Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
05:12:31 (8480): wrapper (7.7.26015): starting
05:12:31 (8480): 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=4446890115
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._047586.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4446890115
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-14 05:11:57,179 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26237 s
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 15174
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 15174
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446890115 has completed
2019-08-14 05:11:57,180 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-14 05:11:57,190 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446890115
2019-08-14 05:11:58,193 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [15174]
2019-08-14 05:11:58,194 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 15174
2019-08-14 05:11:58,194 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-14 05:11:59,199 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-14 05:11:59,199 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=15174
2019-08-14 05:11:59,252 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [15174] (in reverse order)
2019-08-14 05:11:59,293 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-14 05:11:59,294 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-14 05:11:59,294 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-14 05:11:59,294 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-14 05:11:59,803 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-14 05:12:08,837 | INFO     | monitor             | pilot.control.monitor            | control                   | 7157 s have passed since pilot start
2019-08-14 05:12:09,841 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-14 05:12:09,841 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-14 05:12:09,895 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35840327680 B)
2019-08-14 05:12:09,896 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-14 05:12:09,896 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-14 05:12:09,900 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-14 05:12:09,901 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-14 05:12:09,901 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-14 05:12:09,919 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-14 05:12:10,055 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-14 05:12:10,116 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-14 05:12:10,116 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job, started 139800364328704)>, <ExcThread(queue_monitor, started 139799356757760)>, <ExcThread(create_data_payload, started 139800322365184)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(execute_payloads, started 139799365150464)>, <ExcThread(queue_monitoring, started 139799952344832)>, <ExcThread(failed_post, started 139799935559424)>, <ExcThread(copytool_in, started 139799927166720)>, <ExcThread(validate, started 139800347543296)>, <ExcThread(payload, started 139800339150592)>]
2019-08-14 05:12:10,324 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-14 05:12:10,337 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-14 05:12:10,377 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-14 05:12:10,418 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-14 05:12:10,418 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job, started 139800364328704)>, <ExcThread(queue_monitor, started 139799356757760)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(queue_monitoring, started 139799952344832)>, <ExcThread(failed_post, started 139799935559424)>, <ExcThread(copytool_in, started 139799927166720)>, <ExcThread(payload, started 139800339150592)>]
2019-08-14 05:12:10,453 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-14 05:12:10,473 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-14 05:12:10,719 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-14 05:12:10,720 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job, started 139800364328704)>, <ExcThread(queue_monitor, started 139799356757760)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(queue_monitoring, started 139799952344832)>, <ExcThread(copytool_in, started 139799927166720)>, <ExcThread(payload, started 139800339150592)>]
2019-08-14 05:12:10,766 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-14 05:12:10,813 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-14 05:12:10,814 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-14 05:12:10,921 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-14 05:12:10,921 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(queue_monitor, started 139799356757760)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(queue_monitoring, started 139799952344832)>, <ExcThread(copytool_in, started 139799927166720)>, <ExcThread(payload, started 139800339150592)>]
2019-08-14 05:12:10,971 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-14 05:12:10,972 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-14 05:12:11,022 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-14 05:12:11,022 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(queue_monitor, started 139799356757760)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(queue_monitoring, started 139799952344832)>, <ExcThread(copytool_in, started 139799927166720)>]
2019-08-14 05:12:11,199 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-14 05:12:11,207 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-14 05:12:11,207 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-14 05:12:11,223 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-14 05:12:11,223 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(copytool_out, started 139800330757888)>, <ExcThread(queue_monitoring, started 139799952344832)>]
2019-08-14 05:12:11,767 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-14 05:12:11,828 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-14 05:12:11,828 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job_monitor, started 139799373543168)>, <ExcThread(queue_monitoring, started 139799952344832)>]
2019-08-14 05:12:13,474 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-14 05:12:13,539 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-14 05:12:13,539 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139800580601600)>, <ExcThread(job_monitor, started 139799373543168)>]
2019-08-14 05:12:15,872 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-14 05:12:15,872 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-14 05:12:15,954 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-14 05:12:15,955 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-14 05:12:15,955 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-14 05:12:16 UTC [wrapper] ==== pilot stdout END ====
2019-08-14 05:12:16 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-14 05:12:16 UTC [wrapper] Pilot exit status: 0
2019-08-14 05:12:16 UTC [wrapper] STATUSCODE: 0
2019-08-14 05:12:16 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 14 05:12 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

2019-08-14 05:12:16 UTC [wrapper] Test setup, not cleaning
2019-08-14 05:12:16 UTC [wrapper] ==== wrapper stdout END ====
2019-08-14 05:12:16 UTC [wrapper] ==== wrapper stderr END ====
2019-08-14 05:12:16 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7182
2019-08-14 05:12:16 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7182.06s
KernelTime=222.90s
UserTime=26130.22s
CPUUsage=366%
MaxResidentMemory=1944652kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=291363
MinorPageFaults=13308476
Swaps=0
ForcedSwitches=3053322
WaitSwitches=5802361
Inputs=70653912
Outputs=481832
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 379640
drwxrwx--x. 6 grid grid      4096 Aug 14 07:12 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409110 Aug 14 05:12 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517511 Aug 14 05:12 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 14 05:12 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 14 05:12 APPS
-rw-------. 1 grid grid       538 Aug 14 05:12 .asetup
-rw-------. 1 grid grid       826 Aug 14 05:13 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 14 05:12 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 07:12 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 14 07:05 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 374823834 Aug 14 05:12 EVNT.17323813._000928.pool.root.1
-rw-------. 1 grid grid     62395 Aug 14 07:11 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 14 05:12 init_data.xml
-rw-rw-r--. 1 grid grid    261623 Aug 14 05:12 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 14 05:12 job.xml
-rw-------. 1 grid grid    438956 Aug 14 07:12 log.18604976._047586.job.log.1
-rw-------. 1 grid grid    816094 Aug 14 07:11 log.18604976._047586.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 14 07:12 output.list
-rw-------. 1 grid grid      2872 Aug 13 13:40 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 13:29 pilot2.tar.gz
-rw-------. 1 grid grid     10239 Aug 14 07:12 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 13:40 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 14 05:12 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 14 05:12 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 13:40 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 07:12 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 07:12 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 07:12 shared
-rw-rw-r--. 1 grid grid      8688 Aug 14 05:12 start_atlas.sh
-rw-rw-r--. 1 grid grid     18042 Aug 14 07:12 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 14 05:12 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 14 07:12 wrapper_checkpoint.txt
-rw-------. 1 grid grid       516 Aug 14 07:12 XYrMDmCLkHvnShfckohDCDFpABFKDmABFKDmq5MaDmABFKDmBTOPgn.diag

running start_atlas return value is 0
Parent exit 0
child process exit 0
07:12:16 (8480): run_atlas exited; CPU time 26130.604490
07:12:16 (8480): called boinc_finish(0)

</stderr_txt>
]]>

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