Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
04:08:55 (4777): wrapper (7.7.26015): starting
04:08:55 (4777): wrapper: running run_atlas (--nthreads 4)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '4']
THREADS=4
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.6.1810 (Core) 

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is not installed, using version from CVMFS
Testing the function of Singularity...
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
Singularity Works...

copy /home/grid/slots/0/shared/ATLAS.root_0
copy /home/grid/slots/0/shared/input.tar.gz
copy /home/grid/slots/0/shared/RTE.tar.gz
copy /home/grid/slots/0/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=4;start atlas job with grep: pandaJobData.out: No such file or directory
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
running cmd return value is 0
Moving ./HITS.18722432._013117.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442814046
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722432
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 05:14:43,072 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 42056 s
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 11447
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 11447
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442814046 has completed
2019-08-11 05:14:43,073 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 05:14:43,081 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442814046
2019-08-11 05:14:44,086 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11447]
2019-08-11 05:14:44,086 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11447
2019-08-11 05:14:44,086 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 05:14:45,092 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 05:14:45,092 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11447
2019-08-11 05:14:45,146 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11447] (in reverse order)
2019-08-11 05:14:45,188 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 05:14:45,188 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 05:14:45,188 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 05:14:45,188 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-11 05:14:45,699 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 05:14:55,749 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 05:14:55,749 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 05:14:55,787 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35473326080 B)
2019-08-11 05:14:55,787 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-11 05:14:55,787 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 05:14:55,826 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 05:14:55,878 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-11 05:14:55,879 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(job, started 139849970038528)>, <ExcThread(copytool_in, started 139849403184896)>, <ExcThread(validate_pre, started 139849428363008)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>, <ExcThread(data, started 139849961645824)>, <ExcThread(validate_post, started 139849394792192)>, <ExcThread(execute_payloads, started 139848891492096)>, <ExcThread(payload, started 139849944860416)>, <ExcThread(failed_post, started 139849386399488)>, <ExcThread(validate, started 139849953253120)>, <ExcThread(create_data_payload, started 139849936467712)>]
2019-08-11 05:14:56,014 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 05:14:56,019 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 05:14:56,098 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 05:14:56,281 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-11 05:14:56,281 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(job, started 139849970038528)>, <ExcThread(copytool_in, started 139849403184896)>, <ExcThread(validate_pre, started 139849428363008)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>, <ExcThread(data, started 139849961645824)>, <ExcThread(validate_post, started 139849394792192)>, <ExcThread(execute_payloads, started 139848891492096)>, <ExcThread(payload, started 139849944860416)>, <ExcThread(create_data_payload, started 139849936467712)>]
2019-08-11 05:14:56,400 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 05:14:56,515 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 05:14:56,589 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 05:14:56,590 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 05:14:56,590 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-11 05:14:56,591 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(job, started 139849970038528)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>, <ExcThread(data, started 139849961645824)>, <ExcThread(validate_post, started 139849394792192)>, <ExcThread(execute_payloads, started 139848891492096)>, <ExcThread(create_data_payload, started 139849936467712)>]
2019-08-11 05:14:56,710 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 05:14:56,711 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 05:14:56,760 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 05:14:56,792 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-11 05:14:56,792 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(job, started 139849970038528)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>, <ExcThread(validate_post, started 139849394792192)>, <ExcThread(execute_payloads, started 139848891492096)>, <ExcThread(create_data_payload, started 139849936467712)>]
2019-08-11 05:14:56,814 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 05:14:56,814 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 05:14:56,858 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 05:14:56,893 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-11 05:14:56,893 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>, <ExcThread(execute_payloads, started 139848891492096)>, <ExcThread(create_data_payload, started 139849936467712)>]
2019-08-11 05:14:57,018 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 05:14:57,090 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 05:14:57,095 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-11 05:14:57,095 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>, <ExcThread(queue_monitor, started 139848899884800)>]
2019-08-11 05:14:57,461 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 05:14:57,461 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 05:14:57,499 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 05:14:57,499 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>, <ExcThread(copytool_out, started 139849928075008)>]
2019-08-11 05:14:57,761 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 05:14:57,801 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 05:14:57,802 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(queue_monitoring, started 139849419970304)>, <ExcThread(job_monitor, started 139849411577600)>]
2019-08-11 05:14:59,016 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 05:14:59,112 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 05:14:59,112 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139850186311424)>, <ExcThread(job_monitor, started 139849411577600)>]
2019-08-11 05:15:28,376 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-11 05:15:28,376 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 05:15:28,421 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 05:15:28,422 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 05:15:28,422 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 05:15:28 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 05:15:28 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 05:15:28 UTC [wrapper] Pilot exit status: 0
2019-08-11 05:15:28 UTC [wrapper] STATUSCODE: 0
2019-08-11 05:15:28 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 11 04:09 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

2019-08-11 05:15:28 UTC [wrapper] Test setup, not cleaning
2019-08-11 05:15:28 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 05:15:28 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11190.62s
KernelTime=332.70s
UserTime=41873.33s
CPUUsage=377%
MaxResidentMemory=1944648kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=371824
MinorPageFaults=16007915
Swaps=0
ForcedSwitches=4867859
WaitSwitches=7416911
Inputs=90130576
Outputs=759760
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 231032
drwxrwx--x. 7 grid grid      4096 Aug 11 07:15 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 11 04:09 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506453 Aug 11 04:09 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 11 04:08 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 11 04:08 APPS
drwxr-xr-x. 2 grid grid         6 Aug 11 04:09 .arc
-rw-------. 1 grid grid       538 Aug 11 04:09 .asetup
-rw-------. 1 grid grid       826 Aug 11 04:09 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 11 04:08 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 11 07:15 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 11 07:08 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 222357438 Aug 11 04:08 EVNT.18605781._000266.pool.root.1
-rw-------. 1 grid grid    123039 Aug 11 07:14 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 11 04:08 init_data.xml
-rw-rw-r--. 1 grid grid    262343 Aug 11 04:08 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 11 04:08 job.xml
-rw-------. 1 grid grid    636331 Aug 11 07:15 log.18722432._013117.job.log.1
-rw-------. 1 grid grid    853740 Aug 11 07:14 log.18722432._013117.job.log.tgz.1
-rw-------. 1 grid grid       517 Aug 11 07:15 LTNODmp2iGvnShfckohDCDFpABFKDmABFKDmwFiYDmABFKDmB0wtXo.diag
-rw-------. 1 grid grid       391 Aug 11 07:15 output.list
-rw-------. 1 grid grid      2957 Aug 10 18:05 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 17:33 pilot2.tar.gz
-rw-------. 1 grid grid     11285 Aug 11 07:15 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 10 18:05 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 11 04:08 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 11 04:08 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 18:05 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 11 07:15 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 11 07:15 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 11 07:15 shared
-rw-rw-r--. 1 grid grid      8688 Aug 11 04:08 start_atlas.sh
-rw-rw-r--. 1 grid grid     19160 Aug 11 07:15 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 11 04:08 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 11 07:15 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
07:15:29 (4777): run_atlas exited; CPU time 41873.685676
07:15:29 (4777): called boinc_finish(0)

</stderr_txt>
]]>

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