Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
09:25:48 (26121): wrapper (7.7.26015): starting
09:25:48 (26121): 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.18722298._013625.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 12:08:53,168 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442652707
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 12:08:53,169 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 64715 s
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 326
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 326
2019-08-11 12:08:53,170 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 12:08:53,171 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 12:08:53,171 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 12:08:53,171 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 12:08:53,171 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442652707 has completed
2019-08-11 12:08:53,171 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 12:08:53,182 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442652707
2019-08-11 12:08:54,187 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [326]
2019-08-11 12:08:54,187 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 326
2019-08-11 12:08:54,187 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 12:08:55,193 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 12:08:55,193 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=326
2019-08-11 12:08:55,254 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [326] (in reverse order)
2019-08-11 12:08:55,305 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 12:08:55,305 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 12:08:55,305 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 12:08:55,305 | 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 12:08:55,816 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 12:09:05,830 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 12:09:05,831 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 12:09:05,877 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34703671296 B)
2019-08-11 12:09:05,877 | 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 12:09:05,878 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 12:09:05,910 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 12:09:05,920 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 12:09:05,926 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 12:09:05,933 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 12:09:06,198 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-11 12:09:06,199 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(job, started 139800911542016)>, <ExcThread(validate_post, started 139800329819904)>, <ExcThread(payload, started 139800877971200)>, <ExcThread(data, started 139800894756608)>, <ExcThread(validate, started 139800903149312)>, <ExcThread(copytool_in, started 139800380176128)>, <ExcThread(execute_payloads, started 139799834912512)>, <ExcThread(create_data_payload, started 139800869578496)>, <ExcThread(failed_post, started 139799843305216)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(copytool_out, started 139800886363904)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:06,332 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 12:09:06,332 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 12:09:06,500 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 12:09:06,500 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 12:09:06,516 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 12:09:06,528 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-11 12:09:06,529 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(validate_post, started 139800329819904)>, <ExcThread(data, started 139800894756608)>, <ExcThread(validate, started 139800903149312)>, <ExcThread(copytool_in, started 139800380176128)>, <ExcThread(execute_payloads, started 139799834912512)>, <ExcThread(create_data_payload, started 139800869578496)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(copytool_out, started 139800886363904)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:06,795 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 12:09:06,795 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 12:09:06,831 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-11 12:09:06,831 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(validate_post, started 139800329819904)>, <ExcThread(validate, started 139800903149312)>, <ExcThread(copytool_in, started 139800380176128)>, <ExcThread(execute_payloads, started 139799834912512)>, <ExcThread(create_data_payload, started 139800869578496)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(copytool_out, started 139800886363904)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:06,911 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 12:09:06,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-11 12:09:06,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(validate_post, started 139800329819904)>, <ExcThread(validate, started 139800903149312)>, <ExcThread(copytool_in, started 139800380176128)>, <ExcThread(execute_payloads, started 139799834912512)>, <ExcThread(create_data_payload, started 139800869578496)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:07,098 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 12:09:07,101 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 12:09:07,134 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-11 12:09:07,134 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(validate_post, started 139800329819904)>, <ExcThread(validate, started 139800903149312)>, <ExcThread(execute_payloads, started 139799834912512)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:07,245 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 12:09:07,268 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 12:09:07,270 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 12:09:07,335 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 12:09:07,335 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>, <ExcThread(queue_monitor, started 139800338212608)>]
2019-08-11 12:09:07,665 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 12:09:07,665 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 12:09:07,738 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 12:09:07,738 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(job_monitor, started 139800346605312)>, <ExcThread(queue_monitoring, started 139800861185792)>]
2019-08-11 12:09:08,927 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 12:09:08,947 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 12:09:08,947 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139801127814912)>, <ExcThread(job_monitor, started 139800346605312)>]
2019-08-11 12:09:18,806 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-11 12:09:18,807 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 12:09:18,814 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 12:09:18,814 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 12:09:18,815 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 12:09:19 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 12:09:19 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 12:09:19 UTC [wrapper] Pilot exit status: 0
2019-08-11 12:09:19 UTC [wrapper] STATUSCODE: 0
2019-08-11 12:09:19 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 09:26 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 12:09:19 UTC [wrapper] Test setup, not cleaning
2019-08-11 12:09:19 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 12:09:19 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=17004.32s
KernelTime=490.60s
UserTime=64444.79s
CPUUsage=381%
MaxResidentMemory=1945232kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=484890
MinorPageFaults=19706714
Swaps=0
ForcedSwitches=7430396
WaitSwitches=10217973
Inputs=117042896
Outputs=963472
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 288228
drwxrwx--x. 7 grid grid      4096 Aug 11 14:09 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 11 09:26 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506674 Aug 11 09:26 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 11 09:25 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 11 09:25 APPS
drwxr-xr-x. 2 grid grid         6 Aug 11 09:26 .arc
-rw-------. 1 grid grid       538 Aug 11 09:25 .asetup
-rw-------. 1 grid grid       826 Aug 11 09:26 .asetup.save
-rw-------. 1 grid grid       519 Aug 11 14:09 bbVLDmNzRGvnShfckohDCDFpABFKDmABFKDmvMFYDmABFKDmX8QBnm.diag
-rw-rw-r--. 1 grid grid         0 Aug 11 09:25 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 11 14:09 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 11 13:59 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 280780791 Aug 11 09:25 EVNT.18605754._000263.pool.root.1
-rw-------. 1 grid grid     92769 Aug 11 14:08 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 11 09:25 init_data.xml
-rw-rw-r--. 1 grid grid    262337 Aug 11 09:25 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 11 09:25 job.xml
-rw-------. 1 grid grid    814049 Aug 11 14:09 log.18722298._013625.job.log.1
-rw-------. 1 grid grid    857881 Aug 11 14:08 log.18722298._013625.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 11 14:09 output.list
-rw-------. 1 grid grid      2914 Aug  9 23:52 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 23:25 pilot2.tar.gz
-rw-------. 1 grid grid     10596 Aug 11 14:09 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 23:52 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 11 09:25 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 11 09:25 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 23:52 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 11 14:09 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 11 14:09 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 11 14:09 shared
-rw-rw-r--. 1 grid grid      8688 Aug 11 09:25 start_atlas.sh
-rw-rw-r--. 1 grid grid     18727 Aug 11 14:09 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 11 09:25 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 11 14:09 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
14:09:20 (26121): run_atlas exited; CPU time 64445.156073
14:09:20 (26121): called boinc_finish(0)

</stderr_txt>
]]>

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