Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
08:00:37 (17875): wrapper (7.7.26015): starting
08:00:37 (17875): wrapper: running run_atlas (--nthreads 4)
2019-08-17 08:00:37,283: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 08:00:37,283: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-17 08:00:37,284: THREADS=4

2019-08-17 08:00:37,286: Checking for CVMFS
2019-08-17 08:00:38,996: CVMFS is installed
2019-08-17 08:00:39,000: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-17 08:00:39,000: This is not SLC6, need to run with Singularity....
2019-08-17 08:00:39,000: Checking Singularity...
2019-08-17 08:00:39,003: Singularity is not installed, using version from CVMFS
2019-08-17 08:00:39,003: Testing the function of Singularity...
2019-08-17 08:00:39,004: 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 08:00:39,283: Singularity Works...
2019-08-17 08:00:39,283: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-17 08:00:39,853: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-17 08:00:39,854: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-17 08:00:39,854: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-17 08:00:39,854: export ATHENA_PROC_NUMBER=4;
2019-08-17 08:00:39,879: start atlas job with PandaID=4448403219
2019-08-17 08:00:39,879: 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
2019-08-17 12:31:35,280: running cmd return value is 0
2019-08-17 12:31:35,283: Moving ./HITS.18722495._009913.pool.root.1 to shared/HITS.pool.root.1
2019-08-17 12:31:35,283: *****************The last 100 lines of the pilot log******************
2019-08-17 12:31:35,292: 2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4448403219
2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722495
2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-17 10:30:45,894 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 62042 s
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 24576
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 24576
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 10:30:45,895 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 10:30:45,896 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4448403219 has completed
2019-08-17 10:30:45,896 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 10:30:45,902 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4448403219
2019-08-17 10:30:46,908 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [24576]
2019-08-17 10:30:46,908 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 24576
2019-08-17 10:30:46,908 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 10:30:47,913 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 10:30:47,914 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=24576
2019-08-17 10:30:47,964 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [24576] (in reverse order)
2019-08-17 10:30:48,007 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 10:30:48,007 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 10:30:48,007 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 10:30:48,007 | 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 10:30:48,518 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 10:30:58,550 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 10:30:58,550 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-17 10:30:58,599 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35019292672 B)
2019-08-17 10:30:58,600 | 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 10:30:58,600 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 10:30:58,644 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 10:30:58,725 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 10:30:58,725 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 10:30:58,781 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 10:30:58,846 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 10:30:58,859 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 10:30:58,939 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-17 10:30:58,940 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job, started 140288111752960)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(monitor, started 140287716353792)>, <ExcThread(validate_pre, started 140287707961088)>, <ExcThread(copytool_out, started 140288069789440)>, <ExcThread(payload, started 140288078182144)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(validate_post, started 140287682782976)>, <ExcThread(failed_post, started 140287112374016)>, <ExcThread(create_data_payload, started 140288086574848)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:30:59,303 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 10:30:59,306 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-17 10:30:59,306 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job, started 140288111752960)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(validate_pre, started 140287707961088)>, <ExcThread(copytool_out, started 140288069789440)>, <ExcThread(payload, started 140288078182144)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(validate_post, started 140287682782976)>, <ExcThread(failed_post, started 140287112374016)>, <ExcThread(create_data_payload, started 140288086574848)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:30:59,313 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 10:30:59,328 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 10:30:59,328 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 10:30:59,339 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 10:30:59,339 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 10:30:59,407 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-17 10:30:59,407 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(validate_pre, started 140287707961088)>, <ExcThread(copytool_out, started 140288069789440)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(validate_post, started 140287682782976)>, <ExcThread(failed_post, started 140287112374016)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:30:59,421 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 10:30:59,627 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 10:30:59,645 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 10:30:59,710 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-17 10:30:59,710 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(validate_post, started 140287682782976)>, <ExcThread(failed_post, started 140287112374016)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:30:59,987 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 10:31:00,012 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 10:31:00,012 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(failed_post, started 140287112374016)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:31:00,101 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 10:31:00,113 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 10:31:00,113 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(queue_monitoring, started 140287691175680)>, <ExcThread(queue_monitor, started 140287674390272)>]
2019-08-17 10:31:00,364 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 10:31:00,365 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 10:31:00,415 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 10:31:00,416 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>, <ExcThread(queue_monitoring, started 140287691175680)>]
2019-08-17 10:31:02,422 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 10:31:02,429 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 10:31:02,429 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140288328025856)>, <ExcThread(job_monitor, started 140287699568384)>]
2019-08-17 10:31:34,809 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-17 10:31:34,809 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 10:31:34,851 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 10:31:34,852 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 10:31:34,852 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 10:31:35 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 10:31:35 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 10:31:35 UTC [wrapper] Pilot exit status: 0
2019-08-17 10:31:35 UTC [wrapper] STATUSCODE: 0
2019-08-17 10:31:35 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 17 08:00 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

2019-08-17 10:31:35 UTC [wrapper] Test setup, not cleaning
2019-08-17 10:31:35 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 10:31:35 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 10:31:35 UTC [wrapper] wrapper wrapperexiting ec=0, duration=16255
2019-08-17 10:31:35 UTC [wrapper] apfmon messages muted
2019-08-17 12:31:35,296: ***************diag file************
2019-08-17 12:31:35,296: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=16255.03s
KernelTime=435.18s
UserTime=61806.16s
CPUUsage=382%
MaxResidentMemory=1945344kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=470663
MinorPageFaults=19257506
Swaps=0
ForcedSwitches=7105188
WaitSwitches=10027052
Inputs=113686768
Outputs=934824
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-17 12:31:35,307: ******************************WorkDir***********************
2019-08-17 12:31:35,308: total 245812
drwxrwx--x. 6 grid grid      4096 Aug 17 12:31 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       519 Aug 17 12:31 6dRMDmLGtIvnShfckohDCDFpABFKDmABFKDmdabKDmABFKDmQNorqn.diag
-rw-------. 1 grid grid   7417847 Aug 17 08:00 agis_ddmendpoints.json
-rw-------. 1 grid grid   4399560 Aug 17 08:00 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 17 08:00 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 17 08:00 APPS
-rw-------. 1 grid grid       538 Aug 17 08:00 .asetup
-rw-------. 1 grid grid       826 Aug 17 08:01 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 17 08:00 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 17 12:31 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 17 12:22 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 237537444 Aug 17 08:00 EVNT.18605790._000178.pool.root.1
-rw-------. 1 grid grid     69544 Aug 17 12:30 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 17 08:00 init_data.xml
-rw-rw-r--. 1 grid grid    261630 Aug 17 08:00 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 17 08:00 job.xml
-rw-------. 1 grid grid    758458 Aug 17 12:31 log.18722495._009913.job.log.1
-rw-------. 1 grid grid    845590 Aug 17 12:30 log.18722495._009913.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 17 12:31 output.list
-rw-------. 1 grid grid      2949 Aug 16 17:24 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 16 17:23 pilot2.tar.gz
-rw-------. 1 grid grid     10109 Aug 17 12:31 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 16 17:22 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 17 08:00 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 17 08:00 run_atlas
-rwx------. 1 grid grid     12641 Aug 16 17:24 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 17 12:31 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 17 12:31 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 17 12:31 shared
-rw-rw-r--. 1 grid grid      8688 Aug 17 08:00 start_atlas.sh
-rw-rw-r--. 1 grid grid     18717 Aug 17 12:31 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 17 08:00 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 17 12:31 wrapper_checkpoint.txt

2019-08-17 12:31:35,308: running start_atlas return value is 0
2019-08-17 12:31:35,308: Parent exit 0
2019-08-17 12:31:35,310: child process exit 0
12:31:35 (17875): run_atlas exited; CPU time 61806.551079
12:31:35 (17875): called boinc_finish(0)

</stderr_txt>
]]>

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