Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
09:23:00 (26199): wrapper (7.7.26015): starting
09:23:00 (26199): 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=4446336337
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.18604991._045837.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-14 09:24:45,572 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4446336337
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604991
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-14 09:24:45,573 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 27016 s
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 393
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 393
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 09:24:45,574 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446336337 has completed
2019-08-14 09:24:45,575 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-14 09:24:45,582 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446336337
2019-08-14 09:24:46,588 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [393]
2019-08-14 09:24:46,588 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 393
2019-08-14 09:24:46,588 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-14 09:24:47,593 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-14 09:24:47,594 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=393
2019-08-14 09:24:47,643 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [393] (in reverse order)
2019-08-14 09:24:47,685 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-14 09:24:47,685 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-14 09:24:47,685 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-14 09:24:47,685 | 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 09:24:48,195 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-14 09:24:58,240 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-14 09:24:58,241 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-14 09:24:58,274 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35681992704 B)
2019-08-14 09:24:58,274 | 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 09:24:58,274 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-14 09:24:58,301 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-14 09:24:58,348 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-14 09:24:58,348 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(job, started 140047090411264)>, <ExcThread(copytool_in, started 140046359308032)>, <ExcThread(execute_payloads, started 140046350915328)>, <ExcThread(copytool_out, started 140046980073216)>, <ExcThread(failed_post, started 140046376093440)>, <ExcThread(validate, started 140047082018560)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(create_data_payload, started 140046996858624)>, <ExcThread(queue_monitoring, started 140046392878848)>, <ExcThread(data, started 140047005251328)>, <ExcThread(validate_post, started 140046384486144)>, <ExcThread(validate_pre, started 140046954895104)>, <ExcThread(payload, started 140046988465920)>, <ExcThread(queue_monitor, started 140046367700736)>]
2019-08-14 09:24:58,522 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-14 09:24:58,602 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-14 09:24:58,626 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-14 09:24:58,705 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-14 09:24:58,705 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-14 09:24:58,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-14 09:24:58,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(job, started 140047090411264)>, <ExcThread(copytool_in, started 140046359308032)>, <ExcThread(execute_payloads, started 140046350915328)>, <ExcThread(copytool_out, started 140046980073216)>, <ExcThread(validate, started 140047082018560)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(create_data_payload, started 140046996858624)>, <ExcThread(queue_monitoring, started 140046392878848)>, <ExcThread(data, started 140047005251328)>, <ExcThread(queue_monitor, started 140046367700736)>]
2019-08-14 09:24:59,028 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-14 09:24:59,116 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-14 09:24:59,117 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-14 09:24:59,123 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-14 09:24:59,217 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-14 09:24:59,217 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(job, started 140047090411264)>, <ExcThread(copytool_in, started 140046359308032)>, <ExcThread(copytool_out, started 140046980073216)>, <ExcThread(validate, started 140047082018560)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(create_data_payload, started 140046996858624)>, <ExcThread(queue_monitoring, started 140046392878848)>, <ExcThread(queue_monitor, started 140046367700736)>]
2019-08-14 09:24:59,336 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-14 09:24:59,336 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-14 09:24:59,372 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-14 09:24:59,417 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-14 09:24:59,418 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-14 09:24:59,419 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-14 09:24:59,419 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(copytool_out, started 140046980073216)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(queue_monitoring, started 140046392878848)>, <ExcThread(queue_monitor, started 140046367700736)>]
2019-08-14 09:25:00,016 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-14 09:25:00,017 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-14 09:25:00,017 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-14 09:25:00,023 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-14 09:25:00,023 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(copytool_out, started 140046980073216)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(queue_monitoring, started 140046392878848)>]
2019-08-14 09:25:00,124 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-14 09:25:00,225 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-14 09:25:00,225 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(job_monitor, started 140046401271552)>, <ExcThread(queue_monitoring, started 140046392878848)>]
2019-08-14 09:25:03,018 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-14 09:25:03,044 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-14 09:25:03,044 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140047306684160)>, <ExcThread(job_monitor, started 140046401271552)>]
2019-08-14 09:25:19,263 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-14 09:25:19,263 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-14 09:25:19,263 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-14 09:25:19,264 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-14 09:25:19,264 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-14 09:25:19 UTC [wrapper] ==== pilot stdout END ====
2019-08-14 09:25:19 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-14 09:25:19 UTC [wrapper] Pilot exit status: 0
2019-08-14 09:25:19 UTC [wrapper] STATUSCODE: 0
2019-08-14 09:25:19 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 09:23 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 09:25:19 UTC [wrapper] Test setup, not cleaning
2019-08-14 09:25:19 UTC [wrapper] ==== wrapper stdout END ====
2019-08-14 09:25:19 UTC [wrapper] ==== wrapper stderr END ====
2019-08-14 09:25:19 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7332
2019-08-14 09:25:19 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7332.16s
KernelTime=229.83s
UserTime=26905.41s
CPUUsage=370%
MaxResidentMemory=1944820kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=293004
MinorPageFaults=13371281
Swaps=0
ForcedSwitches=3138217
WaitSwitches=5886942
Inputs=71281448
Outputs=498840
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 383384
drwxrwx--x. 6 grid grid      4096 Aug 14 11:25 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 14 11:25 4mgNDmPvdHvnShfckohDCDFpABFKDmABFKDmNyBaDmABFKDmdzx5Sm.diag
-rw-------. 1 grid grid   7409110 Aug 14 09:23 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517155 Aug 14 09:23 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 14 09:23 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 14 09:23 APPS
-rw-------. 1 grid grid       538 Aug 14 09:23 .asetup
-rw-------. 1 grid grid       826 Aug 14 09:24 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 14 09:23 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 11:24 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 14 11:20 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 378584498 Aug 14 09:23 EVNT.17323818._001242.pool.root.1
-rw-------. 1 grid grid     94114 Aug 14 11:24 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 14 09:23 init_data.xml
-rw-rw-r--. 1 grid grid    261623 Aug 14 09:23 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 14 09:22 job.xml
-rw-------. 1 grid grid    471210 Aug 14 11:25 log.18604991._045837.job.log.1
-rw-------. 1 grid grid    828876 Aug 14 11:24 log.18604991._045837.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 14 11:25 output.list
-rw-------. 1 grid grid      2871 Aug 13 06:49 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 06:30 pilot2.tar.gz
-rw-------. 1 grid grid      9700 Aug 14 11:25 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 06:47 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 14 09:23 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 14 09:22 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 06:49 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 11:25 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 11:25 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 11:25 shared
-rw-rw-r--. 1 grid grid      8688 Aug 14 09:23 start_atlas.sh
-rw-rw-r--. 1 grid grid     17930 Aug 14 11:25 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 14 09:22 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 14 11:24 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
11:25:19 (26199): run_atlas exited; CPU time 26905.819088
11:25:19 (26199): called boinc_finish(0)

</stderr_txt>
]]>

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