Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
15:04:54 (17371): wrapper (7.7.26015): starting
15:04:54 (17371): 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.18722398._015476.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442626047
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 15:15:21,456 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 29048 s
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 24042
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 24042
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 15:15:21,457 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442626047 has completed
2019-08-10 15:15:21,458 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 15:15:21,465 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442626047
2019-08-10 15:15:22,470 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [24042]
2019-08-10 15:15:22,470 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 24042
2019-08-10 15:15:22,470 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 15:15:23,472 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 15:15:23,472 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=24042
2019-08-10 15:15:23,538 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [24042] (in reverse order)
2019-08-10 15:15:23,589 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 15:15:23,590 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 15:15:23,590 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 15:15:23,590 | 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 15:15:24,103 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 15:15:34,154 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 15:15:34,154 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 15:15:34,189 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36562796544 B)
2019-08-10 15:15:34,189 | 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 15:15:34,189 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 15:15:34,462 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-10 15:15:34,463 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job, started 140031972325120)>, <ExcThread(failed_post, started 140030899123968)>, <ExcThread(validate_post, started 140031402424064)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(execute_payloads, started 140030890731264)>, <ExcThread(monitor, started 140031427602176)>, <ExcThread(copytool_in, started 140031385638656)>, <ExcThread(validate_pre, started 140031921968896)>, <ExcThread(data, started 140031963932416)>, <ExcThread(copytool_out, started 140031947147008)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>, <ExcThread(validate, started 140031955539712)>, <ExcThread(payload, started 140031938754304)>, <ExcThread(create_data_payload, started 140031930361600)>]
2019-08-10 15:15:34,519 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 15:15:34,525 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 15:15:34,818 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 15:15:34,818 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 15:15:34,874 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 15:15:34,892 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-10 15:15:34,892 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job, started 140031972325120)>, <ExcThread(failed_post, started 140030899123968)>, <ExcThread(validate_post, started 140031402424064)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(copytool_in, started 140031385638656)>, <ExcThread(validate_pre, started 140031921968896)>, <ExcThread(data, started 140031963932416)>, <ExcThread(copytool_out, started 140031947147008)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>, <ExcThread(validate, started 140031955539712)>, <ExcThread(create_data_payload, started 140031930361600)>]
2019-08-10 15:15:34,915 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 15:15:34,968 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 15:15:34,969 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 15:15:35,094 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-10 15:15:35,094 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job, started 140031972325120)>, <ExcThread(failed_post, started 140030899123968)>, <ExcThread(validate_post, started 140031402424064)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(copytool_in, started 140031385638656)>, <ExcThread(validate_pre, started 140031921968896)>, <ExcThread(copytool_out, started 140031947147008)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>, <ExcThread(validate, started 140031955539712)>]
2019-08-10 15:15:35,114 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 15:15:35,161 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 15:15:35,295 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-10 15:15:35,295 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job, started 140031972325120)>, <ExcThread(failed_post, started 140030899123968)>, <ExcThread(validate_post, started 140031402424064)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(copytool_out, started 140031947147008)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>, <ExcThread(validate, started 140031955539712)>]
2019-08-10 15:15:35,521 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 15:15:35,521 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 15:15:35,526 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 15:15:35,597 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 15:15:35,598 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(failed_post, started 140030899123968)>, <ExcThread(validate_post, started 140031402424064)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>, <ExcThread(validate, started 140031955539712)>]
2019-08-10 15:15:35,605 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 15:15:35,621 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 15:15:35,677 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 15:15:35,699 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 15:15:35,699 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(queue_monitor, started 140031394031360)>, <ExcThread(queue_monitoring, started 140031419209472)>]
2019-08-10 15:15:35,957 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 15:15:35,957 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 15:15:35,971 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 15:15:36,001 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 15:15:36,001 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job_monitor, started 140031410816768)>, <ExcThread(queue_monitoring, started 140031419209472)>]
2019-08-10 15:15:38,973 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 15:15:39,023 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 15:15:39,023 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140032188598016)>, <ExcThread(job_monitor, started 140031410816768)>]
2019-08-10 15:16:04,223 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 15:16:04,223 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 15:16:04,299 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 15:16:04,300 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 15:16:04,300 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 15:16:04 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 15:16:04 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 15:16:04 UTC [wrapper] Pilot exit status: 0
2019-08-10 15:16:04 UTC [wrapper] STATUSCODE: 0
2019-08-10 15:16:04 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 15:05 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 15:16:04 UTC [wrapper] Test setup, not cleaning
2019-08-10 15:16:04 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 15:16:04 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7867.60s
KernelTime=250.93s
UserTime=28916.13s
CPUUsage=370%
MaxResidentMemory=1944564kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=306155
MinorPageFaults=13903654
Swaps=0
ForcedSwitches=3383237
WaitSwitches=6008475
Inputs=74345336
Outputs=626296
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216780
drwxrwx--x. 7 grid grid      4096 Aug 10 17:16 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408901 Aug 10 15:05 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506548 Aug 10 15:05 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 15:04 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 15:04 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 15:05 .arc
-rw-------. 1 grid grid       538 Aug 10 15:04 .asetup
-rw-------. 1 grid grid       826 Aug 10 15:05 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 15:04 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 17:16 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 10 17:09 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207992661 Aug 10 15:04 EVNT.18605775._000304.pool.root.1
-rw-------. 1 grid grid     81121 Aug 10 17:15 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 15:04 init_data.xml
-rw-rw-r--. 1 grid grid    262349 Aug 10 15:04 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 15:04 job.xml
-rw-------. 1 grid grid    479688 Aug 10 17:16 log.18722398._015476.job.log.1
-rw-------. 1 grid grid    825897 Aug 10 17:15 log.18722398._015476.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 17:16 output.list
-rw-------. 1 grid grid      2957 Aug  9 22:41 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 22:32 pilot2.tar.gz
-rw-------. 1 grid grid     10791 Aug 10 17:16 pilotlog.txt
-rw-------. 1 grid grid       516 Aug 10 17:16 PjmLDmdsQGvnShfckohDCDFpABFKDmABFKDm9VDYDmABFKDmeBaUqm.diag
-rw-r--r--. 1 grid grid      4468 Aug  9 22:41 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 15:04 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 15:04 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 22:41 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 17:16 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 17:16 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 17:16 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 15:04 start_atlas.sh
-rw-rw-r--. 1 grid grid     18931 Aug 10 17:16 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 15:04 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 10 17:16 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
17:16:05 (17371): run_atlas exited; CPU time 28916.487792
17:16:05 (17371): called boinc_finish(0)

</stderr_txt>
]]>

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