Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
06:24:52 (5341): wrapper (7.7.26015): starting
06:24:52 (5341): 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 installed, version singularity version 3.2.1-1
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 /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 = 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.18722465._007201.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 08:26:27,855 | DEBUG    | queue_monitor       | pilot.control.job                | send_state                | wrote heartbeat to file /home/grid/slots/0/heartbeat.json
2019-08-09 08:26:27,855 | INFO     | queue_monitor       | pilot.control.job                | queue_monitor             | job 4441063689 was dequeued from the monitored payloads queue
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4441063689
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722465
2019-08-09 08:26:28,677 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 55005 s
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 12104
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 12104
2019-08-09 08:26:28,678 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-09 08:26:28,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 08:26:28,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 08:26:28,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 08:26:28,679 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441063689 has completed
2019-08-09 08:26:28,679 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 08:26:28,688 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4441063689
2019-08-09 08:26:29,689 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [12104]
2019-08-09 08:26:29,690 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 12104
2019-08-09 08:26:29,690 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 08:26:30,695 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 08:26:30,695 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=12104
2019-08-09 08:26:30,750 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [12104] (in reverse order)
2019-08-09 08:26:30,796 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 08:26:30,796 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 08:26:30,796 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 08:26:30,796 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-09 08:26:31,306 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 08:26:41,348 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 08:26:41,348 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-09 08:26:41,384 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34493956096 B)
2019-08-09 08:26:41,385 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-09 08:26:41,385 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 08:26:41,406 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 08:26:41,407 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 08:26:41,501 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 08:26:41,760 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-09 08:26:41,761 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(job, started 140062169720576)>, <ExcThread(queue_monitor, started 140061609805568)>, <ExcThread(create_data_payload, started 140062144542464)>, <ExcThread(validate_post, started 140061601412864)>, <ExcThread(execute_payloads, started 140061500765952)>, <ExcThread(data, started 140062152935168)>, <ExcThread(failed_post, started 140061593020160)>, <ExcThread(validate, started 140062161327872)>, <ExcThread(copytool_in, started 140061584627456)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>, <ExcThread(monitor, started 140061634983680)>, <ExcThread(copytool_out, started 140062127757056)>, <ExcThread(payload, started 140062136149760)>]
2019-08-09 08:26:41,881 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 08:26:41,957 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 08:26:42,020 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 08:26:42,020 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 08:26:42,116 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 08:26:42,249 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 08:26:42,249 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 08:26:42,263 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-09 08:26:42,263 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(queue_monitor, started 140061609805568)>, <ExcThread(create_data_payload, started 140062144542464)>, <ExcThread(execute_payloads, started 140061500765952)>, <ExcThread(data, started 140062152935168)>, <ExcThread(validate, started 140062161327872)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>, <ExcThread(monitor, started 140061634983680)>, <ExcThread(copytool_out, started 140062127757056)>]
2019-08-09 08:26:42,285 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 08:26:42,285 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 08:26:42,303 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 08:26:42,364 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-09 08:26:42,365 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(queue_monitor, started 140061609805568)>, <ExcThread(create_data_payload, started 140062144542464)>, <ExcThread(execute_payloads, started 140061500765952)>, <ExcThread(validate, started 140062161327872)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>, <ExcThread(copytool_out, started 140062127757056)>]
2019-08-09 08:26:42,407 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 08:26:42,466 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 08:26:42,466 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(queue_monitor, started 140061609805568)>, <ExcThread(create_data_payload, started 140062144542464)>, <ExcThread(execute_payloads, started 140061500765952)>, <ExcThread(validate, started 140062161327872)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>]
2019-08-09 08:26:42,650 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 08:26:42,654 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 08:26:42,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 08:26:42,668 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(queue_monitor, started 140061609805568)>, <ExcThread(create_data_payload, started 140062144542464)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>]
2019-08-09 08:26:42,787 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 08:26:42,840 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 08:26:42,840 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 08:26:42,869 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 08:26:42,869 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(job_monitor, started 140061626590976)>, <ExcThread(queue_monitoring, started 140061618198272)>]
2019-08-09 08:26:44,407 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 08:26:44,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 08:26:44,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140062385993472)>, <ExcThread(job_monitor, started 140061626590976)>]
2019-08-09 08:27:05,550 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-09 08:27:05,551 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 08:27:05,650 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 08:27:05,651 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 08:27:05,651 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 08:27:05 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 08:27:05 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 08:27:05 UTC [wrapper] Pilot exit status: 0
2019-08-09 08:27:05 UTC [wrapper] STATUSCODE: 0
2019-08-09 08:27:05 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  9 06:25 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

2019-08-09 08:27:05 UTC [wrapper] Test setup, not cleaning
2019-08-09 08:27:05 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 08:27:05 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=14528.44s
KernelTime=447.45s
UserTime=54767.22s
CPUUsage=380%
MaxResidentMemory=1944644kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=433742
MinorPageFaults=18112802
Swaps=0
ForcedSwitches=6396571
WaitSwitches=8959965
Inputs=105071424
Outputs=872736
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 236704
drwxrwx--x. 7 grid grid      4096 Aug  9 10:27 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       518 Aug  9 10:27 7x1LDmrD6FvnShfckohDCDFpABFKDmABFKDmtodXDmABFKDmzZ4SDo.diag
-rw-------. 1 grid grid   7409227 Aug  9 06:25 agis_ddmendpoints.json
-rw-------. 1 grid grid   4533855 Aug  9 06:25 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  9 06:24 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  9 06:24 APPS
drwxr-xr-x. 2 grid grid         6 Aug  9 06:25 .arc
-rw-------. 1 grid grid       538 Aug  9 06:25 .asetup
-rw-------. 1 grid grid       826 Aug  9 06:25 .asetup.save
-rw-r--r--. 1 grid grid         0 Aug  9 06:24 boinc_lockfile
-rw-r--r--. 1 grid grid      8192 Aug  9 10:26 boinc_mmap_file
-rw-r--r--. 1 grid grid       537 Aug  9 10:16 boinc_task_state.xml
-rw-r--r--. 1 grid grid 228077937 Aug  9 06:24 EVNT.18605785._000145.pool.root.1
-rw-------. 1 grid grid     97707 Aug  9 10:26 heartbeat.json
-rw-r--r--. 1 grid grid      5857 Aug  9 06:24 init_data.xml
-rw-r--r--. 1 grid grid    262348 Aug  9 06:24 input.tar.gz
-rw-r--r--. 1 grid grid       112 Aug  9 06:24 job.xml
-rw-------. 1 grid grid    729625 Aug  9 10:27 log.18722465._007201.job.log.1
-rw-------. 1 grid grid    849782 Aug  9 10:26 log.18722465._007201.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug  9 10:27 output.list
-rw-------. 1 grid grid      2955 Aug  9 00:37 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 00:23 pilot2.tar.gz
-rw-------. 1 grid grid      9781 Aug  9 10:27 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 00:35 queuedata.json
-rw-r--r--. 1 grid grid       815 Aug  9 06:24 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  9 06:24 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 00:37 runpilot2-wrapper.sh
-rw-r--r--. 1 grid grid       692 Aug  9 10:27 runtime_log
-rw-r--r--. 1 grid grid      6807 Aug  9 10:27 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug  9 10:27 shared
-rw-r--r--. 1 grid grid      8688 Aug  9 06:24 start_atlas.sh
-rw-r--r--. 1 grid grid     18142 Aug  9 10:27 stderr.txt
-rw-r--r--. 1 grid grid       107 Aug  9 06:24 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 grid grid        28 Aug  9 10:26 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
10:27:06 (5341): run_atlas exited; CPU time 54767.623079
10:27:06 (5341): called boinc_finish(0)

</stderr_txt>
]]>

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