Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:09:24 (27206): wrapper (7.7.26015): starting
14:09:24 (27206): 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 grep: pandaJobData.out: No such file or directory
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.18722398._017843.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442993106
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 14:08:37,086 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26481 s
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 1449
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 1449
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442993106 has completed
2019-08-11 14:08:37,087 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 14:08:37,097 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442993106
2019-08-11 14:08:38,102 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [1449]
2019-08-11 14:08:38,103 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 1449
2019-08-11 14:08:38,103 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 14:08:39,104 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 14:08:39,105 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=1449
2019-08-11 14:08:39,164 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [1449] (in reverse order)
2019-08-11 14:08:39,214 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 14:08:39,215 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 14:08:39,215 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 14:08:39,215 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-11 14:08:39,725 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 14:08:45,477 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-11 14:08:49,774 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 14:08:49,774 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 14:08:49,818 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34895560704 B)
2019-08-11 14:08:49,819 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-11 14:08:49,819 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 14:08:49,825 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 14:08:49,834 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 14:08:49,838 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 14:08:50,036 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 14:08:50,113 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 14:08:50,120 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-11 14:08:50,121 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job, started 139865418229504)>, <ExcThread(execute_payloads, started 139864267814656)>, <ExcThread(create_data_payload, started 139865307985664)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(copytool_out, started 139865324771072)>, <ExcThread(validate, started 139865333163776)>, <ExcThread(data, started 139865341556480)>, <ExcThread(copytool_in, started 139864787900160)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(payload, started 139865316378368)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:50,222 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 14:08:50,222 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 14:08:50,423 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-11 14:08:50,424 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job, started 139865418229504)>, <ExcThread(execute_payloads, started 139864267814656)>, <ExcThread(create_data_payload, started 139865307985664)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(copytool_out, started 139865324771072)>, <ExcThread(validate, started 139865333163776)>, <ExcThread(data, started 139865341556480)>, <ExcThread(copytool_in, started 139864787900160)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:50,510 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 14:08:50,526 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 14:08:50,526 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 14:08:50,625 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-11 14:08:50,625 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job, started 139865418229504)>, <ExcThread(execute_payloads, started 139864267814656)>, <ExcThread(create_data_payload, started 139865307985664)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(copytool_out, started 139865324771072)>, <ExcThread(copytool_in, started 139864787900160)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:50,652 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 14:08:50,653 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 14:08:50,729 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 14:08:50,730 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 14:08:50,733 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-11 14:08:50,734 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(copytool_out, started 139865324771072)>, <ExcThread(copytool_in, started 139864787900160)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:50,835 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 14:08:50,935 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-11 14:08:50,935 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(copytool_in, started 139864787900160)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:51,001 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 14:08:51,036 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 14:08:51,036 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(queue_monitoring, started 139865291200256)>, <ExcThread(queue_monitor, started 139864762722048)>]
2019-08-11 14:08:51,061 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 14:08:51,583 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 14:08:51,583 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 14:08:51,641 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 14:08:51,641 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job_monitor, started 139864779507456)>, <ExcThread(queue_monitoring, started 139865291200256)>]
2019-08-11 14:08:54,063 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 14:08:54,158 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 14:08:54,159 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139865634502400)>, <ExcThread(job_monitor, started 139864779507456)>]
2019-08-11 14:09:47,049 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-08-11 14:09:47,049 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 14:09:47,119 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 14:09:47,119 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 14:09:47,119 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 14:09:47 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 14:09:47 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 14:09:47 UTC [wrapper] Pilot exit status: 0
2019-08-11 14:09:47 UTC [wrapper] STATUSCODE: 0
2019-08-11 14:09:47 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 11 14:09 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

2019-08-11 14:09:47 UTC [wrapper] Test setup, not cleaning
2019-08-11 14:09:47 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 14:09:47 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7219.86s
KernelTime=231.21s
UserTime=26360.36s
CPUUsage=368%
MaxResidentMemory=1945228kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=291268
MinorPageFaults=13454348
Swaps=0
ForcedSwitches=3145660
WaitSwitches=5650796
Inputs=70730128
Outputs=584480
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216440
drwxrwx--x. 7 grid grid      4096 Aug 11 16:09 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 11 14:09 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506622 Aug 11 14:09 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 11 14:09 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 11 14:09 APPS
drwxr-xr-x. 2 grid grid         6 Aug 11 14:09 .arc
-rw-------. 1 grid grid       538 Aug 11 14:09 .asetup
-rw-------. 1 grid grid       826 Aug 11 14:10 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 11 14:09 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 11 16:09 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 11 16:03 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207656438 Aug 11 14:09 EVNT.18605775._000351.pool.root.1
-rw-------. 1 grid grid       516 Aug 11 16:09 GUFLDmnLtGvnShfckohDCDFpABFKDmABFKDmd4yYDmABFKDmc8hhon.diag
-rw-------. 1 grid grid     88929 Aug 11 16:08 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 11 14:09 init_data.xml
-rw-rw-r--. 1 grid grid    262355 Aug 11 14:09 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 11 14:09 job.xml
-rw-------. 1 grid grid    461440 Aug 11 16:09 log.18722398._017843.job.log.1
-rw-------. 1 grid grid    826309 Aug 11 16:08 log.18722398._017843.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 11 16:09 output.list
-rw-------. 1 grid grid      2957 Aug 11 05:05 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 04:33 pilot2.tar.gz
-rw-------. 1 grid grid     10335 Aug 11 16:09 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 05:00 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 11 14:09 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 11 14:09 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 05:05 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 11 16:09 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 11 16:09 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 11 16:09 shared
-rw-rw-r--. 1 grid grid      8688 Aug 11 14:09 start_atlas.sh
-rw-rw-r--. 1 grid grid     18346 Aug 11 16:09 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 11 14:09 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 11 16:09 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
16:09:47 (27206): run_atlas exited; CPU time 26360.750533
16:09:47 (27206): called boinc_finish(0)

</stderr_txt>
]]>

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