Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:10:57 (30546): wrapper (7.7.26015): starting
14:10:57 (30546): 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 PandaID=4443004956
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._016798.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-15 16:55:51,353 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 65437 s
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 4845
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 4845
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443004956 has completed
2019-08-15 16:55:51,354 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-15 16:55:51,361 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443004956
2019-08-15 16:55:52,366 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [4845]
2019-08-15 16:55:52,367 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 4845
2019-08-15 16:55:52,367 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-15 16:55:53,369 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-15 16:55:53,369 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=4845
2019-08-15 16:55:53,420 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [4845] (in reverse order)
2019-08-15 16:55:53,461 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-15 16:55:53,461 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-15 16:55:53,462 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-15 16:55:53,462 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-15 16:55:53,970 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-15 16:56:03,612 | INFO     | monitor             | pilot.control.monitor            | control                   | 17083 s have passed since pilot start
2019-08-15 16:56:03,990 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-15 16:56:03,990 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-15 16:56:04,022 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35624321024 B)
2019-08-15 16:56:04,023 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-15 16:56:04,023 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-15 16:56:04,026 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-15 16:56:04,027 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job, started 140532622329600)>, <ExcThread(monitor, started 140532504311552)>, <ExcThread(failed_post, started 140531967440640)>, <ExcThread(validate_pre, started 140532512704256)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(execute_payloads, started 140531959047936)>, <ExcThread(payload, started 140532521096960)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(data, started 140532613936896)>, <ExcThread(queue_monitoring, started 140532495918848)>, <ExcThread(create_data_payload, started 140532001011456)>, <ExcThread(validate_post, started 140532487526144)>, <ExcThread(validate, started 140532537882368)>]
2019-08-15 16:56:04,167 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-15 16:56:04,529 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-15 16:56:04,529 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job, started 140532622329600)>, <ExcThread(monitor, started 140532504311552)>, <ExcThread(validate_pre, started 140532512704256)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(execute_payloads, started 140531959047936)>, <ExcThread(payload, started 140532521096960)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(data, started 140532613936896)>, <ExcThread(queue_monitoring, started 140532495918848)>, <ExcThread(create_data_payload, started 140532001011456)>, <ExcThread(validate_post, started 140532487526144)>, <ExcThread(validate, started 140532537882368)>]
2019-08-15 16:56:04,617 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-15 16:56:04,631 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-15 16:56:04,783 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-15 16:56:04,783 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-15 16:56:04,817 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-15 16:56:04,835 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-15 16:56:04,870 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-15 16:56:04,926 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-15 16:56:04,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-15 16:56:04,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(execute_payloads, started 140531959047936)>, <ExcThread(payload, started 140532521096960)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(data, started 140532613936896)>, <ExcThread(queue_monitoring, started 140532495918848)>, <ExcThread(validate, started 140532537882368)>]
2019-08-15 16:56:04,966 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-15 16:56:04,966 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-15 16:56:05,046 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-15 16:56:05,046 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-15 16:56:05,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-15 16:56:05,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(execute_payloads, started 140531959047936)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(queue_monitoring, started 140532495918848)>, <ExcThread(validate, started 140532537882368)>]
2019-08-15 16:56:05,237 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-15 16:56:05,250 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-15 16:56:05,251 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(queue_monitoring, started 140532495918848)>, <ExcThread(validate, started 140532537882368)>]
2019-08-15 16:56:05,350 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-15 16:56:05,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-15 16:56:05,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(copytool_in, started 140531992618752)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(queue_monitoring, started 140532495918848)>]
2019-08-15 16:56:05,397 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-15 16:56:05,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-15 16:56:05,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(queue_monitor, started 140531950655232)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(queue_monitoring, started 140532495918848)>]
2019-08-15 16:56:05,817 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-15 16:56:05,818 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-15 16:56:05,855 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-15 16:56:05,855 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(copytool_out, started 140532529489664)>, <ExcThread(queue_monitoring, started 140532495918848)>]
2019-08-15 16:56:05,927 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-15 16:56:05,956 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-15 16:56:05,956 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>, <ExcThread(queue_monitoring, started 140532495918848)>]
2019-08-15 16:56:07,836 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-15 16:56:07,869 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-15 16:56:07,870 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140532838602496)>, <ExcThread(job_monitor, started 140531975833344)>]
2019-08-15 16:56:12,231 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-15 16:56:12,232 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-15 16:56:12,300 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-15 16:56:12,300 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-15 16:56:12,300 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-15 16:56:12 UTC [wrapper] ==== pilot stdout END ====
2019-08-15 16:56:12 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-15 16:56:12 UTC [wrapper] Pilot exit status: 0
2019-08-15 16:56:12 UTC [wrapper] STATUSCODE: 0
2019-08-15 16:56:12 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 15 14:11 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

2019-08-15 16:56:12 UTC [wrapper] Test setup, not cleaning
2019-08-15 16:56:12 UTC [wrapper] ==== wrapper stdout END ====
2019-08-15 16:56:12 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=17107.14s
KernelTime=455.02s
UserTime=65196.18s
CPUUsage=383%
MaxResidentMemory=1944500kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=484951
MinorPageFaults=19809689
Swaps=0
ForcedSwitches=7504945
WaitSwitches=10506615
Inputs=117138336
Outputs=972744
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 285948
drwxrwx--x. 7 grid grid      4096 Aug 15 18:56 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409162 Aug 15 14:11 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438557 Aug 15 14:11 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 14:11 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 14:11 APPS
drwxr-xr-x. 2 grid grid         6 Aug 15 14:11 .arc
-rw-------. 1 grid grid       538 Aug 15 14:11 .asetup
-rw-------. 1 grid grid       826 Aug 15 14:12 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 14:10 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 15 18:56 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 15 18:47 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 278511355 Aug 15 14:11 EVNT.18605754._000325.pool.root.1
-rw-------. 1 grid grid     93114 Aug 15 18:55 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 14:10 init_data.xml
-rw-rw-r--. 1 grid grid    262340 Aug 15 14:11 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 14:10 job.xml
-rw-------. 1 grid grid    816898 Aug 15 18:56 log.18722298._016798.job.log.1
-rw-------. 1 grid grid    856584 Aug 15 18:55 log.18722298._016798.job.log.tgz.1
-rw-------. 1 grid grid       519 Aug 15 18:56 NjtKDmYiwGvnShfckohDCDFpABFKDmABFKDmCh4YDmABFKDmAAqkTm.diag
-rw-------. 1 grid grid       391 Aug 15 18:56 output.list
-rw-------. 1 grid grid      2916 Aug 11 08:41 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 08:27 pilot2.tar.gz
-rw-------. 1 grid grid     12107 Aug 15 18:56 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 08:41 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 15 14:11 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 14:10 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 08:41 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 15 18:56 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 15 18:56 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 15 18:56 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 14:11 start_atlas.sh
-rw-rw-r--. 1 grid grid     19489 Aug 15 18:56 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 14:10 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 15 18:56 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
18:56:12 (30546): run_atlas exited; CPU time 65196.586277
18:56:12 (30546): called boinc_finish(0)

</stderr_txt>
]]>

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