Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
23:50:30 (12340): wrapper (7.7.26015): starting
23:50:30 (12340): wrapper: running run_atlas (--nthreads 4)
2019-08-22 23:50:30,837: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-22 23:50:30,837: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-22 23:50:30,838: THREADS=4

2019-08-22 23:50:30,840: Checking for CVMFS
2019-08-22 23:50:32,089: CVMFS is installed
2019-08-22 23:50:32,093: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-22 23:50:32,093: This is not SLC6, need to run with Singularity....
2019-08-22 23:50:32,093: Checking Singularity...
2019-08-22 23:50:32,096: Singularity is not installed, using version from CVMFS
2019-08-22 23:50:32,096: Testing the function of Singularity...
2019-08-22 23:50:32,096: 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 23:50:32,334: Singularity Works...
2019-08-22 23:50:32,335: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-22 23:50:32,774: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-22 23:50:32,775: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-22 23:50:32,775: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-22 23:50:32,776: export ATHENA_PROC_NUMBER=4;
2019-08-22 23:50:32,798: start atlas job with PandaID=4454254509
2019-08-22 23:50:32,799: 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
2019-08-23 03:35:51,046: running cmd return value is 0
2019-08-23 03:35:51,049: Moving ./HITS.18722261._018054.pool.root.1 to shared/HITS.pool.root.1
2019-08-23 03:35:51,050: *****************The last 100 lines of the pilot log******************
2019-08-23 03:35:51,060: 2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-23 01:34:37,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 51119 s
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 19139
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 19139
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4454254509 has completed
2019-08-23 01:34:37,681 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-23 01:34:37,693 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4454254509
2019-08-23 01:34:38,698 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [19139]
2019-08-23 01:34:38,699 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 19139
2019-08-23 01:34:38,699 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-23 01:34:39,703 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-23 01:34:39,704 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=19139
2019-08-23 01:34:39,767 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [19139] (in reverse order)
2019-08-23 01:34:39,812 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-23 01:34:39,812 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-23 01:34:39,812 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-23 01:34:39,812 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-23 01:34:40,325 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-23 01:34:50,046 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-23 01:34:50,375 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-23 01:34:50,375 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-23 01:34:50,415 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36022779904 B)
2019-08-23 01:34:50,415 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-23 01:34:50,415 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-23 01:34:50,420 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-23 01:34:50,451 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-23 01:34:50,533 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-23 01:34:50,533 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-23 01:34:50,548 | WARNING  | job_monitor         | pilot.util.common                | should_abort              | job:job_monitor:received graceful stop - abort after this iteration
2019-08-23 01:34:50,576 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-23 01:34:50,577 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-23 01:34:50,581 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-23 01:34:50,581 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job, started 139946402711296)>, <ExcThread(validate_pre, started 139945872193280)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(validate, started 139946385925888)>, <ExcThread(create_data_payload, started 139946360747776)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(validate_post, started 139945830229760)>, <ExcThread(failed_post, started 139945335322368)>, <ExcThread(copytool_in, started 139945847015168)>, <ExcThread(copytool_out, started 139946377533184)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:50,757 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-23 01:34:50,783 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-23 01:34:50,783 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job, started 139946402711296)>, <ExcThread(validate_pre, started 139945872193280)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(validate, started 139946385925888)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(validate_post, started 139945830229760)>, <ExcThread(failed_post, started 139945335322368)>, <ExcThread(copytool_in, started 139945847015168)>, <ExcThread(copytool_out, started 139946377533184)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:50,804 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-23 01:34:50,984 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-23 01:34:50,984 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job, started 139946402711296)>, <ExcThread(validate_pre, started 139945872193280)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(validate, started 139946385925888)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(validate_post, started 139945830229760)>, <ExcThread(copytool_in, started 139945847015168)>, <ExcThread(copytool_out, started 139946377533184)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:51,038 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-23 01:34:51,042 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-23 01:34:51,185 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-23 01:34:51,186 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job, started 139946402711296)>, <ExcThread(validate_pre, started 139945872193280)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(validate, started 139946385925888)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(copytool_out, started 139946377533184)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:51,236 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-23 01:34:51,387 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-23 01:34:51,387 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job, started 139946402711296)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(validate, started 139946385925888)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(copytool_out, started 139946377533184)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:51,421 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-23 01:34:51,561 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-23 01:34:51,562 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-23 01:34:51,562 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-23 01:34:51,588 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-23 01:34:51,588 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(execute_payloads, started 139945326929664)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:51,736 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-23 01:34:51,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-23 01:34:51,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(queue_monitor, started 139945821837056)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:52,089 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-23 01:34:52,158 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-23 01:34:52,158 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-23 01:34:52,193 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-23 01:34:52,193 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job_monitor, started 139945838622464)>, <ExcThread(queue_monitoring, started 139945863800576)>]
2019-08-23 01:34:55,091 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-23 01:34:55,114 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-23 01:34:55,114 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139946618984192)>, <ExcThread(job_monitor, started 139945838622464)>]
2019-08-23 01:35:50,572 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 122 s)
2019-08-23 01:35:50,572 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-23 01:35:50,598 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-23 01:35:50,598 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-23 01:35:50,598 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-23 01:35:50 UTC [wrapper] ==== pilot stdout END ====
2019-08-23 01:35:50 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-23 01:35:50 UTC [wrapper] Pilot exit status: 0
2019-08-23 01:35:50 UTC [wrapper] STATUSCODE: 0
2019-08-23 01:35:50 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 23:50 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

2019-08-23 01:35:50 UTC [wrapper] Test setup, not cleaning
2019-08-23 01:35:50 UTC [wrapper] ==== wrapper stdout END ====
2019-08-23 01:35:50 UTC [wrapper] ==== wrapper stderr END ====
2019-08-23 01:35:50 UTC [wrapper] wrapper wrapperexiting ec=0, duration=13517
2019-08-23 01:35:50 UTC [wrapper] apfmon messages muted
2019-08-23 03:35:51,063: ***************diag file************
2019-08-23 03:35:51,064: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=13517.88s
KernelTime=382.78s
UserTime=50901.48s
CPUUsage=379%
MaxResidentMemory=1945360kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=419936
MinorPageFaults=17569391
Swaps=0
ForcedSwitches=5906444
WaitSwitches=8397887
Inputs=101611592
Outputs=844528
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-23 03:35:51,074: ******************************WorkDir***********************
2019-08-23 03:35:51,074: total 273600
drwxrwx--x. 6 grid grid      4096 Aug 23 03:35 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7460931 Aug 22 23:50 agis_ddmendpoints.json
-rw-------. 1 grid grid   4339152 Aug 22 23:50 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 22 23:50 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 22 23:50 APPS
-rw-------. 1 grid grid       538 Aug 22 23:50 .asetup
-rw-------. 1 grid grid       826 Aug 22 23:51 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 22 23:50 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 23 03:35 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 23 03:27 boinc_task_state.xml
-rw-------. 1 grid grid       518 Aug 23 03:35 Cc0LDmM9UKvnShfckohDCDFpABFKDmABFKDmC4FNDmABFKDm6Arurn.diag
-rw-rw-r--. 1 grid grid 266027633 Aug 22 23:50 EVNT.18605752._000351.pool.root.1
-rw-------. 1 grid grid    107484 Aug 23 03:34 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 22 23:50 init_data.xml
-rw-rw-r--. 1 grid grid    263687 Aug 22 23:50 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 22 23:50 job.xml
-rw-------. 1 grid grid    686343 Aug 23 03:35 log.18722261._018054.job.log.1
-rw-------. 1 grid grid    850014 Aug 23 03:34 log.18722261._018054.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 23 03:35 output.list
-rw-------. 1 grid grid      2922 Aug 21 04:03 pandaJobData.out
drwx------. 3 grid grid       174 Aug 19 14:00 pilot2
-rw-r--r--. 1 grid grid    255033 Aug 21 03:22 pilot2.tar.gz
-rw-------. 1 grid grid     11588 Aug 23 03:35 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 21 04:00 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 22 23:50 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 22 23:50 run_atlas
-rwx------. 1 grid grid     12641 Aug 21 04:03 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 23 03:35 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 23 03:35 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 23 03:35 shared
-rw-rw-r--. 1 grid grid      8688 Aug 22 23:50 start_atlas.sh
-rw-rw-r--. 1 grid grid     19598 Aug 23 03:35 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 22 23:50 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 23 03:35 wrapper_checkpoint.txt

2019-08-23 03:35:51,075: running start_atlas return value is 0
2019-08-23 03:35:51,075: Parent exit 0
2019-08-23 03:35:51,076: child process exit 0
03:35:52 (12340): run_atlas exited; CPU time 50901.904154
03:35:52 (12340): called boinc_finish(0)

</stderr_txt>
]]>

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