Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
19:23:45 (11845): wrapper (7.7.26015): starting
19:23:45 (11845): wrapper: running run_atlas (--nthreads 4)
2019-08-22 19:23:45,912: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-22 19:23:45,912: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-22 19:23:45,913: THREADS=4

2019-08-22 19:23:45,914: Checking for CVMFS
2019-08-22 19:23:47,372: CVMFS is installed
2019-08-22 19:23:47,376: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-22 19:23:47,376: This is not SLC6, need to run with Singularity....
2019-08-22 19:23:47,376: Checking Singularity...
2019-08-22 19:23:47,379: Singularity is not installed, using version from CVMFS
2019-08-22 19:23:47,379: Testing the function of Singularity...
2019-08-22 19:23:47,379: 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 19:23:47,599: Singularity Works...
2019-08-22 19:23:47,599: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-22 19:23:47,964: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-22 19:23:47,965: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-22 19:23:47,965: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-22 19:23:47,965: export ATHENA_PROC_NUMBER=4;
2019-08-22 19:23:47,984: start atlas job with PandaID=4454236255
2019-08-22 19:23:47,984: 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 23:50:25,997: running cmd return value is 0
2019-08-22 23:50:26,001: Moving ./HITS.18722495._013396.pool.root.1 to shared/HITS.pool.root.1
2019-08-22 23:50:26,001: *****************The last 100 lines of the pilot log******************
2019-08-22 23:50:26,009: 2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4454236255
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722495
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 60298 s
2019-08-22 21:49:23,025 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 18644
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 18644
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4454236255 has completed
2019-08-22 21:49:23,026 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-22 21:49:23,036 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4454236255
2019-08-22 21:49:23,951 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-22 21:49:24,041 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [18644]
2019-08-22 21:49:24,041 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 18644
2019-08-22 21:49:24,041 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-22 21:49:25,043 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-22 21:49:25,043 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=18644
2019-08-22 21:49:25,091 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [18644] (in reverse order)
2019-08-22 21:49:25,132 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-22 21:49:25,133 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-22 21:49:25,133 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-22 21:49:25,133 | 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 21:49:25,646 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-22 21:49:35,694 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-22 21:49:35,694 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-22 21:49:35,741 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36354129920 B)
2019-08-22 21:49:35,742 | 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 21:49:35,742 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-22 21:49:35,745 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-22 21:49:35,745 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-22 21:49:35,813 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-22 21:49:35,813 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-22 21:49:35,924 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-22 21:49:35,924 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(job, started 140000298899200)>, <ExcThread(copytool_in, started 139999760611072)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(execute_payloads, started 139999156631296)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>, <ExcThread(create_data_payload, started 140000273721088)>, <ExcThread(validate_pre, started 139999727040256)>, <ExcThread(data, started 140000282113792)>, <ExcThread(validate_post, started 139999718647552)>, <ExcThread(validate, started 140000290506496)>, <ExcThread(failed_post, started 139999710254848)>, <ExcThread(monitor, started 139999743825664)>, <ExcThread(copytool_out, started 140000256935680)>]
2019-08-22 21:49:36,187 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-22 21:49:36,187 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-22 21:49:36,228 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-22 21:49:36,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-22 21:49:36,230 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(copytool_in, started 139999760611072)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(execute_payloads, started 139999156631296)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>, <ExcThread(create_data_payload, started 140000273721088)>, <ExcThread(validate_pre, started 139999727040256)>, <ExcThread(data, started 140000282113792)>, <ExcThread(validate_post, started 139999718647552)>, <ExcThread(validate, started 140000290506496)>, <ExcThread(failed_post, started 139999710254848)>, <ExcThread(copytool_out, started 140000256935680)>]
2019-08-22 21:49:36,285 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-22 21:49:36,425 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-22 21:49:36,431 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-22 21:49:36,431 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(copytool_in, started 139999760611072)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(execute_payloads, started 139999156631296)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>, <ExcThread(create_data_payload, started 140000273721088)>, <ExcThread(data, started 140000282113792)>, <ExcThread(validate_post, started 139999718647552)>, <ExcThread(failed_post, started 139999710254848)>, <ExcThread(copytool_out, started 140000256935680)>]
2019-08-22 21:49:36,692 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-22 21:49:36,746 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-22 21:49:36,829 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-22 21:49:36,830 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-22 21:49:36,834 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-22 21:49:36,834 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(copytool_in, started 139999760611072)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(execute_payloads, started 139999156631296)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>, <ExcThread(validate_post, started 139999718647552)>, <ExcThread(failed_post, started 139999710254848)>]
2019-08-22 21:49:36,994 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-22 21:49:37,034 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-22 21:49:37,035 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-22 21:49:37,036 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(copytool_in, started 139999760611072)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>, <ExcThread(validate_post, started 139999718647552)>]
2019-08-22 21:49:37,047 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-22 21:49:37,094 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-22 21:49:37,137 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-22 21:49:37,137 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(job_monitor, started 139999752218368)>, <ExcThread(queue_monitor, started 139999735432960)>]
2019-08-22 21:49:37,534 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-22 21:49:37,534 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-22 21:49:37,540 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-22 21:49:37,540 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(queue_monitoring, started 140000248542976)>, <ExcThread(job_monitor, started 139999752218368)>]
2019-08-22 21:49:38,747 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-22 21:49:38,747 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-22 21:49:38,748 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140000515172096)>, <ExcThread(job_monitor, started 139999752218368)>]
2019-08-22 21:50:25,552 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-22 21:50:25,552 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-22 21:50:25,570 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-22 21:50:25,570 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-22 21:50:25,571 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-22 21:50:25 UTC [wrapper] ==== pilot stdout END ====
2019-08-22 21:50:25 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-22 21:50:25 UTC [wrapper] Pilot exit status: 0
2019-08-22 21:50:25 UTC [wrapper] STATUSCODE: 0
2019-08-22 21:50:25 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 19:24 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 21:50:25 UTC [wrapper] Test setup, not cleaning
2019-08-22 21:50:25 UTC [wrapper] ==== wrapper stdout END ====
2019-08-22 21:50:25 UTC [wrapper] ==== wrapper stderr END ====
2019-08-22 21:50:25 UTC [wrapper] wrapper wrapperexiting ec=0, duration=15997
2019-08-22 21:50:25 UTC [wrapper] apfmon messages muted
2019-08-22 23:50:26,013: ***************diag file************
2019-08-22 23:50:26,013: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15997.66s
KernelTime=436.01s
UserTime=60053.50s
CPUUsage=378%
MaxResidentMemory=1945324kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=466222
MinorPageFaults=19178493
Swaps=0
ForcedSwitches=6927295
WaitSwitches=9752957
Inputs=112494448
Outputs=956624
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-22 23:50:26,024: ******************************WorkDir***********************
2019-08-22 23:50:26,024: total 247360
drwxrwx--x. 6 grid grid      4096 Aug 22 23:50 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7460931 Aug 22 19:24 agis_ddmendpoints.json
-rw-------. 1 grid grid   4338944 Aug 22 19:24 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 22 19:23 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 22 19:23 APPS
-rw-------. 1 grid grid       538 Aug 22 19:23 .asetup
-rw-------. 1 grid grid       826 Aug 22 19:24 .asetup.save
-rw-------. 1 grid grid       518 Aug 22 23:50 bj5NDmyiTKvnShfckohDCDFpABFKDmABFKDmw5CNDmABFKDmeNuNam.diag
-rw-rw-r--. 1 grid grid         0 Aug 22 19:23 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 22 23:49 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 22 23:39 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 239122199 Aug 22 19:23 EVNT.18605790._000249.pool.root.1
-rw-------. 1 grid grid     84400 Aug 22 23:49 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 22 19:23 init_data.xml
-rw-rw-r--. 1 grid grid    263692 Aug 22 19:23 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 22 19:23 job.xml
-rw-------. 1 grid grid    747236 Aug 22 23:50 log.18722495._013396.job.log.1
-rw-------. 1 grid grid    848549 Aug 22 23:49 log.18722495._013396.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 22 23:50 output.list
-rw-------. 1 grid grid      2950 Aug 21 02:32 pandaJobData.out
drwx------. 3 grid grid       174 Aug 19 14:00 pilot2
-rw-r--r--. 1 grid grid    255033 Aug 21 02:30 pilot2.tar.gz
-rw-------. 1 grid grid     10690 Aug 22 23:50 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 21 02:30 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 22 19:23 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 22 19:23 run_atlas
-rwx------. 1 grid grid     12641 Aug 21 02:32 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 22 23:50 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 22 23:50 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 22 23:50 shared
-rw-rw-r--. 1 grid grid      8688 Aug 22 19:23 start_atlas.sh
-rw-rw-r--. 1 grid grid     19305 Aug 22 23:50 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 22 19:23 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 22 23:50 wrapper_checkpoint.txt

2019-08-22 23:50:26,024: running start_atlas return value is 0
2019-08-22 23:50:26,024: Parent exit 0
2019-08-22 23:50:26,026: child process exit 0
23:50:26 (11845): run_atlas exited; CPU time 60053.926898
23:50:26 (11845): called boinc_finish(0)

</stderr_txt>
]]>

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