Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
19:15:29 (12364): wrapper (7.7.26015): starting
19:15:29 (12364): 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=4446599382
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.18604991._046290.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 19:12:48,843 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 19:12:48,843 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 19:12:48,843 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 19:12:48,843 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 25824 s
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 19054
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 19054
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446599382 has completed
2019-08-13 19:12:48,844 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 19:12:48,853 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446599382
2019-08-13 19:12:49,858 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [19054]
2019-08-13 19:12:49,858 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 19054
2019-08-13 19:12:49,858 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 19:12:50,864 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 19:12:50,864 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=19054
2019-08-13 19:12:50,917 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [19054] (in reverse order)
2019-08-13 19:12:50,957 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 19:12:50,958 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 19:12:50,958 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 19:12:50,958 | 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 19:12:51,468 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 19:12:56,893 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 19:13:01,508 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 19:13:01,509 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 19:13:01,543 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34341912576 B)
2019-08-13 19:13:01,544 | 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 19:13:01,544 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 19:13:01,559 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 19:13:01,587 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-13 19:13:01,588 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(job, started 140663820834560)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(copytool_in, started 140663182055168)>, <ExcThread(payload, started 140663710533376)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(create_data_payload, started 140663718926080)>, <ExcThread(failed_post, started 140663165269760)>, <ExcThread(validate, started 140663812441856)>, <ExcThread(validate_post, started 140663190447872)>, <ExcThread(data, started 140663735711488)>, <ExcThread(execute_payloads, started 140663148484352)>, <ExcThread(validate_pre, started 140663685355264)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:01,677 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 19:13:01,706 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 19:13:01,955 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 19:13:01,955 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 19:13:01,990 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-13 19:13:01,990 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(copytool_in, started 140663182055168)>, <ExcThread(payload, started 140663710533376)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(create_data_payload, started 140663718926080)>, <ExcThread(failed_post, started 140663165269760)>, <ExcThread(validate_post, started 140663190447872)>, <ExcThread(data, started 140663735711488)>, <ExcThread(validate_pre, started 140663685355264)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:02,031 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 19:13:02,057 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 19:13:02,057 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 19:13:02,189 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 19:13:02,191 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 19:13:02,191 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(create_data_payload, started 140663718926080)>, <ExcThread(validate_post, started 140663190447872)>, <ExcThread(data, started 140663735711488)>, <ExcThread(validate_pre, started 140663685355264)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:02,240 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 19:13:02,256 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 19:13:02,256 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 19:13:02,292 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 19:13:02,292 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(create_data_payload, started 140663718926080)>, <ExcThread(validate_post, started 140663190447872)>, <ExcThread(validate_pre, started 140663685355264)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:02,535 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 19:13:02,594 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 19:13:02,594 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(create_data_payload, started 140663718926080)>, <ExcThread(validate_pre, started 140663685355264)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:02,946 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 19:13:02,972 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 19:13:02,997 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 19:13:02,997 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>, <ExcThread(copytool_out, started 140663727318784)>]
2019-08-13 19:13:03,241 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 19:13:03,299 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 19:13:03,299 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitor, started 140663156877056)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>]
2019-08-13 19:13:03,347 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 19:13:03,350 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 19:13:03,350 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 19:13:03,400 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 19:13:03,401 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(queue_monitoring, started 140663702140672)>, <ExcThread(job_monitor, started 140663173662464)>]
2019-08-13 19:13:06,348 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 19:13:06,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 19:13:06,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140664037107456)>, <ExcThread(job_monitor, started 140663173662464)>]
2019-08-13 19:13:58,497 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-13 19:13:58,497 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 19:13:58,554 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 19:13:58,554 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 19:13:58,554 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 19:13:58 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 19:13:58 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 19:13:58 UTC [wrapper] Pilot exit status: 0
2019-08-13 19:13:58 UTC [wrapper] STATUSCODE: 0
2019-08-13 19:13:58 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 13 19:15 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

2019-08-13 19:13:58 UTC [wrapper] Test setup, not cleaning
2019-08-13 19:13:58 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 19:13:58 UTC [wrapper] ==== wrapper stderr END ====
2019-08-13 19:13:58 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7107
2019-08-13 19:13:58 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7107.11s
KernelTime=230.44s
UserTime=25706.65s
CPUUsage=364%
MaxResidentMemory=1945180kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=291119
MinorPageFaults=13250467
Swaps=0
ForcedSwitches=2984872
WaitSwitches=5729606
Inputs=70717192
Outputs=508120
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 379476
drwxrwx--x. 6 grid grid      4096 Aug 13 21:13 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409110 Aug 13 19:15 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517756 Aug 13 19:15 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 19:15 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 19:15 APPS
-rw-------. 1 grid grid       538 Aug 13 19:15 .asetup
-rw-------. 1 grid grid       826 Aug 13 19:16 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 19:15 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 21:13 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 13 21:06 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 374661598 Aug 13 19:15 EVNT.17323818._001251.pool.root.1
-rw-------. 1 grid grid     62577 Aug 13 21:12 heartbeat.json
-rw-rw-r--. 1 grid grid      5863 Aug 13 19:15 init_data.xml
-rw-rw-r--. 1 grid grid    261611 Aug 13 19:15 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 13 19:15 job.xml
-rw-------. 1 grid grid    434055 Aug 13 21:13 log.18604991._046290.job.log.1
-rw-------. 1 grid grid    818719 Aug 13 21:12 log.18604991._046290.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug 13 21:13 mDZLDmqdhHvnShfckohDCDFpABFKDmABFKDm9HIaDmABFKDmF8ozEn.diag
-rw-------. 1 grid grid       391 Aug 13 21:13 output.list
-rw-------. 1 grid grid      2871 Aug 13 10:47 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 10:28 pilot2.tar.gz
-rw-------. 1 grid grid     11321 Aug 13 21:13 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 10:47 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 19:15 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 19:15 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 10:47 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 21:13 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 21:13 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 21:13 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 19:15 start_atlas.sh
-rw-rw-r--. 1 grid grid     18839 Aug 13 21:13 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 19:15 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 13 21:13 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
21:13:59 (12364): run_atlas exited; CPU time 25707.047848
21:13:59 (12364): called boinc_finish(0)

</stderr_txt>
]]>

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