Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
06:31:00 (13764): wrapper (7.7.26015): starting
06:31:00 (13764): 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.18605019._041156.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 06:03:45,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 06:03:45,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 06:03:45,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 06:03:45,651 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 20130 s
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 20441
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 20441
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 06:03:45,652 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442593762 has completed
2019-08-10 06:03:45,653 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 06:03:45,659 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442593762
2019-08-10 06:03:46,661 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [20441]
2019-08-10 06:03:46,661 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 20441
2019-08-10 06:03:46,662 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 06:03:47,666 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 06:03:47,667 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=20441
2019-08-10 06:03:47,724 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [20441] (in reverse order)
2019-08-10 06:03:47,769 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 06:03:47,769 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 06:03:47,769 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 06:03:47,770 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-10 06:03:48,281 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 06:03:51,593 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 06:03:58,309 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 06:03:58,310 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 06:03:58,353 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34500247552 B)
2019-08-10 06:03:58,354 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-10 06:03:58,354 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 06:03:58,723 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-10 06:03:58,724 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(job, started 140221205841664)>, <ExcThread(monitor, started 140220808816384)>, <ExcThread(execute_payloads, started 140220196443904)>, <ExcThread(payload, started 140221163878144)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(validate_pre, started 140220792030976)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(failed_post, started 140220204836608)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(data, started 140221197448960)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>, <ExcThread(copytool_in, started 140220766852864)>, <ExcThread(create_data_payload, started 140221180663552)>]
2019-08-10 06:03:58,739 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 06:03:59,124 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 06:03:59,126 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 06:03:59,127 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-10 06:03:59,127 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(job, started 140221205841664)>, <ExcThread(payload, started 140221163878144)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(validate_pre, started 140220792030976)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(failed_post, started 140220204836608)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(data, started 140221197448960)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>, <ExcThread(create_data_payload, started 140221180663552)>]
2019-08-10 06:03:59,178 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 06:03:59,178 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 06:03:59,309 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 06:03:59,309 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 06:03:59,353 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 06:03:59,353 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 06:03:59,360 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-10 06:03:59,361 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(validate_pre, started 140220792030976)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(failed_post, started 140220204836608)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>, <ExcThread(create_data_payload, started 140221180663552)>]
2019-08-10 06:03:59,396 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 06:03:59,520 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 06:03:59,562 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-10 06:03:59,562 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(failed_post, started 140220204836608)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>, <ExcThread(create_data_payload, started 140221180663552)>]
2019-08-10 06:03:59,565 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 06:03:59,663 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-10 06:03:59,663 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(failed_post, started 140220204836608)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>]
2019-08-10 06:03:59,732 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 06:03:59,764 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 06:03:59,765 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(validate, started 140221189056256)>, <ExcThread(validate_post, started 140220775245568)>, <ExcThread(queue_monitor, started 140220213229312)>]
2019-08-10 06:03:59,768 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 06:03:59,842 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 06:03:59,865 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-10 06:03:59,866 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>, <ExcThread(queue_monitor, started 140220213229312)>]
2019-08-10 06:04:00,042 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 06:04:00,119 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 06:04:00,119 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 06:04:00,168 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 06:04:00,168 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(copytool_out, started 140221172270848)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>]
2019-08-10 06:04:00,397 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 06:04:00,470 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 06:04:00,471 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(queue_monitoring, started 140220800423680)>, <ExcThread(job_monitor, started 140220783638272)>]
2019-08-10 06:04:03,044 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 06:04:03,090 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 06:04:03,090 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140221422114560)>, <ExcThread(job_monitor, started 140220783638272)>]
2019-08-10 06:04:53,193 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-08-10 06:04:53,194 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 06:04:53,239 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 06:04:53,239 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 06:04:53,239 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 06:04:53 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 06:04:53 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 06:04:53 UTC [wrapper] Pilot exit status: 0
2019-08-10 06:04:53 UTC [wrapper] STATUSCODE: 0
2019-08-10 06:04:53 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 10 06:31 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

2019-08-10 06:04:53 UTC [wrapper] Test setup, not cleaning
2019-08-10 06:04:53 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 06:04:53 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5630.36s
KernelTime=198.64s
UserTime=20032.31s
CPUUsage=359%
MaxResidentMemory=1945224kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=261107
MinorPageFaults=12435769
Swaps=0
ForcedSwitches=2395071
WaitSwitches=4914145
Inputs=63460072
Outputs=502256
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 383176
drwxrwx--x. 7 grid grid      4096 Aug 10 08:04 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408903 Aug 10 06:31 agis_ddmendpoints.json
-rw-------. 1 grid grid   4507217 Aug 10 06:31 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 06:31 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 06:31 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 06:31 .arc
-rw-------. 1 grid grid       538 Aug 10 06:31 .asetup
-rw-------. 1 grid grid       826 Aug 10 06:32 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 06:31 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 08:04 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 10 07:58 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 378520676 Aug 10 06:31 EVNT.17323843._000819.pool.root.1
-rw-------. 1 grid grid     55507 Aug 10 08:03 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 06:31 init_data.xml
-rw-rw-r--. 1 grid grid    262342 Aug 10 06:31 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 06:30 job.xml
-rw-------. 1 grid grid    377600 Aug 10 08:04 log.18605019._041156.job.log.1
-rw-------. 1 grid grid    812303 Aug 10 08:03 log.18605019._041156.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug 10 08:04 mFyKDmyzPGvnShfckohDCDFpABFKDmABFKDmPtBYDmABFKDmkGN84m.diag
-rw-------. 1 grid grid       391 Aug 10 08:04 output.list
-rw-------. 1 grid grid      2886 Aug  9 21:44 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 21:23 pilot2.tar.gz
-rw-------. 1 grid grid     12202 Aug 10 08:04 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 21:40 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 06:31 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 06:30 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 21:44 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 08:04 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 08:04 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 08:04 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 06:31 start_atlas.sh
-rw-rw-r--. 1 grid grid     19618 Aug 10 08:04 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 06:30 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 10 08:04 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
08:04:53 (13764): run_atlas exited; CPU time 20032.694410
08:04:53 (13764): called boinc_finish(0)

</stderr_txt>
]]>

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