Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
05:41:33 (25843): wrapper (7.7.26015): starting
05:41:33 (25843): 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=4449868145
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._051936.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 05:46:35,339 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-16 05:46:35,339 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 05:46:35,339 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 05:46:35,339 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 05:46:35,339 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 27847 s
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 32507
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 32507
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4449868145 has completed
2019-08-16 05:46:35,340 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 05:46:35,349 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4449868145
2019-08-16 05:46:36,355 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [32507]
2019-08-16 05:46:36,355 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 32507
2019-08-16 05:46:36,355 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 05:46:37,357 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 05:46:37,357 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=32507
2019-08-16 05:46:37,413 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [32507] (in reverse order)
2019-08-16 05:46:37,457 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 05:46:37,457 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 05:46:37,457 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 05:46:37,458 | 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 05:46:37,968 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 05:46:48,004 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 05:46:48,004 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 05:46:48,039 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34670116864 B)
2019-08-16 05:46:48,040 | 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 05:46:48,040 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 05:46:48,059 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 05:46:48,120 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 05:46:48,120 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 05:46:48,185 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 05:46:48,206 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 05:46:48,220 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 05:46:48,221 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job, started 140684811736832)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(copytool_in, started 140684245845760)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(validate_pre, started 140684769773312)>, <ExcThread(execute_payloads, started 140683667044096)>, <ExcThread(create_data_payload, started 140684786558720)>, <ExcThread(queue_monitoring, started 140684262631168)>, <ExcThread(failed_post, started 140684220667648)>, <ExcThread(payload, started 140684778166016)>]
2019-08-16 05:46:48,228 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 05:46:48,228 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 05:46:48,422 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 05:46:48,422 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(copytool_in, started 140684245845760)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(validate_pre, started 140684769773312)>, <ExcThread(execute_payloads, started 140683667044096)>, <ExcThread(create_data_payload, started 140684786558720)>, <ExcThread(queue_monitoring, started 140684262631168)>, <ExcThread(failed_post, started 140684220667648)>, <ExcThread(payload, started 140684778166016)>]
2019-08-16 05:46:48,580 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 05:46:48,581 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 05:46:48,623 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-16 05:46:48,624 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(validate_pre, started 140684769773312)>, <ExcThread(execute_payloads, started 140683667044096)>, <ExcThread(queue_monitoring, started 140684262631168)>, <ExcThread(failed_post, started 140684220667648)>, <ExcThread(payload, started 140684778166016)>]
2019-08-16 05:46:48,831 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 05:46:48,853 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 05:46:49,026 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-16 05:46:49,026 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(queue_monitoring, started 140684262631168)>, <ExcThread(failed_post, started 140684220667648)>, <ExcThread(payload, started 140684778166016)>]
2019-08-16 05:46:49,031 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 05:46:49,031 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 05:46:49,121 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 05:46:49,127 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 05:46:49,127 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(queue_monitoring, started 140684262631168)>, <ExcThread(failed_post, started 140684220667648)>]
2019-08-16 05:46:49,285 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 05:46:49,329 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 05:46:49,329 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(queue_monitor, started 140684229060352)>, <ExcThread(queue_monitoring, started 140684262631168)>]
2019-08-16 05:46:49,833 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 05:46:49,833 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 05:46:49,883 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 05:46:49,933 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 05:46:49,933 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(copytool_out, started 140684761380608)>, <ExcThread(queue_monitoring, started 140684262631168)>]
2019-08-16 05:46:50,121 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 05:46:50,135 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 05:46:50,135 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>, <ExcThread(queue_monitoring, started 140684262631168)>]
2019-08-16 05:46:52,884 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 05:46:52,953 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 05:46:52,954 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140685028009728)>, <ExcThread(job_monitor, started 140684237453056)>]
2019-08-16 05:47:21,847 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-16 05:47:21,848 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 05:47:21,948 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 05:47:21,949 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 05:47:21,949 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 05:47:22 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 05:47:22 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 05:47:22 UTC [wrapper] Pilot exit status: 0
2019-08-16 05:47:22 UTC [wrapper] STATUSCODE: 0
2019-08-16 05:47:22 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 05:41 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 05:47:22 UTC [wrapper] Test setup, not cleaning
2019-08-16 05:47:22 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 05:47:22 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 05:47:22 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7546
2019-08-16 05:47:22 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7546.02s
KernelTime=237.16s
UserTime=27730.29s
CPUUsage=370%
MaxResidentMemory=1945076kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=296233
MinorPageFaults=13516711
Swaps=0
ForcedSwitches=3213341
WaitSwitches=5943974
Inputs=72105616
Outputs=507304
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 381152
drwxrwx--x. 6 grid grid      4096 Aug 16 07:47 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7413078 Aug 16 05:41 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438118 Aug 16 05:41 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 05:41 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 05:41 APPS
-rw-------. 1 grid grid       538 Aug 16 05:41 .asetup
-rw-------. 1 grid grid       826 Aug 16 05:42 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 05:41 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 07:47 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 16 07:41 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 376410754 Aug 16 05:41 EVNT.17323813._001012.pool.root.1
-rw-------. 1 grid grid     71147 Aug 16 07:46 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 05:41 init_data.xml
-rw-rw-r--. 1 grid grid    261620 Aug 16 05:41 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 16 05:41 job.xml
-rw-------. 1 grid grid    456732 Aug 16 07:47 log.18604976._051936.job.log.1
-rw-------. 1 grid grid    826104 Aug 16 07:46 log.18604976._051936.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 07:47 output.list
-rw-------. 1 grid grid      2872 Aug 15 16:56 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 15 16:29 pilot2.tar.gz
-rw-------. 1 grid grid     10824 Aug 16 07:47 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 15 16:56 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 05:41 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 05:41 run_atlas
-rwx------. 1 grid grid     12641 Aug 15 16:56 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 07:47 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 07:47 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 07:47 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 05:41 start_atlas.sh
-rw-rw-r--. 1 grid grid     18482 Aug 16 07:47 stderr.txt
-rw-------. 1 grid grid       516 Aug 16 07:47 T54NDmbMWIvnShfckohDCDFpABFKDmABFKDmeLbbDmABFKDmadaBmm.diag
-rw-rw-r--. 1 grid grid       107 Aug 16 05:41 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 16 07:47 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
07:47:22 (25843): run_atlas exited; CPU time 27730.710487
07:47:22 (25843): called boinc_finish(0)

</stderr_txt>
]]>

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