Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
19:35:54 (23889): wrapper (7.7.26015): starting
19:35:54 (23889): 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.18604991._040013.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-08 19:40:30,120 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-08 19:40:30,120 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 27224 s
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 30556
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 30556
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4437461520 has completed
2019-08-08 19:40:30,121 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-08 19:40:30,131 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4437461520
2019-08-08 19:40:31,136 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [30556]
2019-08-08 19:40:31,137 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 30556
2019-08-08 19:40:31,137 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-08 19:40:32,140 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-08 19:40:32,140 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=30556
2019-08-08 19:40:32,201 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [30556] (in reverse order)
2019-08-08 19:40:32,252 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-08 19:40:32,252 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-08 19:40:32,252 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-08 19:40:32,252 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-08 19:40:32,764 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-08 19:40:42,810 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-08 19:40:42,810 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-08 19:40:42,848 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34974203904 B)
2019-08-08 19:40:42,848 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-08 19:40:42,848 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-08 19:40:42,878 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-08 19:40:42,908 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-08 19:40:42,911 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-08 19:40:42,987 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-08 19:40:43,154 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-08 19:40:43,155 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(job, started 139997324404480)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(validate_post, started 139996891682560)>, <ExcThread(data, started 139997307619072)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(validate, started 139997316011776)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(create_data_payload, started 139996942038784)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(payload, started 139997290833664)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:43,353 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-08 19:40:43,353 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-08 19:40:43,457 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-08 19:40:43,457 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(job, started 139997324404480)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(validate_post, started 139996891682560)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(validate, started 139997316011776)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(create_data_payload, started 139996942038784)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(payload, started 139997290833664)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:43,463 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-08 19:40:43,463 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-08 19:40:43,520 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-08 19:40:43,520 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-08 19:40:43,558 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-08 19:40:43,558 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(validate_post, started 139996891682560)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(validate, started 139997316011776)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(create_data_payload, started 139996942038784)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:43,601 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-08 19:40:43,659 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-08 19:40:43,659 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(validate_post, started 139996891682560)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(create_data_payload, started 139996942038784)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:43,828 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-08 19:40:43,861 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-08 19:40:43,861 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(validate_post, started 139996891682560)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:43,969 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-08 19:40:44,063 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-08 19:40:44,063 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(copytool_in, started 139996908467968)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:44,119 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-08 19:40:44,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-08 19:40:44,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(validate_pre, started 139996925253376)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:44,240 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-08 19:40:44,265 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-08 19:40:44,265 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(queue_monitor, started 139996379989760)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:44,314 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-08 19:40:44,602 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-08 19:40:44,602 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-08 19:40:44,668 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-08 19:40:44,669 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(copytool_out, started 139997299226368)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:45,314 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-08 19:40:45,374 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-08 19:40:45,374 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(queue_monitoring, started 139996933646080)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:40:45,879 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-08 19:40:45,979 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-08 19:40:45,979 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139997540677376)>, <ExcThread(job_monitor, started 139996405167872)>]
2019-08-08 19:41:29,323 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-08 19:41:29,323 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-08 19:41:29,369 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-08 19:41:29,369 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-08 19:41:29,370 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-08 19:41:29 UTC [wrapper] ==== pilot stdout END ====
2019-08-08 19:41:29 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-08 19:41:29 UTC [wrapper] Pilot exit status: 0
2019-08-08 19:41:29 UTC [wrapper] STATUSCODE: 0
2019-08-08 19:41:29 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  8 19:36 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

2019-08-08 19:41:29 UTC [wrapper] Test setup, not cleaning
2019-08-08 19:41:29 UTC [wrapper] ==== wrapper stdout END ====
2019-08-08 19:41:29 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7530.81s
KernelTime=247.44s
UserTime=27106.57s
CPUUsage=363%
MaxResidentMemory=1944284kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=295515
MinorPageFaults=13488587
Swaps=0
ForcedSwitches=3167646
WaitSwitches=5832508
Inputs=71876704
Outputs=517344
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 381572
drwxrwx--x. 7 grid grid      4096 Aug  8 21:41 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409227 Aug  8 19:36 agis_ddmendpoints.json
-rw-------. 1 grid grid   4533639 Aug  8 19:36 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  8 19:35 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  8 19:35 APPS
drwxr-xr-x. 2 grid grid         6 Aug  8 19:36 .arc
-rw-------. 1 grid grid       538 Aug  8 19:36 .asetup
-rw-------. 1 grid grid       826 Aug  8 19:37 .asetup.save
-rw-r--r--. 1 grid grid         0 Aug  8 19:35 boinc_lockfile
-rw-r--r--. 1 grid grid      8192 Aug  8 21:41 boinc_mmap_file
-rw-r--r--. 1 grid grid       536 Aug  8 21:33 boinc_task_state.xml
-rw-r--r--. 1 grid grid 376732058 Aug  8 19:35 EVNT.17323818._001149.pool.root.1
-rw-------. 1 grid grid     78455 Aug  8 21:40 heartbeat.json
-rw-r--r--. 1 grid grid      5853 Aug  8 19:35 init_data.xml
-rw-r--r--. 1 grid grid    262345 Aug  8 19:35 input.tar.gz
-rw-r--r--. 1 grid grid       112 Aug  8 19:35 job.xml
-rw-------. 1 grid grid    464608 Aug  8 21:41 log.18604991._040013.job.log.1
-rw-------. 1 grid grid    819776 Aug  8 21:40 log.18604991._040013.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug  8 21:41 OtWLDmQzyFvnShfckohDCDFpABFKDmABFKDmzxIXDmABFKDm3HnLqm.diag
-rw-------. 1 grid grid       391 Aug  8 21:41 output.list
-rw-------. 1 grid grid      2872 Aug  8 16:54 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  8 16:25 pilot2.tar.gz
-rw-------. 1 grid grid     12434 Aug  8 21:41 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  8 16:50 queuedata.json
-rw-r--r--. 1 grid grid       815 Aug  8 19:35 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  8 19:35 run_atlas
-rwx------. 1 grid grid     15232 Aug  8 16:54 runpilot2-wrapper.sh
-rw-r--r--. 1 grid grid       692 Aug  8 21:41 runtime_log
-rw-r--r--. 1 grid grid      6807 Aug  8 21:41 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug  8 21:41 shared
-rw-r--r--. 1 grid grid      8688 Aug  8 19:35 start_atlas.sh
-rw-r--r--. 1 grid grid     19570 Aug  8 21:41 stderr.txt
-rw-r--r--. 1 grid grid       107 Aug  8 19:35 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 grid grid        27 Aug  8 21:41 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
21:41:30 (23889): run_atlas exited; CPU time 27107.004865
21:41:30 (23889): called boinc_finish(0)

</stderr_txt>
]]>

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