Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
00:05:21 (31626): wrapper (7.7.26015): starting
00:05:21 (31626): wrapper: running run_atlas (--nthreads 4)
2019-08-18 00:05:21,595: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-18 00:05:21,595: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-18 00:05:21,596: THREADS=4

2019-08-18 00:05:21,597: Checking for CVMFS
2019-08-18 00:05:23,329: CVMFS is installed
2019-08-18 00:05:23,333: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-18 00:05:23,333: This is not SLC6, need to run with Singularity....
2019-08-18 00:05:23,333: Checking Singularity...
2019-08-18 00:05:23,336: Singularity is not installed, using version from CVMFS
2019-08-18 00:05:23,336: Testing the function of Singularity...
2019-08-18 00:05:23,336: 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
2019-08-18 00:05:23,537: Singularity Works...
2019-08-18 00:05:23,537: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-18 00:05:23,967: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-18 00:05:23,969: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-18 00:05:23,969: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-18 00:05:23,969: export ATHENA_PROC_NUMBER=4;
2019-08-18 00:05:23,992: start atlas job with PandaID=4448525072
2019-08-18 00:05:23,992: 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
2019-08-18 04:41:41,657: running cmd return value is 0
2019-08-18 04:41:41,661: Moving ./HITS.18722495._010146.pool.root.1 to shared/HITS.pool.root.1
2019-08-18 04:41:41,662: *****************The last 100 lines of the pilot log******************
2019-08-18 04:41:41,671: 2019-08-18 02:41:07,327 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4448525072
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722495
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-18 02:41:07,328 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 63446 s
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 6000
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 6000
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4448525072 has completed
2019-08-18 02:41:07,329 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-18 02:41:07,336 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4448525072
2019-08-18 02:41:08,338 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [6000]
2019-08-18 02:41:08,339 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 6000
2019-08-18 02:41:08,339 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-18 02:41:09,339 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-18 02:41:09,339 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=6000
2019-08-18 02:41:09,391 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [6000] (in reverse order)
2019-08-18 02:41:09,434 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-18 02:41:09,434 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-18 02:41:09,434 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-18 02:41:09,434 | 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 02:41:09,944 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-18 02:41:19,991 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-18 02:41:19,992 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-18 02:41:20,048 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35691429888 B)
2019-08-18 02:41:20,048 | 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 02:41:20,048 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-18 02:41:20,054 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-18 02:41:20,070 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-18 02:41:20,070 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-18 02:41:20,070 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-18 02:41:20,190 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-18 02:41:20,273 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-18 02:41:20,273 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(data, started 140334999750400)>, <ExcThread(validate_post, started 140334096971520)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(queue_monitor, started 140334088578816)>, <ExcThread(payload, started 140334633842432)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(failed_post, started 140334080186112)>, <ExcThread(execute_payloads, started 140334071793408)>, <ExcThread(validate_pre, started 140334617057024)>, <ExcThread(create_data_payload, started 140334991357696)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:20,389 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-18 02:41:20,575 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-18 02:41:20,575 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(data, started 140334999750400)>, <ExcThread(validate_post, started 140334096971520)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(queue_monitor, started 140334088578816)>, <ExcThread(payload, started 140334633842432)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(execute_payloads, started 140334071793408)>, <ExcThread(validate_pre, started 140334617057024)>, <ExcThread(create_data_payload, started 140334991357696)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:20,592 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-18 02:41:20,769 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-18 02:41:20,856 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-18 02:41:20,873 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-18 02:41:20,873 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-18 02:41:20,877 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-18 02:41:20,877 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(data, started 140334999750400)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(queue_monitor, started 140334088578816)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(execute_payloads, started 140334071793408)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:20,883 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-18 02:41:20,884 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-18 02:41:20,978 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-18 02:41:20,979 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(queue_monitor, started 140334088578816)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(execute_payloads, started 140334071793408)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:21,190 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-18 02:41:21,363 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-18 02:41:21,382 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-18 02:41:21,382 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(queue_monitor, started 140334088578816)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:21,455 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-18 02:41:21,821 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-18 02:41:21,821 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-18 02:41:21,886 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-18 02:41:21,886 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(job_monitor, started 140334583486208)>, <ExcThread(copytool_out, started 140334982964992)>]
2019-08-18 02:41:22,191 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-18 02:41:22,289 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-18 02:41:22,289 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(queue_monitoring, started 140334625449728)>, <ExcThread(job_monitor, started 140334583486208)>]
2019-08-18 02:41:24,457 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-18 02:41:24,505 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-18 02:41:24,506 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140335232808704)>, <ExcThread(job_monitor, started 140334583486208)>]
2019-08-18 02:41:41,151 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-18 02:41:41,151 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-18 02:41:41,219 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-18 02:41:41,220 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-18 02:41:41,220 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-18 02:41:41 UTC [wrapper] ==== pilot stdout END ====
2019-08-18 02:41:41 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-18 02:41:41 UTC [wrapper] Pilot exit status: 0
2019-08-18 02:41:41 UTC [wrapper] STATUSCODE: 0
2019-08-18 02:41:41 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 18 00:05 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

2019-08-18 02:41:41 UTC [wrapper] Test setup, not cleaning
2019-08-18 02:41:41 UTC [wrapper] ==== wrapper stdout END ====
2019-08-18 02:41:41 UTC [wrapper] ==== wrapper stderr END ====
2019-08-18 02:41:41 UTC [wrapper] wrapper wrapperexiting ec=0, duration=16577
2019-08-18 02:41:41 UTC [wrapper] apfmon messages muted
2019-08-18 04:41:41,675: ***************diag file************
2019-08-18 04:41:41,675: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=16577.28s
KernelTime=440.93s
UserTime=63216.74s
CPUUsage=384%
MaxResidentMemory=1923188kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=479716
MinorPageFaults=19547759
Swaps=0
ForcedSwitches=7284717
WaitSwitches=10236018
Inputs=115847296
Outputs=948296
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-18 04:41:41,687: ******************************WorkDir***********************
2019-08-18 04:41:41,687: total 247744
drwxrwx--x. 6 grid grid      4096 Aug 18 04:41 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       519 Aug 18 04:41 61PODmHywIvnShfckohDCDFpABFKDmABFKDmqbhKDmABFKDmw6UMGn.diag
-rw-------. 1 grid grid   7417898 Aug 18 00:05 agis_ddmendpoints.json
-rw-------. 1 grid grid   4400484 Aug 18 00:05 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 18 00:05 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 18 00:05 APPS
-rw-------. 1 grid grid       538 Aug 18 00:05 .asetup
-rw-------. 1 grid grid       826 Aug 18 00:06 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 18 00:05 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 18 04:41 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 18 04:32 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 239476647 Aug 18 00:05 EVNT.18605790._000190.pool.root.1
-rw-------. 1 grid grid     77282 Aug 18 04:41 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 18 00:05 init_data.xml
-rw-rw-r--. 1 grid grid    261611 Aug 18 00:05 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 18 00:05 job.xml
-rw-------. 1 grid grid    782985 Aug 18 04:41 log.18722495._010146.job.log.1
-rw-------. 1 grid grid    849922 Aug 18 04:40 log.18722495._010146.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 18 04:41 output.list
-rw-------. 1 grid grid      2948 Aug 16 21:21 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 16 20:30 pilot2.tar.gz
-rw-------. 1 grid grid     10073 Aug 18 04:41 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 16 21:21 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 18 00:05 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 18 00:05 run_atlas
-rwx------. 1 grid grid     12641 Aug 16 21:21 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 18 04:41 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 18 04:41 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 18 04:41 shared
-rw-rw-r--. 1 grid grid      8688 Aug 18 00:05 start_atlas.sh
-rw-rw-r--. 1 grid grid     18675 Aug 18 04:41 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 18 00:05 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 18 04:41 wrapper_checkpoint.txt

2019-08-18 04:41:41,687: running start_atlas return value is 0
2019-08-18 04:41:41,687: Parent exit 0
2019-08-18 04:41:41,689: child process exit 0
04:41:42 (31626): run_atlas exited; CPU time 63217.140872
04:41:42 (31626): called boinc_finish(0)

</stderr_txt>
]]>

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