Stderr output

<core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
04:47:07 (52003): wrapper (7.7.26015): starting
04:47:07 (52003): 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=4442981970
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.18722432._013761.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442981970
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722432
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 13:01:58,921 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 53086 s
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 18434
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 18434
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 8
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442981970 has completed
2019-08-13 13:01:58,922 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 13:01:58,927 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc2/slots/1/PanDA_Pilot-4442981970
2019-08-13 13:01:59,932 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [18434]
2019-08-13 13:01:59,933 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 18434
2019-08-13 13:01:59,933 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 13:02:00,937 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 13:02:00,937 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=18434
2019-08-13 13:02:01,063 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [18434] (in reverse order)
2019-08-13 13:02:01,168 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 13:02:01,169 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 13:02:01,169 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 13:02:01,169 | 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 13:02:01,675 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 13:02:11,725 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 13:02:11,726 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc2/slots/1
2019-08-13 13:02:11,752 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (274616811520 B)
2019-08-13 13:02:11,752 | 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 13:02:11,752 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 13:02:11,787 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 13:02:11,789 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 13:02:11,831 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 13:02:12,007 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 13:02:12,007 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 13:02:12,015 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-13 13:02:12,016 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(job, started 139658500855552)>, <ExcThread(validate, started 139658492462848)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(failed_post, started 139657497011968)>, <ExcThread(copytool_in, started 139658067420928)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(execute_payloads, started 139657488619264)>, <ExcThread(validate_post, started 139658059028224)>, <ExcThread(payload, started 139658458892032)>, <ExcThread(validate_pre, started 139658084206336)>, <ExcThread(copytool_out, started 139658467284736)>]
2019-08-13 13:02:12,059 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 13:02:12,059 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 13:02:12,217 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-13 13:02:12,217 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(job, started 139658500855552)>, <ExcThread(validate, started 139658492462848)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(failed_post, started 139657497011968)>, <ExcThread(copytool_in, started 139658067420928)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(execute_payloads, started 139657488619264)>, <ExcThread(validate_post, started 139658059028224)>, <ExcThread(validate_pre, started 139658084206336)>, <ExcThread(copytool_out, started 139658467284736)>]
2019-08-13 13:02:12,223 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 13:02:12,371 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 13:02:12,371 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 13:02:12,382 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-13 13:02:12,382 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(validate, started 139658492462848)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(copytool_in, started 139658067420928)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(execute_payloads, started 139657488619264)>, <ExcThread(validate_post, started 139658059028224)>, <ExcThread(validate_pre, started 139658084206336)>, <ExcThread(copytool_out, started 139658467284736)>]
2019-08-13 13:02:12,525 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 13:02:12,583 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 13:02:12,583 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(validate, started 139658492462848)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(copytool_in, started 139658067420928)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(execute_payloads, started 139657488619264)>, <ExcThread(validate_pre, started 139658084206336)>, <ExcThread(copytool_out, started 139658467284736)>]
2019-08-13 13:02:12,686 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 13:02:12,784 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 13:02:12,785 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(copytool_in, started 139658067420928)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(execute_payloads, started 139657488619264)>, <ExcThread(validate_pre, started 139658084206336)>, <ExcThread(copytool_out, started 139658467284736)>]
2019-08-13 13:02:12,787 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 13:02:12,834 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 13:02:12,858 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 13:02:12,885 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 13:02:12,886 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(queue_monitoring, started 139658100991744)>, <ExcThread(validate_pre, started 139658084206336)>]
2019-08-13 13:02:12,987 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 13:02:13,021 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 13:02:13,087 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 13:02:13,087 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(queue_monitor, started 139657505404672)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(queue_monitoring, started 139658100991744)>]
2019-08-13 13:02:13,265 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 13:02:13,265 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 13:02:13,288 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 13:02:13,289 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(job_monitor, started 139658075813632)>, <ExcThread(queue_monitoring, started 139658100991744)>]
2019-08-13 13:02:16,022 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 13:02:16,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 13:02:16,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139658716337920)>, <ExcThread(job_monitor, started 139658075813632)>]
2019-08-13 13:02:44,260 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-13 13:02:44,260 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 13:02:44,263 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 13:02:44,263 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 13:02:44,263 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 13:02:44 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 13:02:44 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 13:02:44 UTC [wrapper] Pilot exit status: 0
2019-08-13 13:02:44 UTC [wrapper] STATUSCODE: 0
2019-08-13 13:02:44 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 04:47 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 13:02:44 UTC [wrapper] Test setup, not cleaning
2019-08-13 13:02:44 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 13:02:44 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8135.57s
KernelTime=590.92s
UserTime=52628.57s
CPUUsage=654%
MaxResidentMemory=1983480kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=475850
MinorPageFaults=26144540
Swaps=0
ForcedSwitches=286723
WaitSwitches=8190796
Inputs=84623976
Outputs=752608
SocketReceived=0
SocketSent=0
Signals=0

nodename=wHewitt@d8
exitcode=0
******************************WorkDir***********************
total 230136
drwxrwxrwx  7 root root      4096 Aug 13 07:02 .
drwxrwxrwx 33 root root      4096 Aug 12 15:18 ..
-rw-------  1 root root       493 Aug 13 07:02 3CnKDmYnnGvnShfckohDCDFpABFKDmABFKDmclpYDmABFKDmNBDtOn.diag
-rw-------  1 root root   7409065 Aug 13 04:47 agis_ddmendpoints.json
-rw-------  1 root root   4517399 Aug 13 04:47 agis_schedconf.cvmfs.json
drwx------  2 root root      4096 Aug 13 04:47 .alrb
drwxr-xr-x  3 root root      4096 Aug 13 04:47 APPS
drwxr-xr-x  2 root root      4096 Aug 13 04:47 .arc
-rw-------  1 root root       543 Aug 13 04:47 .asetup
-rw-------  1 root root       829 Aug 13 04:47 .asetup.save
-rw-r--r--  1 root root         0 Aug 13 04:47 boinc_lockfile
-rw-r--r--  1 root root      8192 Aug 13 07:02 boinc_mmap_file
-rw-r--r--  1 root root       536 Aug 13 06:46 boinc_task_state.xml
-rw-r--r--  1 root root 221140412 Aug 13 04:47 EVNT.18605781._000281.pool.root.1
-rw-------  1 root root    110278 Aug 13 07:01 heartbeat.json
-rw-r--r--  1 root root      8513 Aug 13 04:47 init_data.xml
-rw-r--r--  1 root root    262346 Aug 13 04:47 input.tar.gz
-rw-r--r--  1 root root       112 Aug 13 04:47 job.xml
-rw-------  1 root root    577839 Aug 13 07:02 log.18722432._013761.job.log.1
-rw-------  1 root root   1186260 Aug 13 07:01 log.18722432._013761.job.log.tgz.1
-rw-------  1 root root       391 Aug 13 07:02 output.list
-rw-------  1 4871 1028      2957 Aug 10 15:09 pandaJobData.out
drwxr-xr-x  3  320  320      4096 Aug  7 05:02 pilot2
-rw-r--r--  1 root root    253018 Aug 10 14:38 pilot2.tar.gz
-rw-------  1 root root     11183 Aug 13 07:02 pilotlog.txt
-rw-r--r--  1 root root      4468 Aug 10 15:09 queuedata.json
-rw-r--r--  1 root root       815 Aug 13 04:47 RTE.tar.gz
-rwxr-xr-x  1 root root      8779 Aug 13 04:47 run_atlas
-rwx------  1 4871 1028     15232 Aug 10 15:09 runpilot2-wrapper.sh
-rw-r--r--  1 root root       692 Aug 13 07:02 runtime_log
-rw-r--r--  1 root root      6844 Aug 13 07:02 runtime_log.err
drwxrwx--x  2 root root      4096 Aug 13 07:02 shared
-rw-r--r--  1 root root      8688 Aug 13 04:47 start_atlas.sh
-rw-r--r--  1 root root     18870 Aug 13 07:02 stderr.txt
-rw-r--r--  1 root root       107 Aug 13 04:47 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--  1 root root        27 Aug 13 07:02 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
07:02:45 (52003): run_atlas exited; CPU time 52628.708000
07:02:45 (52003): called boinc_finish(0)

</stderr_txt>
]]>

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