Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
07:15:33 (670): wrapper (7.7.26015): starting
07:15:33 (670): 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._007716.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4436883055
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 07:25:13,114 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 28631 s
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7432
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7432
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4436883055 has completed
2019-08-11 07:25:13,115 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 07:25:13,126 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4436883055
2019-08-11 07:25:14,131 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7432]
2019-08-11 07:25:14,131 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7432
2019-08-11 07:25:14,131 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 07:25:15,132 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 07:25:15,132 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7432
2019-08-11 07:25:15,196 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7432] (in reverse order)
2019-08-11 07:25:15,240 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 07:25:15,241 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 07:25:15,241 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 07:25:15,241 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-11 07:25:15,249 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 07:25:18,222 | INFO     | monitor             | pilot.control.monitor            | control                   | 7766 s have passed since pilot start
2019-08-11 07:25:25,280 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 07:25:25,280 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 07:25:25,386 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35333865472 B)
2019-08-11 07:25:25,386 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-11 07:25:25,386 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 07:25:25,405 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 07:25:25,406 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 07:25:25,406 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | will abort 
2019-08-11 07:25:25,406 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 07:25:25,407 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 07:25:25,482 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 07:25:25,482 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 07:25:25,522 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 07:25:25,531 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 07:25:25,624 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 07:25:25,657 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-11 07:25:25,658 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(job, started 140086084679424)>, <ExcThread(data, started 140086076286720)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(copytool_in, started 140085458630400)>, <ExcThread(execute_payloads, started 140085416666880)>, <ExcThread(validate_post, started 140085450237696)>, <ExcThread(validate, started 140085995501312)>, <ExcThread(create_data_payload, started 140085953537792)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:25,758 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 07:25:25,758 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 07:25:25,808 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 07:25:25,859 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 07:25:25,859 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 07:25:25,859 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 07:25:25,860 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-11 07:25:25,860 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(validate_post, started 140085450237696)>, <ExcThread(validate, started 140085995501312)>, <ExcThread(create_data_payload, started 140085953537792)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:25,961 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-11 07:25:25,962 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(validate_post, started 140085450237696)>, <ExcThread(validate, started 140085995501312)>, <ExcThread(create_data_payload, started 140085953537792)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:25,994 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 07:25:26,062 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-11 07:25:26,063 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(validate_post, started 140085450237696)>, <ExcThread(validate, started 140085995501312)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:26,109 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 07:25:26,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-11 07:25:26,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(validate, started 140085995501312)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:26,212 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 07:25:26,265 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 07:25:26,265 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>, <ExcThread(copytool_out, started 140085987108608)>]
2019-08-11 07:25:26,407 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | aborting
2019-08-11 07:25:26,407 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 07:25:26,466 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 07:25:26,467 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(queue_monitoring, started 140085970323200)>, <ExcThread(job_monitor, started 140085425059584)>]
2019-08-11 07:25:28,626 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 07:25:28,683 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 07:25:28,684 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140086298830592)>, <ExcThread(job_monitor, started 140085425059584)>]
2019-08-11 07:25:43,163 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-11 07:25:43,164 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 07:25:43,196 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 07:25:43,197 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 07:25:43,197 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 07:25:43 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 07:25:43 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 07:25:43 UTC [wrapper] Pilot exit status: 0
2019-08-11 07:25:43 UTC [wrapper] STATUSCODE: 0
2019-08-11 07:25:43 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 11 07:15 pilot
-rwx------.  1 grid grid 20463 Jul 25 16:38 pilot.py
-rw-------.  1 grid grid     8 Jul 31 19:00 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-11 07:25:43 UTC [wrapper] Test setup, not cleaning
2019-08-11 07:25:43 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 07:25:43 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7806.60s
KernelTime=265.96s
UserTime=28508.76s
CPUUsage=368%
MaxResidentMemory=1945132kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=304751
MinorPageFaults=13842863
Swaps=0
ForcedSwitches=3480029
WaitSwitches=6892889
Inputs=74016840
Outputs=605040
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216320
drwxrwx--x. 7 grid grid      4096 Aug 11 09:25 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 11 07:15 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506453 Aug 11 07:15 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 11 07:15 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 11 07:15 APPS
drwxr-xr-x. 2 grid grid         6 Aug 11 07:15 .arc
-rw-------. 1 grid grid       538 Aug 11 07:15 .asetup
-rw-------. 1 grid grid       826 Aug 11 07:16 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 11 07:15 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 11 09:25 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 11 09:18 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207520687 Aug 11 07:15 EVNT.18605775._000152.pool.root.1
-rw-------. 1 grid grid     81065 Aug 11 09:25 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 11 07:15 init_data.xml
-rw-rw-r--. 1 grid grid    261806 Aug 11 07:15 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 11 07:15 job.xml
-rw-------. 1 grid grid    482202 Aug 11 09:25 log.18722398._007716.job.log.1
-rw-------. 1 grid grid    829613 Aug 11 09:25 log.18722398._007716.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 11 09:25 output.list
-rw-------. 1 grid grid      2956 Aug  3 08:53 pandaJobData.out
-rw-------. 1 grid grid       516 Aug 11 09:25 pdvMDm352DvnShfckohDCDFpABFKDmABFKDmu2mSDmABFKDmpPGBnm.diag
drwx------. 3 grid grid       174 Jul 31 19:00 pilot2
-rw-r--r--. 1 grid grid    252463 Aug  1 05:54 pilot2.tar.gz
-rw-------. 1 grid grid     10225 Aug 11 09:25 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  3 08:53 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 11 07:15 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 11 07:15 run_atlas
-rwx------. 1 grid grid     15232 Aug  3 08:53 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 11 09:25 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 11 09:25 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 11 09:25 shared
-rw-rw-r--. 1 grid grid      8688 Aug 11 07:15 start_atlas.sh
-rw-rw-r--. 1 grid grid     17918 Aug 11 09:25 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 11 07:15 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 11 09:25 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
09:25:43 (670): run_atlas exited; CPU time 28509.154082
09:25:43 (670): called boinc_finish(0)

</stderr_txt>
]]>

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