Stderr output

<core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
07:02:49 (34849): wrapper (7.7.26015): starting
07:02:49 (34849): wrapper: running run_atlas (--nthreads 8)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '8']
THREADS=8
Checking for CVMFS
CVMFS is installed
OS:cat: /etc/redhat-release: No such file or directory

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is installed, version 2.4.2-dist
Testing the function of Singularity...
Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
Singularity Works...

copy /var/lib/boinc2/slots/1/shared/RTE.tar.gz
copy /var/lib/boinc2/slots/1/shared/ATLAS.root_0
copy /var/lib/boinc2/slots/1/shared/input.tar.gz
copy /var/lib/boinc2/slots/1/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=8;start atlas job with PandaID=4442745579
cmd = singularity exec --pwd /var/lib/boinc2/slots/1 -B /cvmfs,/var /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.18722398._016210.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 14:51:23,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442745579
2019-08-13 14:51:23,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-13 14:51:23,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 35389 s
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 14:51:23,256 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 2894
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 2894
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 8
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442745579 has completed
2019-08-13 14:51:23,257 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 14:51:23,262 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc2/slots/1/PanDA_Pilot-4442745579
2019-08-13 14:51:24,267 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2894]
2019-08-13 14:51:24,267 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2894
2019-08-13 14:51:24,267 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 14:51:25,272 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 14:51:25,272 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2894
2019-08-13 14:51:25,398 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2894] (in reverse order)
2019-08-13 14:51:25,529 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 14:51:25,530 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 14:51:25,530 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 14:51:25,530 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 14:51:26,039 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 14:51:30,417 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-13 14:51:36,087 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 14:51:36,087 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc2/slots/1
2019-08-13 14:51:36,133 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (273018781696 B)
2019-08-13 14:51:36,134 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 14:51:36,134 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 14:51:36,170 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 14:51:36,176 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 14:51:36,207 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 14:51:36,370 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-13 14:51:36,370 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(job, started 140511059539712)>, <ExcThread(copytool_in, started 140509989304064)>, <ExcThread(failed_post, started 140510492604160)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(validate, started 140511042754304)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>, <ExcThread(data, started 140511051147008)>, <ExcThread(create_data_payload, started 140511017576192)>, <ExcThread(execute_payloads, started 140510484211456)>, <ExcThread(validate_pre, started 140511009183488)>, <ExcThread(payload, started 140511025968896)>]
2019-08-13 14:51:36,372 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 14:51:36,522 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 14:51:36,522 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 14:51:36,615 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 14:51:36,657 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 14:51:36,657 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 14:51:36,671 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 14:51:36,672 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(job, started 140511059539712)>, <ExcThread(failed_post, started 140510492604160)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>, <ExcThread(validate_pre, started 140511009183488)>, <ExcThread(payload, started 140511025968896)>]
2019-08-13 14:51:36,810 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 14:51:36,811 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 14:51:36,873 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 14:51:36,873 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(job, started 140511059539712)>, <ExcThread(failed_post, started 140510492604160)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>, <ExcThread(validate_pre, started 140511009183488)>]
2019-08-13 14:51:36,973 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 14:51:36,974 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 14:51:36,974 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 14:51:36,974 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(failed_post, started 140510492604160)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>, <ExcThread(validate_pre, started 140511009183488)>]
2019-08-13 14:51:37,042 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 14:51:37,075 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-13 14:51:37,075 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(failed_post, started 140510492604160)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>]
2019-08-13 14:51:37,133 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 14:51:37,398 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 14:51:37,477 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 14:51:37,478 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitor, started 140509980911360)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>]
2019-08-13 14:51:37,733 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 14:51:37,733 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 14:51:37,779 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 14:51:37,779 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(copytool_out, started 140511034361600)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>]
2019-08-13 14:51:38,133 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 14:51:38,181 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 14:51:38,181 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(queue_monitoring, started 140510509389568)>, <ExcThread(job_monitor, started 140510475818752)>]
2019-08-13 14:51:39,171 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 14:51:39,187 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 14:51:39,187 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140511275022080)>, <ExcThread(job_monitor, started 140510475818752)>]
2019-08-13 14:52:32,017 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-08-13 14:52:32,017 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 14:52:32,099 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 14:52:32,100 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 14:52:32,100 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 14:52:32 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 14:52:32 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 14:52:32 UTC [wrapper] Pilot exit status: 0
2019-08-13 14:52:32 UTC [wrapper] STATUSCODE: 0
2019-08-13 14:52:32 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-rw-r--  1 320 320 11357 Jul 25 08:38 LICENSE
drwxrwxr-x 14 320 320  4096 Aug 13 07:03 pilot
-rwxrwxr-x  1 320 320 20463 Jul 25 08:38 pilot.py
-rw-r--r--  1 320 320     8 Aug  7 05:02 PILOTVERSION
-rw-rw-r--  1 320 320  2251 Jul 25 08:38 README.md
-rw-rw-r--  1 320 320   221 Jul 25 08:38 TODO.md

2019-08-13 14:52:32 UTC [wrapper] Test setup, not cleaning
2019-08-13 14:52:32 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 14:52:32 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6581.47s
KernelTime=425.84s
UserTime=35080.40s
CPUUsage=539%
MaxResidentMemory=1959208kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=547312
MinorPageFaults=22688862
Swaps=0
ForcedSwitches=213079
WaitSwitches=7357070
Inputs=75760232
Outputs=639104
SocketReceived=0
SocketSent=0
Signals=0

nodename=wHewitt@d8
exitcode=0
******************************WorkDir***********************
total 216388
drwxrwxrwx  7 root root      4096 Aug 13 08:52 .
drwxrwxrwx 33 root root      4096 Aug 12 15:18 ..
-rw-------  1 root root   7409065 Aug 13 07:03 agis_ddmendpoints.json
-rw-------  1 root root   4517361 Aug 13 07:03 agis_schedconf.cvmfs.json
drwx------  2 root root      4096 Aug 13 07:02 .alrb
drwxr-xr-x  3 root root      4096 Aug 13 07:02 APPS
drwxr-xr-x  2 root root      4096 Aug 13 07:03 .arc
-rw-------  1 root root       543 Aug 13 07:02 .asetup
-rw-------  1 root root       829 Aug 13 07:03 .asetup.save
-rw-r--r--  1 root root         0 Aug 13 07:02 boinc_lockfile
-rw-r--r--  1 root root      8192 Aug 13 08:52 boinc_mmap_file
-rw-r--r--  1 root root       536 Aug 13 08:42 boinc_task_state.xml
-rw-r--r--  1 root root 207233352 Aug 13 07:02 EVNT.18605775._000318.pool.root.1
-rw-------  1 root root     70399 Aug 13 08:51 heartbeat.json
-rw-r--r--  1 root root      8501 Aug 13 08:34 init_data.xml
-rw-r--r--  1 root root    262345 Aug 13 07:02 input.tar.gz
-rw-r--r--  1 root root       112 Aug 13 07:02 job.xml
-rw-------  1 root root    470591 Aug 13 08:52 log.18722398._016210.job.log.1
-rw-------  1 root root   1165778 Aug 13 08:51 log.18722398._016210.job.log.tgz.1
-rw-------  1 root root       391 Aug 13 08:52 output.list
-rw-------  1 4871 1028      2957 Aug 10 03:08 pandaJobData.out
drwxr-xr-x  3  320  320      4096 Aug  7 05:02 pilot2
-rw-r--r--  1 root root    253018 Aug 10 02:36 pilot2.tar.gz
-rw-------  1 root root     10925 Aug 13 08:52 pilotlog.txt
-rw-r--r--  1 root root      4468 Aug 10 03:08 queuedata.json
-rw-r--r--  1 root root       815 Aug 13 07:02 RTE.tar.gz
-rwxr-xr-x  1 root root      8779 Aug 13 07:02 run_atlas
-rwx------  1 4871 1028     15232 Aug 10 03:08 runpilot2-wrapper.sh
-rw-r--r--  1 root root       692 Aug 13 08:52 runtime_log
-rw-r--r--  1 root root      6844 Aug 13 08:52 runtime_log.err
drwxrwx--x  2 root root      4096 Aug 13 08:52 shared
-rw-r--r--  1 root root      8688 Aug 13 07:02 start_atlas.sh
-rw-r--r--  1 root root     18433 Aug 13 08:52 stderr.txt
-rw-------  1 root root       493 Aug 13 08:52 TkuNDmlXcGvnShfckohDCDFpABFKDmABFKDmugXYDmABFKDmAHdsan.diag
-rw-r--r--  1 root root       107 Aug 13 07:02 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--  1 root root        27 Aug 13 08:52 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
08:52:32 (34849): run_atlas exited; CPU time 35080.616000
08:52:32 (34849): called boinc_finish(0)

</stderr_txt>
]]>

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