Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
17:19:33 (3250): wrapper (7.7.26015): starting
17:19:33 (3250): wrapper: running run_atlas (--nthreads 4)
2019-08-19 17:19:33,936: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-19 17:19:33,936: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-19 17:19:33,937: THREADS=4

2019-08-19 17:19:33,938: Checking for CVMFS
2019-08-19 17:19:40,019: CVMFS is installed
2019-08-19 17:19:40,022: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-19 17:19:40,023: This is not SLC6, need to run with Singularity....
2019-08-19 17:19:40,023: Checking Singularity...
2019-08-19 17:19:40,026: Singularity is not installed, using version from CVMFS
2019-08-19 17:19:40,026: Testing the function of Singularity...
2019-08-19 17:19:40,026: 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
2019-08-19 17:19:40,232: Singularity Works...
2019-08-19 17:19:40,232: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-19 17:19:41,066: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-19 17:19:41,067: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-19 17:19:41,067: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-19 17:19:41,068: export ATHENA_PROC_NUMBER=4;
2019-08-19 17:19:41,095: start atlas job with PandaID=4452122331
2019-08-19 17:19:41,095: 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
2019-08-19 20:37:48,356: running cmd return value is 0
2019-08-19 20:37:48,360: Moving ./HITS.18722222._018367.pool.root.1 to shared/HITS.pool.root.1
2019-08-19 20:37:48,360: *****************The last 100 lines of the pilot log******************
2019-08-19 20:37:48,368: 2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4452122331
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722222
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-19 18:37:25,650 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 44763 s
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 9938
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 9938
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4452122331 has completed
2019-08-19 18:37:25,651 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-19 18:37:25,659 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4452122331
2019-08-19 18:37:26,664 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [9938]
2019-08-19 18:37:26,665 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 9938
2019-08-19 18:37:26,665 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-19 18:37:27,668 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-19 18:37:27,668 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=9938
2019-08-19 18:37:27,785 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [9938] (in reverse order)
2019-08-19 18:37:27,835 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-19 18:37:27,836 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-19 18:37:27,836 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-19 18:37:27,836 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-19 18:37:28,346 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-19 18:37:38,373 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-19 18:37:38,373 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-19 18:37:38,409 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34943795200 B)
2019-08-19 18:37:38,410 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-19 18:37:38,410 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-19 18:37:38,489 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-19 18:37:38,602 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-19 18:37:38,664 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-19 18:37:38,664 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-19 18:37:38,787 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-19 18:37:38,788 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job, started 140546264971008)>, <ExcThread(monitor, started 140545993193216)>, <ExcThread(validate_pre, started 140546001585920)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(create_data_payload, started 140546009978624)>, <ExcThread(validate_post, started 140545481500416)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(copytool_in, started 140545976407808)>, <ExcThread(queue_monitor, started 140545473107712)>, <ExcThread(payload, started 140546026764032)>, <ExcThread(execute_payloads, started 140545456322304)>, <ExcThread(validate, started 140546248185600)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:39,102 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-19 18:37:39,102 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-19 18:37:39,189 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-19 18:37:39,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job, started 140546264971008)>, <ExcThread(monitor, started 140545993193216)>, <ExcThread(validate_pre, started 140546001585920)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(create_data_payload, started 140546009978624)>, <ExcThread(validate_post, started 140545481500416)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(copytool_in, started 140545976407808)>, <ExcThread(queue_monitor, started 140545473107712)>, <ExcThread(execute_payloads, started 140545456322304)>, <ExcThread(validate, started 140546248185600)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:39,233 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-19 18:37:39,350 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-19 18:37:39,384 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-19 18:37:39,385 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-19 18:37:39,391 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-19 18:37:39,391 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job, started 140546264971008)>, <ExcThread(validate_pre, started 140546001585920)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(queue_monitor, started 140545473107712)>, <ExcThread(execute_payloads, started 140545456322304)>, <ExcThread(validate, started 140546248185600)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:39,417 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-19 18:37:39,417 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-19 18:37:39,465 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-19 18:37:39,492 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-19 18:37:39,493 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(validate_pre, started 140546001585920)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(queue_monitor, started 140545473107712)>, <ExcThread(execute_payloads, started 140545456322304)>, <ExcThread(validate, started 140546248185600)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:39,604 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-19 18:37:39,654 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-19 18:37:39,694 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-19 18:37:39,695 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(queue_monitor, started 140545473107712)>, <ExcThread(validate, started 140546248185600)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:39,722 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-19 18:37:39,754 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-19 18:37:39,754 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-19 18:37:39,796 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-19 18:37:39,796 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(queue_monitoring, started 140546018371328)>, <ExcThread(copytool_out, started 140546239792896)>]
2019-08-19 18:37:40,465 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-19 18:37:40,501 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-19 18:37:40,502 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job_monitor, started 140545489893120)>, <ExcThread(queue_monitoring, started 140546018371328)>]
2019-08-19 18:37:41,604 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-19 18:37:41,619 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-19 18:37:41,620 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140546481243904)>, <ExcThread(job_monitor, started 140545489893120)>]
2019-08-19 18:37:47,830 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-19 18:37:47,831 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-19 18:37:47,877 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-19 18:37:47,878 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-19 18:37:47,878 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-19 18:37:48 UTC [wrapper] ==== pilot stdout END ====
2019-08-19 18:37:48 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-19 18:37:48 UTC [wrapper] Pilot exit status: 0
2019-08-19 18:37:48 UTC [wrapper] STATUSCODE: 0
2019-08-19 18:37:48 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 19 17:19 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

2019-08-19 18:37:48 UTC [wrapper] Test setup, not cleaning
2019-08-19 18:37:48 UTC [wrapper] ==== wrapper stdout END ====
2019-08-19 18:37:48 UTC [wrapper] ==== wrapper stderr END ====
2019-08-19 18:37:48 UTC [wrapper] wrapper wrapperexiting ec=0, duration=11887
2019-08-19 18:37:48 UTC [wrapper] apfmon messages muted
2019-08-19 20:37:48,372: ***************diag file************
2019-08-19 20:37:48,373: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11886.85s
KernelTime=341.59s
UserTime=44596.23s
CPUUsage=378%
MaxResidentMemory=1944604kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=385584
MinorPageFaults=16442186
Swaps=0
ForcedSwitches=5218013
WaitSwitches=8002803
Inputs=93553688
Outputs=744112
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-19 20:37:48,389: ******************************WorkDir***********************
2019-08-19 20:37:48,389: total 268028
drwxrwx--x. 6 grid grid      4096 Aug 19 20:37 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7442625 Aug 19 17:19 agis_ddmendpoints.json
-rw-------. 1 grid grid   4371528 Aug 19 17:19 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 19 17:19 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 19 17:19 APPS
-rw-------. 1 grid grid       538 Aug 19 17:19 .asetup
-rw-------. 1 grid grid       826 Aug 19 17:20 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 19 17:19 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 19 20:37 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 19 20:29 boinc_task_state.xml
-rw-------. 1 grid grid       517 Aug 19 20:37 C4lNDmZ2fJvnShfckohDCDFpABFKDmABFKDmrptLDmABFKDmbHbQ9m.diag
-rw-rw-r--. 1 grid grid 260284886 Aug 19 17:19 EVNT.18605748._000432.pool.root.1
-rw-------. 1 grid grid    140291 Aug 19 20:37 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 19 17:19 init_data.xml
-rw-rw-r--. 1 grid grid    261618 Aug 19 17:19 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 19 17:19 job.xml
-rw-------. 1 grid grid    678943 Aug 19 20:37 log.18722222._018367.job.log.1
-rw-------. 1 grid grid    854561 Aug 19 20:37 log.18722222._018367.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 19 20:37 output.list
-rw-------. 1 grid grid      2922 Aug 18 21:29 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 18 20:34 pilot2.tar.gz
-rw-------. 1 grid grid     10512 Aug 19 20:37 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 18 21:25 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 19 17:19 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 19 17:19 run_atlas
-rwx------. 1 grid grid     12641 Aug 18 21:29 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 19 20:37 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 19 20:37 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 19 20:37 shared
-rw-rw-r--. 1 grid grid      8688 Aug 19 17:19 start_atlas.sh
-rw-rw-r--. 1 grid grid     19110 Aug 19 20:37 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 19 17:19 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 19 20:37 wrapper_checkpoint.txt

2019-08-19 20:37:48,390: running start_atlas return value is 0
2019-08-19 20:37:48,390: Parent exit 0
2019-08-19 20:37:48,392: child process exit 0
20:37:48 (3250): run_atlas exited; CPU time 44596.656567
20:37:48 (3250): called boinc_finish(0)

</stderr_txt>
]]>

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