Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
21:41:42 (21500): wrapper (7.7.26015): starting
21:41:42 (21500): 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=4444916299
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.18605019._042490.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-12 21:14:25,473 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4444916299
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18605019
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 19942 s
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 28178
2019-08-12 21:14:25,474 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 28178
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4444916299 has completed
2019-08-12 21:14:25,475 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-12 21:14:25,482 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4444916299
2019-08-12 21:14:26,486 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [28178]
2019-08-12 21:14:26,486 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 28178
2019-08-12 21:14:26,486 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-12 21:14:27,487 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-12 21:14:27,488 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=28178
2019-08-12 21:14:27,536 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [28178] (in reverse order)
2019-08-12 21:14:27,575 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-12 21:14:27,575 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-12 21:14:27,575 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-12 21:14:27,575 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-12 21:14:28,087 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-12 21:14:38,133 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-12 21:14:38,134 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-12 21:14:38,177 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34086060032 B)
2019-08-12 21:14:38,178 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-12 21:14:38,178 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-12 21:14:38,190 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-12 21:14:38,203 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-12 21:14:38,226 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-12 21:14:38,248 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-12 21:14:38,419 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-12 21:14:38,419 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(job, started 140511672297216)>, <ExcThread(create_data_payload, started 140511647119104)>, <ExcThread(data, started 140511655511808)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(execute_payloads, started 140510593283840)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(monitor, started 140511130154752)>, <ExcThread(copytool_in, started 140511104976640)>, <ExcThread(queue_monitor, started 140511096583936)>, <ExcThread(validate_pre, started 140511613548288)>, <ExcThread(payload, started 140511630333696)>]
2019-08-12 21:14:38,576 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-12 21:14:38,576 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-12 21:14:38,714 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-12 21:14:38,821 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-12 21:14:38,822 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(job, started 140511672297216)>, <ExcThread(create_data_payload, started 140511647119104)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(monitor, started 140511130154752)>, <ExcThread(copytool_in, started 140511104976640)>, <ExcThread(queue_monitor, started 140511096583936)>, <ExcThread(validate_pre, started 140511613548288)>, <ExcThread(payload, started 140511630333696)>]
2019-08-12 21:14:38,829 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-12 21:14:38,860 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-12 21:14:38,970 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-12 21:14:38,970 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-12 21:14:39,087 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-12 21:14:39,087 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(copytool_in, started 140511104976640)>, <ExcThread(queue_monitor, started 140511096583936)>, <ExcThread(validate_pre, started 140511613548288)>, <ExcThread(payload, started 140511630333696)>]
2019-08-12 21:14:39,130 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-12 21:14:39,131 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-12 21:14:39,188 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-12 21:14:39,188 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(copytool_in, started 140511104976640)>, <ExcThread(queue_monitor, started 140511096583936)>, <ExcThread(validate_pre, started 140511613548288)>]
2019-08-12 21:14:39,265 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-12 21:14:39,464 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-12 21:14:39,490 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-12 21:14:39,491 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(copytool_in, started 140511104976640)>, <ExcThread(queue_monitor, started 140511096583936)>]
2019-08-12 21:14:39,591 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-12 21:14:39,592 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-12 21:14:39,592 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>, <ExcThread(queue_monitor, started 140511096583936)>]
2019-08-12 21:14:39,905 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-12 21:14:39,905 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-12 21:14:39,995 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-12 21:14:39,996 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(copytool_out, started 140511638726400)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>]
2019-08-12 21:14:40,265 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-12 21:14:40,299 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-12 21:14:40,299 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(queue_monitoring, started 140511121762048)>, <ExcThread(job_monitor, started 140511113369344)>]
2019-08-12 21:14:41,199 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-12 21:14:41,206 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-12 21:14:41,206 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511888570112)>, <ExcThread(job_monitor, started 140511113369344)>]
2019-08-12 21:15:17,819 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-12 21:15:17,819 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-12 21:15:17,869 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-12 21:15:17,870 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-12 21:15:17,870 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-12 21:15:18 UTC [wrapper] ==== pilot stdout END ====
2019-08-12 21:15:18 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-12 21:15:18 UTC [wrapper] Pilot exit status: 0
2019-08-12 21:15:18 UTC [wrapper] STATUSCODE: 0
2019-08-12 21:15:18 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 12 21:42 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

2019-08-12 21:15:18 UTC [wrapper] Test setup, not cleaning
2019-08-12 21:15:18 UTC [wrapper] ==== wrapper stdout END ====
2019-08-12 21:15:18 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5610.29s
KernelTime=195.70s
UserTime=19854.54s
CPUUsage=357%
MaxResidentMemory=1945008kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=260842
MinorPageFaults=12352669
Swaps=0
ForcedSwitches=2342083
WaitSwitches=5127937
Inputs=63674736
Outputs=484720
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 379800
drwxrwx--x. 7 grid grid      4096 Aug 12 23:15 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 12 23:15 2wgLDmCsOHvnShfckohDCDFpABFKDmABFKDm3YnZDmABFKDmZvbAln.diag
-rw-------. 1 grid grid   7409065 Aug 12 21:42 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517799 Aug 12 21:42 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 12 21:41 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 12 21:41 APPS
drwxr-xr-x. 2 grid grid         6 Aug 12 21:42 .arc
-rw-------. 1 grid grid       538 Aug 12 21:41 .asetup
-rw-------. 1 grid grid       826 Aug 12 21:42 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 12 21:41 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 23:15 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 12 23:08 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 375064224 Aug 12 21:41 EVNT.17323843._000832.pool.root.1
-rw-------. 1 grid grid     54971 Aug 12 23:14 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 12 21:41 init_data.xml
-rw-rw-r--. 1 grid grid    262348 Aug 12 21:41 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 12 21:41 job.xml
-rw-------. 1 grid grid    375979 Aug 12 23:15 log.18605019._042490.job.log.1
-rw-------. 1 grid grid    808718 Aug 12 23:14 log.18605019._042490.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 12 23:15 output.list
-rw-------. 1 grid grid      2887 Aug 12 14:44 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 12 14:39 pilot2.tar.gz
-rw-------. 1 grid grid     10796 Aug 12 23:15 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 12 14:40 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 12 21:41 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 12 21:41 run_atlas
-rwx------. 1 grid grid     15232 Aug 12 14:44 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 23:15 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 23:15 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 23:15 shared
-rw-rw-r--. 1 grid grid      8688 Aug 12 21:41 start_atlas.sh
-rw-rw-r--. 1 grid grid     18641 Aug 12 23:15 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 12 21:41 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 12 23:15 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
23:15:18 (21500): run_atlas exited; CPU time 19855.068648
23:15:18 (21500): called boinc_finish(0)

</stderr_txt>
]]>

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