Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
13:18:05 (8085): wrapper (7.7.26015): starting
13:18:05 (8085): 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=4450721651
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._051094.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4450721651
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604991
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 13:17:54,133 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26477 s
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 14777
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 14777
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4450721651 has completed
2019-08-16 13:17:54,134 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 13:17:54,142 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4450721651
2019-08-16 13:17:55,145 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [14777]
2019-08-16 13:17:55,145 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 14777
2019-08-16 13:17:55,145 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 13:17:56,150 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 13:17:56,150 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=14777
2019-08-16 13:17:56,200 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [14777] (in reverse order)
2019-08-16 13:17:56,238 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 13:17:56,238 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 13:17:56,238 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 13:17:56,238 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-16 13:17:56,748 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 13:18:06,799 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 13:18:06,799 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 13:18:06,833 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34190917632 B)
2019-08-16 13:18:06,833 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-16 13:18:06,833 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 13:18:06,860 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 13:18:06,886 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 13:18:06,886 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 13:18:06,988 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-16 13:18:06,988 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(job, started 140393703417600)>, <ExcThread(validate_post, started 140393177917184)>, <ExcThread(failed_post, started 140393169524480)>, <ExcThread(copytool_out, started 140393597355776)>, <ExcThread(validate_pre, started 140393211488000)>, <ExcThread(create_data_payload, started 140393605748480)>, <ExcThread(copytool_in, started 140393203095296)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(monitor, started 140393194702592)>, <ExcThread(validate, started 140393622533888)>, <ExcThread(execute_payloads, started 140392615900928)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(data, started 140393614141184)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:07,079 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 13:18:07,245 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 13:18:07,329 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 13:18:07,341 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 13:18:07,354 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 13:18:07,354 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(job, started 140393703417600)>, <ExcThread(validate_post, started 140393177917184)>, <ExcThread(failed_post, started 140393169524480)>, <ExcThread(copytool_out, started 140393597355776)>, <ExcThread(validate_pre, started 140393211488000)>, <ExcThread(copytool_in, started 140393203095296)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(data, started 140393614141184)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:07,377 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 13:18:07,377 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 13:18:07,465 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 13:18:07,478 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 13:18:07,478 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 13:18:07,486 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-16 13:18:07,487 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(failed_post, started 140393169524480)>, <ExcThread(copytool_out, started 140393597355776)>, <ExcThread(validate_pre, started 140393211488000)>, <ExcThread(copytool_in, started 140393203095296)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:07,797 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 13:18:07,861 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 13:18:07,889 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 13:18:07,890 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(failed_post, started 140393169524480)>, <ExcThread(validate_pre, started 140393211488000)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:08,074 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 13:18:08,091 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 13:18:08,091 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(failed_post, started 140393169524480)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:08,097 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 13:18:08,193 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 13:18:08,193 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>, <ExcThread(queue_monitor, started 140393186309888)>]
2019-08-16 13:18:08,634 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 13:18:08,634 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 13:18:08,640 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 13:18:08,696 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 13:18:08,697 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(job_monitor, started 140393219880704)>, <ExcThread(queue_monitoring, started 140393572177664)>]
2019-08-16 13:18:11,641 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 13:18:11,728 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 13:18:11,728 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140393919690496)>, <ExcThread(job_monitor, started 140393219880704)>]
2019-08-16 13:18:45,553 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 13:18:45,553 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 13:18:45,574 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 13:18:45,575 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 13:18:45,575 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 13:18:45 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 13:18:45 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 13:18:45 UTC [wrapper] Pilot exit status: 0
2019-08-16 13:18:45 UTC [wrapper] STATUSCODE: 0
2019-08-16 13:18:45 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 16 13:18 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

2019-08-16 13:18:45 UTC [wrapper] Test setup, not cleaning
2019-08-16 13:18:45 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 13:18:45 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 13:18:45 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7237
2019-08-16 13:18:45 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7237.50s
KernelTime=226.29s
UserTime=26370.40s
CPUUsage=367%
MaxResidentMemory=1945244kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=289483
MinorPageFaults=13311336
Swaps=0
ForcedSwitches=3076206
WaitSwitches=5927219
Inputs=70662920
Outputs=495720
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 381736
drwxrwx--x. 6 grid grid      4096 Aug 16 15:18 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 16 15:18 18ULDm6PhIvnShfckohDCDFpABFKDmABFKDmIyHKDmABFKDmumM4Jn.diag
-rw-------. 1 grid grid   7416180 Aug 16 13:18 agis_ddmendpoints.json
-rw-------. 1 grid grid   4400266 Aug 16 13:18 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 13:18 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 13:18 APPS
-rw-------. 1 grid grid       538 Aug 16 13:18 .asetup
-rw-------. 1 grid grid       826 Aug 16 13:19 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 13:18 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 15:18 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 16 15:12 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 377059944 Aug 16 13:18 EVNT.17323818._001328.pool.root.1
-rw-------. 1 grid grid     73492 Aug 16 15:17 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 13:18 init_data.xml
-rw-rw-r--. 1 grid grid    261630 Aug 16 13:18 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 16 13:18 job.xml
-rw-------. 1 grid grid    446430 Aug 16 15:18 log.18604991._051094.job.log.1
-rw-------. 1 grid grid    819759 Aug 16 15:17 log.18604991._051094.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 15:18 output.list
-rw-------. 1 grid grid      2873 Aug 16 04:45 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 16 04:29 pilot2.tar.gz
-rw-------. 1 grid grid     10247 Aug 16 15:18 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 16 04:40 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 13:18 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 13:18 run_atlas
-rwx------. 1 grid grid     12641 Aug 16 04:45 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 15:18 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 15:18 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 15:18 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 13:18 start_atlas.sh
-rw-rw-r--. 1 grid grid     18223 Aug 16 15:18 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 16 13:18 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 16 15:18 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
15:18:46 (8085): run_atlas exited; CPU time 26370.806688
15:18:46 (8085): called boinc_finish(0)

</stderr_txt>
]]>

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