Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
11:25:23 (18644): wrapper (7.7.26015): starting
11:25:23 (18644): 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=4444714740
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.18722432._022691.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4444714740
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722432
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-14 12:37:24,533 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 43435 s
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 25316
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 25316
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 12:37:24,534 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4444714740 has completed
2019-08-14 12:37:24,535 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-14 12:37:24,546 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4444714740
2019-08-14 12:37:25,550 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [25316]
2019-08-14 12:37:25,551 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 25316
2019-08-14 12:37:25,551 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-14 12:37:26,552 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-14 12:37:26,552 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=25316
2019-08-14 12:37:26,608 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [25316] (in reverse order)
2019-08-14 12:37:26,653 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-14 12:37:26,653 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-14 12:37:26,653 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-14 12:37:26,653 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-14 12:37:27,163 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-14 12:37:36,862 | INFO     | monitor             | pilot.control.monitor            | control                   | 11515 s have passed since pilot start
2019-08-14 12:37:37,195 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-14 12:37:37,195 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-14 12:37:37,233 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35671506944 B)
2019-08-14 12:37:37,233 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-14 12:37:37,233 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-14 12:37:37,303 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-14 12:37:37,303 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(job, started 139666144110336)>, <ExcThread(copytool_in, started 139665214531328)>, <ExcThread(validate_pre, started 139665726224128)>, <ExcThread(execute_payloads, started 139665197745920)>, <ExcThread(monitor, started 139665734616832)>, <ExcThread(queue_monitor, started 139665222924032)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(failed_post, started 139665206138624)>, <ExcThread(queue_monitoring, started 139665717831424)>, <ExcThread(create_data_payload, started 139666118932224)>, <ExcThread(validate_post, started 139665709438720)>, <ExcThread(data, started 139666127324928)>, <ExcThread(validate, started 139666135717632)>, <ExcThread(payload, started 139665759794944)>]
2019-08-14 12:37:37,496 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-14 12:37:37,496 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-14 12:37:37,513 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-14 12:37:37,556 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-14 12:37:37,747 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-14 12:37:37,808 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-14 12:37:37,809 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(copytool_in, started 139665214531328)>, <ExcThread(validate_pre, started 139665726224128)>, <ExcThread(execute_payloads, started 139665197745920)>, <ExcThread(monitor, started 139665734616832)>, <ExcThread(queue_monitor, started 139665222924032)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(failed_post, started 139665206138624)>, <ExcThread(queue_monitoring, started 139665717831424)>, <ExcThread(validate_post, started 139665709438720)>, <ExcThread(data, started 139666127324928)>, <ExcThread(payload, started 139665759794944)>]
2019-08-14 12:37:37,822 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-14 12:37:37,868 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-14 12:37:37,875 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-14 12:37:38,006 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-14 12:37:38,006 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-14 12:37:38,010 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-14 12:37:38,010 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(validate_pre, started 139665726224128)>, <ExcThread(execute_payloads, started 139665197745920)>, <ExcThread(queue_monitor, started 139665222924032)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(queue_monitoring, started 139665717831424)>, <ExcThread(validate_post, started 139665709438720)>, <ExcThread(data, started 139666127324928)>]
2019-08-14 12:37:38,074 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-14 12:37:38,131 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-14 12:37:38,143 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-14 12:37:38,211 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-14 12:37:38,212 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(queue_monitor, started 139665222924032)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(queue_monitoring, started 139665717831424)>, <ExcThread(data, started 139666127324928)>]
2019-08-14 12:37:38,212 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-14 12:37:38,311 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-14 12:37:38,311 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-14 12:37:38,312 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-14 12:37:38,313 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(queue_monitor, started 139665222924032)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(queue_monitoring, started 139665717831424)>]
2019-08-14 12:37:38,865 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-14 12:37:38,865 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-14 12:37:38,917 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-14 12:37:38,918 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(copytool_out, started 139666110539520)>, <ExcThread(queue_monitoring, started 139665717831424)>]
2019-08-14 12:37:39,213 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-14 12:37:39,220 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-14 12:37:39,220 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(job_monitor, started 139665743009536)>, <ExcThread(queue_monitoring, started 139665717831424)>]
2019-08-14 12:37:40,748 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-14 12:37:40,832 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-14 12:37:40,833 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139666360383232)>, <ExcThread(job_monitor, started 139665743009536)>]
2019-08-14 12:37:52,132 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-14 12:37:52,132 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-14 12:37:52,133 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-14 12:37:52,133 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-14 12:37:52,133 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-14 12:37:52 UTC [wrapper] ==== pilot stdout END ====
2019-08-14 12:37:52 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-14 12:37:52 UTC [wrapper] Pilot exit status: 0
2019-08-14 12:37:52 UTC [wrapper] STATUSCODE: 0
2019-08-14 12:37:52 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 14 11:25 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

2019-08-14 12:37:52 UTC [wrapper] Test setup, not cleaning
2019-08-14 12:37:52 UTC [wrapper] ==== wrapper stdout END ====
2019-08-14 12:37:52 UTC [wrapper] ==== wrapper stderr END ====
2019-08-14 12:37:52 UTC [wrapper] wrapper wrapperexiting ec=0, duration=11546
2019-08-14 12:37:52 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11546.04s
KernelTime=332.68s
UserTime=43270.10s
CPUUsage=377%
MaxResidentMemory=1945260kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=378437
MinorPageFaults=16187007
Swaps=0
ForcedSwitches=4950669
WaitSwitches=7802780
Inputs=92123984
Outputs=757312
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 228640
drwxrwx--x. 6 grid grid      4096 Aug 14 14:37 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       517 Aug 14 14:37 4pJLDmTplHvnShfckohDCDFpABFKDmABFKDmZVPaDmABFKDmwvSSGn.diag
-rw-------. 1 grid grid   7409110 Aug 14 11:25 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517123 Aug 14 11:25 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 14 11:25 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 14 11:25 APPS
-rw-------. 1 grid grid       538 Aug 14 11:25 .asetup
-rw-------. 1 grid grid       826 Aug 14 11:26 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 14 11:25 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 14:37 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 14 14:29 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 219951910 Aug 14 11:25 EVNT.18605781._000279.pool.root.1
-rw-------. 1 grid grid     97723 Aug 14 14:37 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 14 11:25 init_data.xml
-rw-rw-r--. 1 grid grid    261630 Aug 14 11:25 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 14 11:25 job.xml
-rw-------. 1 grid grid    627946 Aug 14 14:37 log.18722432._022691.job.log.1
-rw-------. 1 grid grid    843726 Aug 14 14:37 log.18722432._022691.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 14 14:37 output.list
-rw-------. 1 grid grid      2958 Aug 13 15:15 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 14:32 pilot2.tar.gz
-rw-------. 1 grid grid     10605 Aug 14 14:37 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 15:15 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 14 11:25 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 14 11:25 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 15:15 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 14:37 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 14:37 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 14:37 shared
-rw-rw-r--. 1 grid grid      8688 Aug 14 11:25 start_atlas.sh
-rw-rw-r--. 1 grid grid     18412 Aug 14 14:37 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 14 11:25 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 14 14:37 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
14:37:53 (18644): run_atlas exited; CPU time 43270.483142
14:37:53 (18644): called boinc_finish(0)

</stderr_txt>
]]>

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