Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
23:10:00 (29222): wrapper (7.7.26015): starting
23:10:00 (29222): 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 PandaID=4446298718
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.18604991._045615.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 23:13:13,112 | DEBUG    | queue_monitor       | pilot.control.job                | send_state                | wrote heartbeat to file /home/grid/slots/0/heartbeat.json
2019-08-13 23:13:13,112 | INFO     | queue_monitor       | pilot.control.job                | queue_monitor             | job 4446298718 was dequeued from the monitored payloads queue
2019-08-13 23:13:13,853 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4446298718
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604991
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 23:13:13,854 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 27047 s
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 3503
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 3503
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446298718 has completed
2019-08-13 23:13:13,855 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 23:13:13,864 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446298718
2019-08-13 23:13:14,870 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [3503]
2019-08-13 23:13:14,870 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 3503
2019-08-13 23:13:14,870 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 23:13:15,875 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 23:13:15,876 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=3503
2019-08-13 23:13:15,936 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [3503] (in reverse order)
2019-08-13 23:13:15,984 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 23:13:15,984 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 23:13:15,984 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 23:13:15,985 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 23:13:16,497 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 23:13:26,544 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 23:13:26,545 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 23:13:26,590 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (33992736768 B)
2019-08-13 23:13:26,590 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 23:13:26,590 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 23:13:26,609 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 23:13:26,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-13 23:13:26,668 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(job, started 140011451467520)>, <ExcThread(copytool_in, started 140010783217408)>, <ExcThread(copytool_out, started 140011336873728)>, <ExcThread(queue_monitoring, started 140010825180928)>, <ExcThread(payload, started 140011345266432)>, <ExcThread(job_monitor, started 140010816788224)>, <ExcThread(monitor, started 140010833573632)>, <ExcThread(execute_payloads, started 140010296702720)>, <ExcThread(validate_post, started 140010808395520)>, <ExcThread(data, started 140011362051840)>, <ExcThread(validate, started 140011370444544)>, <ExcThread(queue_monitor, started 140010800002816)>, <ExcThread(validate_pre, started 140011320088320)>, <ExcThread(create_data_payload, started 140011353659136)>, <ExcThread(failed_post, started 140010791610112)>]
2019-08-13 23:13:26,684 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 23:13:26,684 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 23:13:26,879 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 23:13:27,015 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 23:13:27,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-13 23:13:27,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(job, started 140011451467520)>, <ExcThread(copytool_in, started 140010783217408)>, <ExcThread(copytool_out, started 140011336873728)>, <ExcThread(queue_monitoring, started 140010825180928)>, <ExcThread(job_monitor, started 140010816788224)>, <ExcThread(monitor, started 140010833573632)>, <ExcThread(validate_post, started 140010808395520)>, <ExcThread(data, started 140011362051840)>, <ExcThread(validate, started 140011370444544)>, <ExcThread(queue_monitor, started 140010800002816)>, <ExcThread(create_data_payload, started 140011353659136)>, <ExcThread(failed_post, started 140010791610112)>]
2019-08-13 23:13:27,495 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 23:13:27,555 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 23:13:27,610 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 23:13:27,610 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 23:13:27,611 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 23:13:27,676 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 23:13:27,676 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 23:13:27,690 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 23:13:27,690 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 23:13:27,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-13 23:13:27,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(queue_monitoring, started 140010825180928)>, <ExcThread(job_monitor, started 140010816788224)>, <ExcThread(validate_post, started 140010808395520)>, <ExcThread(queue_monitor, started 140010800002816)>, <ExcThread(failed_post, started 140010791610112)>]
2019-08-13 23:13:27,844 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 23:13:27,845 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 23:13:27,903 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 23:13:27,903 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(queue_monitoring, started 140010825180928)>, <ExcThread(job_monitor, started 140010816788224)>, <ExcThread(queue_monitor, started 140010800002816)>]
2019-08-13 23:13:28,046 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 23:13:28,046 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 23:13:28,066 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 23:13:28,105 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 23:13:28,105 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(queue_monitoring, started 140010825180928)>, <ExcThread(job_monitor, started 140010816788224)>]
2019-08-13 23:13:31,068 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 23:13:31,126 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 23:13:31,127 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140011667740416)>, <ExcThread(job_monitor, started 140010816788224)>]
2019-08-13 23:14:09,792 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 23:14:09,792 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 23:14:09,797 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 23:14:09,797 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 23:14:09,797 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 23:14:09 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 23:14:10 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 23:14:10 UTC [wrapper] Pilot exit status: 0
2019-08-13 23:14:10 UTC [wrapper] STATUSCODE: 0
2019-08-13 23:14:10 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 13 23:10 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

2019-08-13 23:14:10 UTC [wrapper] Test setup, not cleaning
2019-08-13 23:14:10 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 23:14:10 UTC [wrapper] ==== wrapper stderr END ====
2019-08-13 23:14:10 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7447
2019-08-13 23:14:10 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7447.00s
KernelTime=234.79s
UserTime=26928.33s
CPUUsage=364%
MaxResidentMemory=1911208kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=300642
MinorPageFaults=13519026
Swaps=0
ForcedSwitches=3158577
WaitSwitches=5721799
Inputs=73031976
Outputs=519392
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 379292
drwxrwx--x. 6 grid grid      4096 Aug 14 01:14 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409110 Aug 13 23:10 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517750 Aug 13 23:10 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 23:10 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 23:10 APPS
-rw-------. 1 grid grid       538 Aug 13 23:10 .asetup
-rw-------. 1 grid grid       826 Aug 13 23:10 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 23:10 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 01:14 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 14 01:06 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 374420785 Aug 13 23:10 EVNT.17323818._001237.pool.root.1
-rw-------. 1 grid grid     79799 Aug 14 01:13 heartbeat.json
-rw-rw-r--. 1 grid grid      5864 Aug 13 23:10 init_data.xml
-rw-rw-r--. 1 grid grid    261625 Aug 13 23:10 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 13 23:09 job.xml
-rw-------. 1 grid grid    459394 Aug 14 01:14 log.18604991._045615.job.log.1
-rw-------. 1 grid grid    823731 Aug 14 01:13 log.18604991._045615.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug 14 01:14 LyILDm2EeHvnShfckohDCDFpABFKDmABFKDmAnCaDmABFKDm4jZhen.diag
-rw-------. 1 grid grid       391 Aug 14 01:14 output.list
-rw-------. 1 grid grid      2872 Aug 13 07:09 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 06:30 pilot2.tar.gz
-rw-------. 1 grid grid      9144 Aug 14 01:14 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 07:07 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 23:10 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 23:09 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 07:09 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 01:14 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 01:14 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 01:14 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 23:10 start_atlas.sh
-rw-rw-r--. 1 grid grid     17744 Aug 14 01:14 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 23:09 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 14 01:14 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
01:14:10 (29222): run_atlas exited; CPU time 26928.747719
01:14:10 (29222): called boinc_finish(0)

</stderr_txt>
]]>

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