Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
12:01:15 (21691): wrapper (7.7.26015): starting
12:01:15 (21691): 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.18722432._012399.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722432
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 13:03:37,763 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 41411 s
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 28364
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 28364
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442732558 has completed
2019-08-10 13:03:37,764 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 13:03:37,772 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442732558
2019-08-10 13:03:38,777 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [28364]
2019-08-10 13:03:38,777 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 28364
2019-08-10 13:03:38,778 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 13:03:39,783 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 13:03:39,783 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=28364
2019-08-10 13:03:39,830 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [28364] (in reverse order)
2019-08-10 13:03:39,872 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 13:03:39,873 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 13:03:39,873 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 13:03:39,873 | 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 13:03:40,383 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 13:03:47,917 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-10 13:03:50,390 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 13:03:50,390 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 13:03:50,431 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34725691392 B)
2019-08-10 13:03:50,432 | 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 13:03:50,432 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 13:03:50,451 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 13:03:50,469 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 13:03:50,473 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 13:03:50,475 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-10 13:03:50,475 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(job, started 140377101305600)>, <ExcThread(payload, started 140377059342080)>, <ExcThread(copytool_out, started 140377067734784)>, <ExcThread(monitor, started 140376711100160)>, <ExcThread(create_data_payload, started 140377076127488)>, <ExcThread(validate_pre, started 140376702707456)>, <ExcThread(execute_payloads, started 140376098727680)>, <ExcThread(validate_post, started 140376677529344)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(failed_post, started 140376669136640)>, <ExcThread(queue_monitor, started 140376090334976)>, <ExcThread(job_monitor, started 140376660743936)>, <ExcThread(data, started 140377084520192)>]
2019-08-10 13:03:50,543 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 13:03:50,730 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 13:03:50,856 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 13:03:50,877 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-10 13:03:50,877 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(job, started 140377101305600)>, <ExcThread(payload, started 140377059342080)>, <ExcThread(copytool_out, started 140377067734784)>, <ExcThread(create_data_payload, started 140377076127488)>, <ExcThread(validate_pre, started 140376702707456)>, <ExcThread(execute_payloads, started 140376098727680)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(queue_monitor, started 140376090334976)>, <ExcThread(job_monitor, started 140376660743936)>, <ExcThread(data, started 140377084520192)>]
2019-08-10 13:03:51,254 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 13:03:51,268 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 13:03:51,268 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 13:03:51,279 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-10 13:03:51,279 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(job, started 140377101305600)>, <ExcThread(payload, started 140377059342080)>, <ExcThread(copytool_out, started 140377067734784)>, <ExcThread(create_data_payload, started 140377076127488)>, <ExcThread(validate_pre, started 140376702707456)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(queue_monitor, started 140376090334976)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:03:51,336 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 13:03:51,336 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 13:03:51,423 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 13:03:51,452 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 13:03:51,480 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 13:03:51,480 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(payload, started 140377059342080)>, <ExcThread(validate_pre, started 140376702707456)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(queue_monitor, started 140376090334976)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:03:51,665 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 13:03:51,665 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 13:03:51,681 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-10 13:03:51,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(validate_pre, started 140376702707456)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(queue_monitor, started 140376090334976)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:03:51,825 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 13:03:51,866 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 13:03:51,867 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 13:03:51,883 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 13:03:51,884 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(validate, started 140377092912896)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:03:51,922 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 13:03:51,984 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 13:03:51,985 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(queue_monitoring, started 140376685922048)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:03:53,474 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 13:03:53,495 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 13:03:53,495 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>, <ExcThread(job_monitor, started 140376660743936)>]
2019-08-10 13:04:49,481 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-10 13:04:49,482 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 13:04:49,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 1 threads
2019-08-10 13:04:49,483 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140377317578496)>]
2019-08-10 13:04:49,483 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | aborting since there is[are] 0 daemon thread[s] which can be ignored
2019-08-10 13:04:49,483 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 13:04:49,483 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 13:04:49,483 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 13:04:49 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 13:04:49 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 13:04:49 UTC [wrapper] Pilot exit status: 0
2019-08-10 13:04:49 UTC [wrapper] STATUSCODE: 0
2019-08-10 13:04:49 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 12:01 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 13:04:49 UTC [wrapper] Test setup, not cleaning
2019-08-10 13:04:49 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 13:04:49 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11011.91s
KernelTime=322.91s
UserTime=41241.34s
CPUUsage=377%
MaxResidentMemory=1944304kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=364322
MinorPageFaults=15847123
Swaps=0
ForcedSwitches=4792061
WaitSwitches=7566801
Inputs=88419416
Outputs=762224
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 231060
drwxrwx--x. 7 grid grid      4096 Aug 10 15:04 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408903 Aug 10 12:01 agis_ddmendpoints.json
-rw-------. 1 grid grid   4507141 Aug 10 12:01 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 12:01 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 12:01 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 12:01 .arc
-rw-------. 1 grid grid       538 Aug 10 12:01 .asetup
-rw-------. 1 grid grid       826 Aug 10 12:02 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 12:01 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 15:04 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 10 14:58 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 222394225 Aug 10 12:01 EVNT.18605781._000252.pool.root.1
-rw-------. 1 grid grid       517 Aug 10 15:04 gUILDma7YGvnShfckohDCDFpABFKDmABFKDmLbRYDmABFKDmckepSm.diag
-rw-------. 1 grid grid    125621 Aug 10 15:03 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 12:01 init_data.xml
-rw-rw-r--. 1 grid grid    262345 Aug 10 12:01 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 12:01 job.xml
-rw-------. 1 grid grid    632089 Aug 10 15:04 log.18722432._012399.job.log.1
-rw-------. 1 grid grid    848643 Aug 10 15:03 log.18722432._012399.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 15:04 output.list
-rw-------. 1 grid grid      2957 Aug 10 07:29 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 07:29 pilot2.tar.gz
-rw-------. 1 grid grid     11193 Aug 10 15:04 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 10 07:29 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 12:01 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 12:01 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 07:29 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 15:04 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 15:04 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 15:04 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 12:01 start_atlas.sh
-rw-rw-r--. 1 grid grid     18750 Aug 10 15:04 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 12:01 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 10 15:04 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
15:04:50 (21691): run_atlas exited; CPU time 41241.700317
15:04:50 (21691): called boinc_finish(0)

</stderr_txt>
]]>

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