 19:24:43,873 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(copytool_out, started 139922316982016)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(queue_monitor, started 139921746540288)>]
2019-08-17 19:24:43,919 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 19:24:43,973 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 19:24:43,974 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(validate_pre, started 139922300196608)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(queue_monitor, started 139921746540288)>]
2019-08-17 19:24:44,239 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 19:24:44,276 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 19:24:44,276 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(job_monitor, started 139921754932992)>, <ExcThread(queue_monitor, started 139921746540288)>]
2019-08-17 19:24:44,557 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 19:24:44,557 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 19:24:44,578 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 19:24:44,578 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(queue_monitoring, started 139921780111104)>, <ExcThread(job_monitor, started 139921754932992)>]
2019-08-17 19:24:46,372 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 19:24:46,389 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 19:24:46,389 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139922775918336)>, <ExcThread(job_monitor, started 139921754932992)>]
2019-08-17 19:25:09,743 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-17 19:25:09,744 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 19:25:09,807 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 19:25:09,807 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 19:25:09,807 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 19:25:10 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 19:25:10 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 19:25:10 UTC [wrapper] Pilot exit status: 0
2019-08-17 19:25:10 UTC [wrapper] STATUSCODE: 0
2019-08-17 19:25:10 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 01:37 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

2019-08-17 19:25:10 UTC [wrapper] Test setup, not cleaning
2019-08-17 19:25:10 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 19:25:10 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 19:25:10 UTC [wrapper] wrapper wrapperexiting ec=0, duration=67698
2019-08-17 19:25:10 UTC [wrapper] apfmon messages muted
2019-08-17 20:25:10,759: ***************diag file************
2019-08-17 20:25:10,760: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=67698.11s
KernelTime=881.35s
UserTime=65793.78s
CPUUsage=98%
MaxResidentMemory=1951496kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=1091403
MinorPageFaults=38651972
Swaps=0
ForcedSwitches=19374975
WaitSwitches=32954285
Inputs=258215752
Outputs=384664
SocketReceived=0
SocketSent=0
Signals=0

nodename=m@TeeC16
exitcode=0
2019-08-17 20:25:10,997: ******************************WorkDir***********************
2019-08-17 20:25:10,997: total 255028
drwxrwx--x 6 m m      4096 Aug 17 20:25 .
drwxrwx--x 6 m m      4096 Aug 17 00:56 ..
-rw------- 1 m m       496 Aug 17 20:25 1lANDmNNvIvnShfckohDCDFpABFKDmABFKDmt2eKDmABFKDmZCTlWo.diag
-rw------- 1 m m   7411700 Aug 17 01:37 agis_ddmendpoints.json
-rw------- 1 m m   4399526 Aug 17 01:37 agis_schedconf.cvmfs.json
drwx------ 2 m m      4096 Aug 17 01:36 .alrb
drwxr-xr-x 3 m m      4096 Aug 17 01:36 APPS
-rw------- 1 m m       541 Aug 17 01:36 .asetup
-rw------- 1 m m       826 Aug 17 01:38 .asetup.save
-rw-rw-r-- 1 m m         0 Aug 17 01:36 boinc_lockfile
-rw-rw-r-- 1 m m      8192 Aug 17 20:24 boinc_mmap_file
-rw-rw-r-- 1 m m       537 Aug 17 20:22 boinc_task_state.xml
-rw-rw-r-- 1 m m 245125002 Aug 17 01:36 EVNT.18605745._000359.pool.root.1
-rw------- 1 m m    103324 Aug 17 20:24 heartbeat.json
-rw-rw-r-- 1 m m      5697 Aug 17 01:36 init_data.xml
-rw-rw-r-- 1 m m    261618 Aug 17 01:36 input.tar.gz
-rw-rw-r-- 1 m m       112 Aug 17 01:36 job.xml
-rw------- 1 m m   2999605 Aug 17 20:25 log.18722183._016981.job.log.1
-rw------- 1 m m    389794 Aug 17 20:24 log.18722183._016981.job.log.tgz.1
-rw------- 1 m m       391 Aug 17 20:25 output.list
-rw------- 1 m m      2921 Aug 16 18:39 pandaJobData.out
drwx------ 3 m m      4096 Aug  7 12:02 pilot2
-rw-r--r-- 1 m m    253018 Aug 16 18:27 pilot2.tar.gz
-rw------- 1 m m     10964 Aug 17 20:25 pilotlog.txt
-rw-r--r-- 1 m m      4468 Aug 16 18:36 queuedata.json
-rw-rw-r-- 1 m m       815 Aug 17 01:36 RTE.tar.gz
-rwxr-xr-x 1 m m      8466 Aug 17 01:36 run_atlas
-rwx------ 1 m m     12641 Aug 16 18:39 runpilot2-wrapper.sh
-rw-rw-r-- 1 m m       692 Aug 17 20:25 runtime_log
-rw-rw-r-- 1 m m      7801 Aug 17 20:25 runtime_log.err
-rw------- 1 m m       248 Aug 17 01:36 setup.sh.local
drwxrwx--x 2 m m      4096 Aug 17 20:25 shared
-rw-rw-r-- 1 m m      8659 Aug 17 01:36 start_atlas.sh
-rw-rw-r-- 1 m m     18999 Aug 17 20:25 stderr.txt
-rw-rw-r-- 1 m m       107 Aug 17 01:36 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r-- 1 m m        28 Aug 17 20:24 wrapper_checkpoint.txt

2019-08-17 20:25:10,997: running start_atlas return value is 0
2019-08-17 20:25:10,997: Parent exit 0
2019-08-17 20:25:10,998: child process exit 0
20:25:11 (31379): run_atlas exited; CPU time 65794.015484
20:25:11 (31379): called boinc_finish(0)

</stderr_txt>
]]>

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