Stderr output

<core_client_version>7.12.0</core_client_version>
<![CDATA[
<stderr_txt>
07:38:52 (3368): wrapper (7.7.26015): starting
07:38:52 (3368): wrapper: running run_atlas (--nthreads 2)
2019-08-17 07:38:52,449: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 07:38:52,458: sys.argv = ['run_atlas', '--nthreads', '2']
2019-08-17 07:38:52,459: THREADS=2

2019-08-17 07:38:52,460: Checking for CVMFS
2019-08-17 07:39:07,432: CVMFS is installed
2019-08-17 07:39:07,435: OS:cat: /etc/redhat-release: No such file or directory
2019-08-17 07:39:07,435: This is not SLC6, need to run with Singularity....
2019-08-17 07:39:07,435: Checking Singularity...
2019-08-17 07:39:07,436: Singularity is not installed, using version from CVMFS
2019-08-17 07:39:07,436: Testing the function of Singularity...
2019-08-17 07:39:07,437: 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
2019-08-17 07:39:11,898: Singularity Works...
2019-08-17 07:39:11,899: copy /var/lib/boinc-client/slots/0/shared/start_atlas.sh
2019-08-17 07:39:11,899: copy /var/lib/boinc-client/slots/0/shared/input.tar.gz
2019-08-17 07:39:11,899: copy /var/lib/boinc-client/slots/0/shared/RTE.tar.gz
2019-08-17 07:39:11,900: copy /var/lib/boinc-client/slots/0/shared/ATLAS.root_0
2019-08-17 07:39:12,628: export ATHENA_PROC_NUMBER=2;
2019-08-17 07:39:13,983: start atlas job with PandaID=4449249163
2019-08-17 07:39:13,983: cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/0 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-08-17 21:11:17,635: running cmd return value is 0
2019-08-17 21:11:17,637: Moving ./HITS.18722261._013777.pool.root.1 to shared/HITS.pool.root.1
2019-08-17 21:11:17,637: *****************The last 100 lines of the pilot log******************
2019-08-17 21:11:17,639: 2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4449249163
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722261
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 19:10:50,053 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 95060 s
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 10591
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 10591
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 2
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4449249163 has completed
2019-08-17 19:10:50,054 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 19:10:50,057 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc-client/slots/0/PanDA_Pilot-4449249163
2019-08-17 19:10:51,063 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [10591]
2019-08-17 19:10:51,063 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 10591
2019-08-17 19:10:51,063 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 19:10:52,066 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 19:10:52,066 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=10591
2019-08-17 19:10:52,106 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [10591] (in reverse order)
2019-08-17 19:10:52,137 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 19:10:52,137 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 19:10:52,137 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 19:10:52,137 | 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 19:10:52,653 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 19:11:03,193 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 19:11:03,193 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc-client/slots/0
2019-08-17 19:11:03,216 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (12986613760 B)
2019-08-17 19:11:03,217 | 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 19:11:03,217 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 19:11:03,237 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 19:11:03,256 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 19:11:03,376 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-17 19:11:03,376 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job, started 140198754703104)>, <ExcThread(payload, started 140198637713152)>, <ExcThread(monitor, started 140198251845376)>, <ExcThread(create_data_payload, started 140198646105856)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(execute_payloads, started 140197664651008)>, <ExcThread(validate_pre, started 140198260238080)>, <ExcThread(validate, started 140198671283968)>, <ExcThread(queue_monitoring, started 140198629320448)>, <ExcThread(copytool_in, started 140198620927744)>, <ExcThread(data, started 140198662891264)>, <ExcThread(queue_monitor, started 140198226667264)>]
2019-08-17 19:11:03,538 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 19:11:03,538 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 19:11:03,623 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 19:11:03,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-17 19:11:03,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job, started 140198754703104)>, <ExcThread(payload, started 140198637713152)>, <ExcThread(create_data_payload, started 140198646105856)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(execute_payloads, started 140197664651008)>, <ExcThread(validate_pre, started 140198260238080)>, <ExcThread(validate, started 140198671283968)>, <ExcThread(queue_monitoring, started 140198629320448)>, <ExcThread(copytool_in, started 140198620927744)>, <ExcThread(queue_monitor, started 140198226667264)>]
2019-08-17 19:11:03,867 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 19:11:04,006 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-17 19:11:04,007 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job, started 140198754703104)>, <ExcThread(payload, started 140198637713152)>, <ExcThread(create_data_payload, started 140198646105856)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(validate_pre, started 140198260238080)>, <ExcThread(validate, started 140198671283968)>, <ExcThread(queue_monitoring, started 140198629320448)>, <ExcThread(copytool_in, started 140198620927744)>, <ExcThread(queue_monitor, started 140198226667264)>]
2019-08-17 19:11:04,015 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 19:11:04,015 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 19:11:04,130 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 19:11:04,132 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 19:11:04,136 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 19:11:04,156 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 19:11:04,215 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-17 19:11:04,215 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job, started 140198754703104)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(queue_monitoring, started 140198629320448)>, <ExcThread(queue_monitor, started 140198226667264)>]
2019-08-17 19:11:04,366 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 19:11:04,366 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 19:11:04,371 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 19:11:04,371 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(queue_monitoring, started 140198629320448)>, <ExcThread(queue_monitor, started 140198226667264)>]
2019-08-17 19:11:04,563 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 19:11:04,636 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 19:11:04,636 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 19:11:04,658 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 19:11:04,686 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 19:11:04,686 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(copytool_out, started 140198654498560)>, <ExcThread(queue_monitoring, started 140198629320448)>]
2019-08-17 19:11:05,564 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 19:11:05,638 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 19:11:05,638 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job_monitor, started 140198243452672)>, <ExcThread(queue_monitoring, started 140198629320448)>]
2019-08-17 19:11:07,663 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 19:11:07,700 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 19:11:07,700 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140198970976000)>, <ExcThread(job_monitor, started 140198243452672)>]
2019-08-17 19:11:17,127 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 63 s)
2019-08-17 19:11:17,127 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 19:11:17,223 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 19:11:17,223 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 19:11:17,224 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 19:11:17 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 19:11:17 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 19:11:17 UTC [wrapper] Pilot exit status: 0
2019-08-17 19:11:17 UTC [wrapper] STATUSCODE: 0
2019-08-17 19:11:17 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------  1 boinc boinc 11357 jul 25 16:38 LICENSE
drwx------ 14 boinc boinc  4096 aug 17 07:40 pilot
-rwx------  1 boinc boinc 20463 jul 25 16:38 pilot.py
-rw-------  1 boinc boinc     8 aug  7 13:02 PILOTVERSION
-rw-------  1 boinc boinc  2251 jul 25 16:38 README.md
-rw-------  1 boinc boinc   221 jul 25 16:38 TODO.md

2019-08-17 19:11:17 UTC [wrapper] Test setup, not cleaning
2019-08-17 19:11:17 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 19:11:17 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 19:11:17 UTC [wrapper] wrapper wrapperexiting ec=0, duration=48719
2019-08-17 19:11:17 UTC [wrapper] apfmon messages muted
2019-08-17 21:11:17,652: ***************diag file************
2019-08-17 21:11:17,652: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=48718.92s
KernelTime=882.72s
UserTime=94679.06s
CPUUsage=196%
MaxResidentMemory=2029488kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=1185446
MinorPageFaults=19977926
Swaps=0
ForcedSwitches=5621046
WaitSwitches=24649511
Inputs=269386832
Outputs=898072
SocketReceived=0
SocketSent=0
Signals=0

nodename=Crystal_Pellet@LinAH125
exitcode=0
2019-08-17 21:11:17,656: ******************************WorkDir***********************
2019-08-17 21:11:17,656: total 277764
drwxrwx--x 6 boinc boinc      4096 aug 17 21:11 .
drwxrwx--x 3 boinc boinc      4096 aug 17 07:38 ..
-rw------- 1 boinc boinc   7417847 aug 17 07:41 agis_ddmendpoints.json
-rw------- 1 boinc boinc   4399560 aug 17 07:41 agis_schedconf.cvmfs.json
drwx------ 2 boinc boinc      4096 aug 17 07:39 .alrb
drwxr-xr-x 3 boinc boinc      4096 aug 17 07:39 APPS
-rw------- 1 boinc boinc       549 aug 17 07:40 .asetup
-rw------- 1 boinc boinc       826 aug 17 07:42 .asetup.save
-rw-r--r-- 1 boinc boinc         0 aug 17 07:38 boinc_lockfile
-rw-r--r-- 1 boinc boinc      8192 aug 17 21:11 boinc_mmap_file
-rw-r--r-- 1 boinc boinc       537 aug 17 21:05 boinc_task_state.xml
-rw-r--r-- 1 boinc boinc 268805505 aug 17 07:39 EVNT.18605752._000265.pool.root.1
-rw------- 1 boinc boinc     82023 aug 17 21:10 heartbeat.json
-rw-r--r-- 1 boinc boinc      5854 aug 17 07:38 init_data.xml
-rw-r--r-- 1 boinc boinc    261615 aug 17 07:39 input.tar.gz
-rw-r--r-- 1 boinc boinc       112 aug 17 07:38 job.xml
-rw------- 1 boinc boinc   2309906 aug 17 21:11 log.18722261._013777.job.log.1
-rw------- 1 boinc boinc    701323 aug 17 21:10 log.18722261._013777.job.log.tgz.1
-rw------- 1 boinc boinc       511 aug 17 21:11 MtTKDm2Z6IvnShfckohDCDFpABFKDmABFKDm7ixKDmABFKDmPDT3gn.diag
-rw------- 1 boinc boinc       391 aug 17 21:11 output.list
-rw------- 1 boinc boinc      2921 aug 17 07:37 pandaJobData.out
drwx------ 3 boinc boinc      4096 aug  7 13:02 pilot2
-rw-r--r-- 1 boinc boinc    253018 aug 17 07:34 pilot2.tar.gz
-rw------- 1 boinc boinc     10402 aug 17 21:11 pilotlog.txt
-rw-r--r-- 1 boinc boinc      4468 aug 17 07:36 queuedata.json
-rw-r--r-- 1 boinc boinc       815 aug 17 07:39 RTE.tar.gz
-rwxr-xr-x 1 boinc boinc      8466 aug 17 07:38 run_atlas
-rwx------ 1 boinc boinc     12641 aug 17 07:37 runpilot2-wrapper.sh
-rw-r--r-- 1 boinc boinc       692 aug 17 21:11 runtime_log
-rw-r--r-- 1 boinc boinc      7057 aug 17 21:11 runtime_log.err
drwxrwx--x 2 boinc boinc      4096 aug 17 21:11 shared
-rw-r--r-- 1 boinc boinc      8688 aug 17 07:39 start_atlas.sh
-rw-r--r-- 1 boinc boinc     19085 aug 17 21:11 stderr.txt
-rw-r--r-- 1 boinc boinc       107 aug 17 07:38 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r-- 1 boinc boinc        28 aug 17 21:11 wrapper_checkpoint.txt

2019-08-17 21:11:17,657: running start_atlas return value is 0
2019-08-17 21:11:17,657: Parent exit 0
2019-08-17 21:11:17,657: child process exit 0
21:11:18 (3368): run_atlas exited; CPU time 94679.890221
21:11:18 (3368): called boinc_finish(0)

</stderr_txt>
]]>

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