Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
10:52:33 (14367): wrapper (7.7.26015): starting
10:52:33 (14367): 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=4446184484
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.18722183._013596.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722183
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 11:16:58,062 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 32106 s
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 21034
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 21034
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446184484 has completed
2019-08-16 11:16:58,063 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 11:16:58,069 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446184484
2019-08-16 11:16:59,075 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [21034]
2019-08-16 11:16:59,075 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 21034
2019-08-16 11:16:59,075 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 11:17:00,080 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 11:17:00,080 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=21034
2019-08-16 11:17:00,133 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [21034] (in reverse order)
2019-08-16 11:17:00,176 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 11:17:00,177 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 11:17:00,177 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 11:17:00,177 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-16 11:17:00,687 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 11:17:10,713 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 11:17:10,714 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 11:17:10,749 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34535899136 B)
2019-08-16 11:17:10,750 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-16 11:17:10,750 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 11:17:10,771 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 11:17:10,780 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 11:17:10,840 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 11:17:10,840 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 11:17:11,031 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 11:17:11,156 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 11:17:11,156 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(copytool_in, started 139969184114432)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(validate_post, started 139969175721728)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(failed_post, started 139968689207040)>, <ExcThread(monitor, started 139969200899840)>, <ExcThread(execute_payloads, started 139968680814336)>, <ExcThread(data, started 139969744840448)>, <ExcThread(payload, started 139969226077952)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:11,415 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 11:17:11,416 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 11:17:11,558 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 11:17:11,558 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(copytool_in, started 139969184114432)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(validate_post, started 139969175721728)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(failed_post, started 139968689207040)>, <ExcThread(monitor, started 139969200899840)>, <ExcThread(execute_payloads, started 139968680814336)>, <ExcThread(payload, started 139969226077952)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:11,649 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 11:17:11,649 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 11:17:11,662 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 11:17:11,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-16 11:17:11,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(copytool_in, started 139969184114432)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(validate_post, started 139969175721728)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(failed_post, started 139968689207040)>, <ExcThread(execute_payloads, started 139968680814336)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:11,691 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 11:17:11,706 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 11:17:11,767 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-16 11:17:11,768 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(copytool_in, started 139969184114432)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(execute_payloads, started 139968680814336)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:12,058 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 11:17:12,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 11:17:12,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(execute_payloads, started 139968680814336)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:12,231 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 11:17:12,247 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 11:17:12,272 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 11:17:12,272 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(queue_monitor, started 139969192507136)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:12,579 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 11:17:12,579 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 11:17:12,581 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 11:17:12,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 11:17:12,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(queue_monitoring, started 139969711269632)>, <ExcThread(copytool_out, started 139969728055040)>]
2019-08-16 11:17:13,248 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 11:17:13,279 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 11:17:13,280 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(job_monitor, started 139969217685248)>, <ExcThread(queue_monitoring, started 139969711269632)>]
2019-08-16 11:17:15,583 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 11:17:15,595 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 11:17:15,596 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139969977898752)>, <ExcThread(job_monitor, started 139969217685248)>]
2019-08-16 11:17:59,303 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-16 11:17:59,304 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 11:17:59,393 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 11:17:59,393 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 11:17:59,393 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 11:17:59 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 11:17:59 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 11:17:59 UTC [wrapper] Pilot exit status: 0
2019-08-16 11:17:59 UTC [wrapper] STATUSCODE: 0
2019-08-16 11:17:59 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 16 10:52 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

2019-08-16 11:17:59 UTC [wrapper] Test setup, not cleaning
2019-08-16 11:17:59 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 11:17:59 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 11:17:59 UTC [wrapper] wrapper wrapperexiting ec=0, duration=8723
2019-08-16 11:17:59 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8723.09s
KernelTime=260.21s
UserTime=31977.29s
CPUUsage=369%
MaxResidentMemory=1945228kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=323292
MinorPageFaults=14364810
Swaps=0
ForcedSwitches=3680839
WaitSwitches=6573042
Inputs=78756760
Outputs=607656
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 252204
drwxrwx--x. 6 grid grid      4096 Aug 16 13:17 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7416180 Aug 16 10:52 agis_ddmendpoints.json
-rw-------. 1 grid grid   4437667 Aug 16 10:52 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 10:52 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 10:52 APPS
-rw-------. 1 grid grid       538 Aug 16 10:52 .asetup
-rw-------. 1 grid grid       826 Aug 16 10:53 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 10:52 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 13:17 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 16 13:09 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 244293991 Aug 16 10:52 EVNT.18605745._000293.pool.root.1
-rw-------. 1 grid grid     79875 Aug 16 13:16 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 10:52 init_data.xml
-rw-rw-r--. 1 grid grid    261610 Aug 16 10:52 input.tar.gz
-rw-------. 1 grid grid       516 Aug 16 13:17 iTEODmbfKIvnShfckohDCDFpABFKDmABFKDmEIJbDmABFKDmc43Ipn.diag
-rw-rw-r--. 1 grid grid       112 Aug 16 10:52 job.xml
-rw-------. 1 grid grid    508513 Aug 16 13:17 log.18722183._013596.job.log.1
-rw-------. 1 grid grid    832761 Aug 16 13:16 log.18722183._013596.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 13:17 output.list
-rw-------. 1 grid grid      2921 Aug 15 04:27 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 15 04:27 pilot2.tar.gz
-rw-------. 1 grid grid     10823 Aug 16 13:17 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 15 04:26 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 10:52 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 10:52 run_atlas
-rwx------. 1 grid grid     12641 Aug 15 04:27 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 13:17 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 13:17 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 13:17 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 10:52 start_atlas.sh
-rw-rw-r--. 1 grid grid     18481 Aug 16 13:17 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 16 10:52 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 16 13:17 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
13:18:00 (14367): run_atlas exited; CPU time 31977.714551
13:18:00 (14367): called boinc_finish(0)

</stderr_txt>
]]>

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