Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:43:05 (10617): wrapper (7.7.26015): starting
14:43:05 (10617): wrapper: running run_atlas (--nthreads 4)
2019-08-22 14:43:05,539: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-22 14:43:05,539: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-22 14:43:05,540: THREADS=4

2019-08-22 14:43:05,542: Checking for CVMFS
2019-08-22 14:43:06,893: CVMFS is installed
2019-08-22 14:43:06,897: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-22 14:43:06,897: This is not SLC6, need to run with Singularity....
2019-08-22 14:43:06,897: Checking Singularity...
2019-08-22 14:43:06,900: Singularity is not installed, using version from CVMFS
2019-08-22 14:43:06,900: Testing the function of Singularity...
2019-08-22 14:43:06,900: 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
2019-08-22 14:43:07,139: Singularity Works...
2019-08-22 14:43:07,139: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-22 14:43:07,569: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-22 14:43:07,570: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-22 14:43:07,571: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-22 14:43:07,571: export ATHENA_PROC_NUMBER=4;
2019-08-22 14:43:07,594: start atlas job with PandaID=4453793567
2019-08-22 14:43:07,594: 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
2019-08-22 19:23:41,394: running cmd return value is 0
2019-08-22 19:23:41,398: Moving ./HITS.18722495._012890.pool.root.1 to shared/HITS.pool.root.1
2019-08-22 19:23:41,399: *****************The last 100 lines of the pilot log******************
2019-08-22 19:23:41,406: 2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4453793567
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722495
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-22 17:22:59,116 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 63744 s
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 17421
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 17421
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4453793567 has completed
2019-08-22 17:22:59,117 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-22 17:22:59,128 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4453793567
2019-08-22 17:23:00,131 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [17421]
2019-08-22 17:23:00,132 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 17421
2019-08-22 17:23:00,132 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-22 17:23:01,134 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-22 17:23:01,134 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=17421
2019-08-22 17:23:01,187 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [17421] (in reverse order)
2019-08-22 17:23:01,227 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-22 17:23:01,227 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-22 17:23:01,228 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-22 17:23:01,228 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-22 17:23:01,738 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-22 17:23:11,786 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-22 17:23:11,787 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-22 17:23:11,826 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36419141632 B)
2019-08-22 17:23:11,827 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-22 17:23:11,827 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-22 17:23:11,865 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-22 17:23:11,882 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-22 17:23:11,882 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job, started 140379870254848)>, <ExcThread(queue_monitor, started 140378724366080)>, <ExcThread(data, started 140379853469440)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(validate, started 140379861862144)>, <ExcThread(copytool_in, started 140379303167744)>, <ExcThread(execute_payloads, started 140379277989632)>, <ExcThread(validate_pre, started 140379811505920)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(validate_post, started 140379319953152)>, <ExcThread(failed_post, started 140379294775040)>, <ExcThread(copytool_out, started 140379845076736)>, <ExcThread(create_data_payload, started 140379836684032)>, <ExcThread(payload, started 140379828291328)>]
2019-08-22 17:23:11,935 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-22 17:23:11,935 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-22 17:23:12,143 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-22 17:23:12,184 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-22 17:23:12,184 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job, started 140379870254848)>, <ExcThread(queue_monitor, started 140378724366080)>, <ExcThread(data, started 140379853469440)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(validate, started 140379861862144)>, <ExcThread(copytool_in, started 140379303167744)>, <ExcThread(execute_payloads, started 140379277989632)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(validate_post, started 140379319953152)>, <ExcThread(failed_post, started 140379294775040)>, <ExcThread(copytool_out, started 140379845076736)>, <ExcThread(create_data_payload, started 140379836684032)>]
2019-08-22 17:23:12,435 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-22 17:23:12,486 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-22 17:23:12,486 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job, started 140379870254848)>, <ExcThread(queue_monitor, started 140378724366080)>, <ExcThread(data, started 140379853469440)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(validate, started 140379861862144)>, <ExcThread(execute_payloads, started 140379277989632)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(validate_post, started 140379319953152)>, <ExcThread(failed_post, started 140379294775040)>, <ExcThread(copytool_out, started 140379845076736)>, <ExcThread(create_data_payload, started 140379836684032)>]
2019-08-22 17:23:12,575 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-22 17:23:12,575 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-22 17:23:12,662 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-22 17:23:12,672 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-22 17:23:12,680 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-22 17:23:12,687 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-22 17:23:12,687 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job, started 140379870254848)>, <ExcThread(queue_monitor, started 140378724366080)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(validate, started 140379861862144)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(failed_post, started 140379294775040)>, <ExcThread(copytool_out, started 140379845076736)>, <ExcThread(create_data_payload, started 140379836684032)>]
2019-08-22 17:23:12,722 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-22 17:23:12,911 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-22 17:23:12,974 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-22 17:23:12,981 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-22 17:23:12,981 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-22 17:23:12,987 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-22 17:23:12,989 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-22 17:23:12,990 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(queue_monitor, started 140378724366080)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(copytool_out, started 140379845076736)>]
2019-08-22 17:23:13,594 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-22 17:23:13,594 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-22 17:23:13,594 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-22 17:23:13,595 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(queue_monitoring, started 140379819898624)>, <ExcThread(copytool_out, started 140379845076736)>]
2019-08-22 17:23:13,722 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-22 17:23:13,796 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-22 17:23:13,797 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job_monitor, started 140379286382336)>, <ExcThread(queue_monitoring, started 140379819898624)>]
2019-08-22 17:23:15,681 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-22 17:23:15,710 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-22 17:23:15,710 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140380086527744)>, <ExcThread(job_monitor, started 140379286382336)>]
2019-08-22 17:23:40,951 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-22 17:23:40,952 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-22 17:23:40,984 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-22 17:23:40,985 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-22 17:23:40,985 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-22 17:23:41 UTC [wrapper] ==== pilot stdout END ====
2019-08-22 17:23:41 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-22 17:23:41 UTC [wrapper] Pilot exit status: 0
2019-08-22 17:23:41 UTC [wrapper] STATUSCODE: 0
2019-08-22 17:23:41 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 22 14:43 pilot
-rwx------.  1 grid grid 20628 Aug 19 14:00 pilot.py
-rw-------.  1 grid grid     9 Aug 19 14:00 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-22 17:23:41 UTC [wrapper] Test setup, not cleaning
2019-08-22 17:23:41 UTC [wrapper] ==== wrapper stdout END ====
2019-08-22 17:23:41 UTC [wrapper] ==== wrapper stderr END ====
2019-08-22 17:23:41 UTC [wrapper] wrapper wrapperexiting ec=0, duration=16834
2019-08-22 17:23:41 UTC [wrapper] apfmon messages muted
2019-08-22 19:23:41,410: ***************diag file************
2019-08-22 19:23:41,410: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=16833.41s
KernelTime=444.24s
UserTime=63508.97s
CPUUsage=379%
MaxResidentMemory=1945292kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=484023
MinorPageFaults=19660058
Swaps=0
ForcedSwitches=7309472
WaitSwitches=10164220
Inputs=116795112
Outputs=955504
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-22 19:23:41,420: ******************************WorkDir***********************
2019-08-22 19:23:41,420: total 246700
drwxrwx--x. 6 grid grid      4096 Aug 22 19:23 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7460931 Aug 22 14:43 agis_ddmendpoints.json
-rw-------. 1 grid grid   4335799 Aug 22 14:43 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 22 14:43 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 22 14:43 APPS
-rw-------. 1 grid grid       538 Aug 22 14:43 .asetup
-rw-------. 1 grid grid       826 Aug 22 14:44 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 22 14:43 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 22 19:23 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 22 19:15 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 238408795 Aug 22 14:43 EVNT.18605790._000239.pool.root.1
-rw-------. 1 grid grid     86856 Aug 22 19:22 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 22 14:43 init_data.xml
-rw-rw-r--. 1 grid grid    263689 Aug 22 14:43 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 22 14:43 job.xml
-rw-------. 1 grid grid    778039 Aug 22 19:23 log.18722495._012890.job.log.1
-rw-------. 1 grid grid    857107 Aug 22 19:22 log.18722495._012890.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 22 19:23 output.list
-rw-------. 1 grid grid      2950 Aug 20 17:53 pandaJobData.out
drwx------. 3 grid grid       174 Aug 19 14:00 pilot2
-rw-r--r--. 1 grid grid    255033 Aug 20 17:32 pilot2.tar.gz
-rw-------. 1 grid grid     10709 Aug 22 19:23 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 20 17:50 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 22 14:43 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 22 14:43 run_atlas
-rwx------. 1 grid grid     12641 Aug 20 17:53 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 22 19:23 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 22 19:23 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 22 19:23 shared
-rw-rw-r--. 1 grid grid      8688 Aug 22 14:43 start_atlas.sh
-rw-rw-r--. 1 grid grid     19317 Aug 22 19:23 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 22 14:43 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 22 19:23 wrapper_checkpoint.txt
-rw-------. 1 grid grid       519 Aug 22 19:23 zyrMDmtcLKvnShfckohDCDFpABFKDmABFKDmxuzMDmABFKDmr1GCmm.diag

2019-08-22 19:23:41,421: running start_atlas return value is 0
2019-08-22 19:23:41,421: Parent exit 0
2019-08-22 19:23:41,423: child process exit 0
19:23:41 (10617): run_atlas exited; CPU time 63509.371167
19:23:41 (10617): called boinc_finish(0)

</stderr_txt>
]]>

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