Stderr output

<core_client_version>7.5.1</core_client_version>
<![CDATA[
<stderr_txt>
10:45:48 (25637): wrapper (7.7.26015): starting
10:45:48 (25637): wrapper: running run_atlas (--nthreads 1)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '1']
THREADS=1
Checking for CVMFS
CVMFS is installed
OS:Scientific Linux release 7.6 (Nitrogen)

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity seems to be installed but not working: %s
 Will use 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 /root/Downloads/BOINC/slots/2/shared/ATLAS.root_0
copy /root/Downloads/BOINC/slots/2/shared/input.tar.gz
copy /root/Downloads/BOINC/slots/2/shared/RTE.tar.gz
copy /root/Downloads/BOINC/slots/2/shared/start_atlas.sh
start atlas job with PandaID=4445586893
cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /root/Downloads/BOINC/slots/2 -B /cvmfs,/root /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._024547.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 06:41:20,666 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 06:41:20,666 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-16 06:41:20,666 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 06:41:20,666 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4445586893
2019-08-16 06:41:20,666 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722432
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 06:41:20,667 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 06:41:20,668 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 06:41:20,674 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 06:41:20,675 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 80390 s
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 5101
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 5101
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 06:41:20,676 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 06:41:20,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 06:41:20,677 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4445586893 has completed
2019-08-16 06:41:20,677 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 06:41:20,679 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /root/Downloads/BOINC/slots/2/PanDA_Pilot-4445586893
2019-08-16 06:41:21,692 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [5101]
2019-08-16 06:41:21,692 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 5101
2019-08-16 06:41:21,692 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 06:41:22,714 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 06:41:22,714 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=5101
2019-08-16 06:41:23,085 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [5101] (in reverse order)
2019-08-16 06:41:23,267 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 06:41:23,268 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 06:41:23,268 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 06:41:23,268 | 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 06:41:23,860 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 06:41:33,915 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 06:41:33,915 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /root/Downloads/BOINC/slots/2
2019-08-16 06:41:34,139 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (7559184384 B)
2019-08-16 06:41:34,140 | 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 06:41:34,140 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 06:41:34,157 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 06:41:34,165 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 06:41:34,558 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-16 06:41:34,568 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(job, started 139821390456576)>, <ExcThread(failed_post, started 139820798023424)>, <ExcThread(data, started 139821373671168)>, <ExcThread(validate, started 139821382063872)>, <ExcThread(validate_post, started 139820806416128)>, <ExcThread(validate_pre, started 139820839986944)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(copytool_in, started 139820831594240)>, <ExcThread(execute_payloads, started 139820244399872)>, <ExcThread(job_monitor, started 139820823201536)>, <ExcThread(create_data_payload, started 139821348493056)>, <ExcThread(queue_monitor, started 139820814808832)>, <ExcThread(payload, started 139821365278464)>, <ExcThread(copytool_out, started 139821356885760)>]
2019-08-16 06:41:34,589 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 06:41:34,630 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 06:41:34,651 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 06:41:34,652 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 06:41:34,866 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 06:41:34,880 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 06:41:34,880 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(job, started 139821390456576)>, <ExcThread(failed_post, started 139820798023424)>, <ExcThread(validate_post, started 139820806416128)>, <ExcThread(validate_pre, started 139820839986944)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(copytool_in, started 139820831594240)>, <ExcThread(job_monitor, started 139820823201536)>, <ExcThread(queue_monitor, started 139820814808832)>, <ExcThread(payload, started 139821365278464)>, <ExcThread(copytool_out, started 139821356885760)>]
2019-08-16 06:41:34,882 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 06:41:35,063 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 06:41:35,122 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 06:41:35,146 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 06:41:35,181 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 06:41:35,181 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 06:41:35,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-16 06:41:35,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(job, started 139821390456576)>, <ExcThread(validate_pre, started 139820839986944)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(job_monitor, started 139820823201536)>, <ExcThread(queue_monitor, started 139820814808832)>, <ExcThread(copytool_out, started 139821356885760)>]
2019-08-16 06:41:35,268 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 06:41:35,268 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 06:41:35,340 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 06:41:35,341 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 06:41:35,348 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 06:41:35,349 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(validate_pre, started 139820839986944)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(job_monitor, started 139820823201536)>, <ExcThread(copytool_out, started 139821356885760)>]
2019-08-16 06:41:35,502 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 06:41:35,552 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 06:41:35,552 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(job_monitor, started 139820823201536)>, <ExcThread(copytool_out, started 139821356885760)>]
2019-08-16 06:41:36,163 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 06:41:36,200 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 06:41:36,201 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(queue_monitoring, started 139821331707648)>, <ExcThread(job_monitor, started 139820823201536)>]
2019-08-16 06:41:37,229 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 06:41:37,333 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 06:41:37,333 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139821607261952)>, <ExcThread(job_monitor, started 139820823201536)>]
2019-08-16 06:41:39,314 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 06:41:39,315 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 06:41:39,359 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 06:41:39,360 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 06:41:39,360 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 06:41:40 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 06:41:40 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 06:41:40 UTC [wrapper] Pilot exit status: 0
2019-08-16 06:41:40 UTC [wrapper] STATUSCODE: 0
2019-08-16 06:41:40 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
insgesamt 44
-rw-rw-r--.  1 root root 11357 25. Jul 16:38 LICENSE
drwxrwxr-x. 14 root root   216 15. Aug 10:50 pilot
-rwxrwxr-x.  1 root root 20463 25. Jul 16:38 pilot.py
-rw-r--r--.  1 root root     8  7. Aug 13:02 PILOTVERSION
-rw-rw-r--.  1 root root  2251 25. Jul 16:38 README.md
-rw-rw-r--.  1 root root   221 25. Jul 16:38 TODO.md

2019-08-16 06:41:41 UTC [wrapper] Test setup, not cleaning
2019-08-16 06:41:41 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 06:41:41 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 06:41:41 UTC [wrapper] wrapper wrapperexiting ec=0, duration=78880
2019-08-16 06:41:41 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=78880.58s
KernelTime=33622.11s
UserTime=79791.05s
CPUUsage=143%
MaxResidentMemory=1949800kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=1361348
MinorPageFaults=41199304
Swaps=0
ForcedSwitches=1585155
WaitSwitches=38896262
Inputs=320023912
Outputs=455800
SocketReceived=0
SocketSent=0
Signals=0

nodename=maeax@RYZSL76
exitcode=0
******************************WorkDir***********************
insgesamt 230816
drwxrwx--x. 6 root root      4096 16. Aug 08:41 .
drwxr-x--x. 8 root root        60 16. Aug 04:13 ..
-rw-------. 1 root root   7409162 15. Aug 10:51 agis_ddmendpoints.json
-rw-------. 1 root root   4438522 15. Aug 10:51 agis_schedconf.cvmfs.json
drwx------. 2 root root         6 15. Aug 10:47 .alrb
drwxr-xr-x. 3 root root        17 15. Aug 10:46 APPS
-rw-------. 1 root root       549 15. Aug 10:48 .asetup
-rw-------. 1 root root       826 15. Aug 11:01 .asetup.save
-rw-r--r--. 1 root root         0 15. Aug 10:45 boinc_lockfile
-rw-r--r--. 1 root root      8192 16. Aug 08:41 boinc_mmap_file
-rw-r--r--. 1 root root       538 16. Aug 08:38 boinc_task_state.xml
-rw-r--r--. 1 root root 219563092 15. Aug 10:46 EVNT.18605781._000494.pool.root.1
-rw-------. 1 root root    104053 16. Aug 08:41 heartbeat.json
-rw-r--r--. 1 root root      5553 15. Aug 10:45 init_data.xml
-rw-r--r--. 1 root root    261627 15. Aug 10:46 input.tar.gz
-rw-r--r--. 1 root root       112 15. Aug 10:45 job.xml
-rw-------. 1 root root   3474930 16. Aug 08:41 log.18722432._024547.job.log.1
-rw-------. 1 root root    419891 16. Aug 08:40 log.18722432._024547.job.log.tgz.1
-rw-------. 1 root root       503 16. Aug 08:41 NRdMDmfl8HvnShfckohDCDFpABFKDmABFKDmsH0aDmABFKDmO9rROn.diag
-rw-------. 1 root root       391 16. Aug 08:41 output.list
-rw-------. 1 root root      2957 14. Aug 15:45 pandaJobData.out
drwxr-xr-x. 3 root root       174  7. Aug 13:02 pilot2
-rw-r--r--. 1 root root    253018 14. Aug 15:26 pilot2.tar.gz
-rw-------. 1 root root      9599 16. Aug 08:41 pilotlog.txt
-rw-r--r--. 1 root root      4468 14. Aug 15:45 queuedata.json
-rw-r--r--. 1 root root       815 15. Aug 10:46 RTE.tar.gz
-rwxr-xr-x. 1 root root      8779 15. Aug 10:45 run_atlas
-rwx------. 1 root root     12641 14. Aug 15:45 runpilot2-wrapper.sh
-rw-r--r--. 1 root root       692 16. Aug 08:41 runtime_log
-rw-r--r--. 1 root root      7312 16. Aug 08:41 runtime_log.err
drwxrwx--x. 2 root root       131 16. Aug 08:41 shared
-rw-r--r--. 1 root root      8659 15. Aug 10:46 start_atlas.sh
-rw-r--r--. 1 root root     17901 16. Aug 08:41 stderr.txt
-rw-r--r--. 1 root root       107 15. Aug 10:45 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 root root        29 16. Aug 08:41 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
08:41:46 (25637): run_atlas exited; CPU time 79795.842795
08:41:46 (25637): called boinc_finish(0)

</stderr_txt>
]]>

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