Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
09:51:39 (12381): wrapper (7.7.26015): starting
09:51:39 (12381): 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=4447864536
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.18604976._049830.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26690 s
2019-08-15 09:51:52,868 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 19073
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 19073
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4447864536 has completed
2019-08-15 09:51:52,869 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-15 09:51:52,878 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4447864536
2019-08-15 09:51:53,884 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [19073]
2019-08-15 09:51:53,884 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 19073
2019-08-15 09:51:53,884 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-15 09:51:54,889 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-15 09:51:54,890 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=19073
2019-08-15 09:51:54,940 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [19073] (in reverse order)
2019-08-15 09:51:54,981 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-15 09:51:54,982 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-15 09:51:54,982 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-15 09:51:54,982 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-15 09:51:55,491 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-15 09:52:05,530 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-15 09:52:05,530 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-15 09:52:05,564 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36003905536 B)
2019-08-15 09:52:05,565 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-15 09:52:05,565 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-15 09:52:05,577 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-15 09:52:05,601 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-15 09:52:05,601 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-15 09:52:05,730 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-15 09:52:05,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-15 09:52:05,909 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(copytool_out, started 140385938552576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(create_data_payload, started 140385946945280)>, <ExcThread(validate_post, started 140385418467072)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(data, started 140385972123392)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(copytool_in, started 140385401681664)>, <ExcThread(monitor, started 140385930159872)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>, <ExcThread(payload, started 140385955337984)>, <ExcThread(failed_post, started 140385384896256)>]
2019-08-15 09:52:06,114 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-15 09:52:06,211 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-15 09:52:06,212 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-15 09:52:06,242 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-15 09:52:06,242 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-15 09:52:06,243 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(copytool_out, started 140385938552576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(validate_post, started 140385418467072)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(data, started 140385972123392)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(copytool_in, started 140385401681664)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>, <ExcThread(failed_post, started 140385384896256)>]
2019-08-15 09:52:06,286 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-15 09:52:06,444 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-15 09:52:06,444 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(copytool_out, started 140385938552576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(validate_post, started 140385418467072)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(data, started 140385972123392)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(copytool_in, started 140385401681664)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,464 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-15 09:52:06,552 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-15 09:52:06,553 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-15 09:52:06,561 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-15 09:52:06,561 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(copytool_out, started 140385938552576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(copytool_in, started 140385401681664)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,577 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-15 09:52:06,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-15 09:52:06,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(copytool_in, started 140385401681664)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,677 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-15 09:52:06,763 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-15 09:52:06,764 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(validate, started 140385963730688)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,802 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-15 09:52:06,864 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-15 09:52:06,865 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(queue_monitor, started 140385393288960)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(validate_pre, started 140385921767168)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,891 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-15 09:52:06,891 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-15 09:52:06,919 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-15 09:52:06,965 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-15 09:52:06,966 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(execute_payloads, started 140384898381568)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:06,979 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-15 09:52:07,067 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-15 09:52:07,067 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(queue_monitoring, started 140385435252480)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:08,732 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-15 09:52:08,778 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-15 09:52:08,778 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140386269816576)>, <ExcThread(job_monitor, started 140385410074368)>]
2019-08-15 09:52:09,229 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-15 09:52:09,229 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-15 09:52:09,282 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-15 09:52:09,282 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-15 09:52:09,282 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-15 09:52:09 UTC [wrapper] ==== pilot stdout END ====
2019-08-15 09:52:09 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-15 09:52:09 UTC [wrapper] Pilot exit status: 0
2019-08-15 09:52:09 UTC [wrapper] STATUSCODE: 0
2019-08-15 09:52:09 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 15 09:51 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

2019-08-15 09:52:09 UTC [wrapper] Test setup, not cleaning
2019-08-15 09:52:09 UTC [wrapper] ==== wrapper stdout END ====
2019-08-15 09:52:09 UTC [wrapper] ==== wrapper stderr END ====
2019-08-15 09:52:09 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7227
2019-08-15 09:52:09 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7226.69s
KernelTime=232.37s
UserTime=26574.05s
CPUUsage=370%
MaxResidentMemory=1945404kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=292144
MinorPageFaults=13351879
Swaps=0
ForcedSwitches=3121660
WaitSwitches=5749793
Inputs=71101096
Outputs=495544
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 380976
drwxrwx--x. 6 grid grid      4096 Aug 15 11:52 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409162 Aug 15 09:51 agis_ddmendpoints.json
-rw-------. 1 grid grid   4448230 Aug 15 09:51 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 09:51 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 09:51 APPS
-rw-------. 1 grid grid       538 Aug 15 09:51 .asetup
-rw-------. 1 grid grid       826 Aug 15 09:52 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 09:51 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 15 11:52 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 15 11:47 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 376218951 Aug 15 09:51 EVNT.17323813._000972.pool.root.1
-rw-------. 1 grid grid       516 Aug 15 11:52 gM3MDmL9xHvnShfckohDCDFpABFKDmABFKDmGljaDmABFKDmmcqyRo.diag
-rw-------. 1 grid grid     78983 Aug 15 11:51 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 09:51 init_data.xml
-rw-rw-r--. 1 grid grid    261626 Aug 15 09:51 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 09:51 job.xml
-rw-------. 1 grid grid    457365 Aug 15 11:52 log.18604976._049830.job.log.1
-rw-------. 1 grid grid    824483 Aug 15 11:51 log.18604976._049830.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 15 11:52 output.list
-rw-------. 1 grid grid      2872 Aug 14 04:25 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 14 03:25 pilot2.tar.gz
-rw-------. 1 grid grid     12038 Aug 15 11:52 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 14 04:20 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 15 09:51 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 09:51 run_atlas
-rwx------. 1 grid grid     12641 Aug 14 04:25 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 15 11:52 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 15 11:52 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 15 11:52 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 09:51 start_atlas.sh
-rw-rw-r--. 1 grid grid     19419 Aug 15 11:52 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 09:51 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 15 11:52 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
11:52:10 (12381): run_atlas exited; CPU time 26574.432971
11:52:10 (12381): called boinc_finish(0)

</stderr_txt>
]]>

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