Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
23:58:56 (3516): wrapper (7.7.26015): starting
23:58:56 (3516): 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.18722298._013837.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 02:07:54,562 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442729299
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 02:07:54,563 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 57125 s
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 10196
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 10196
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 02:07:54,564 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442729299 has completed
2019-08-11 02:07:54,565 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 02:07:54,577 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442729299
2019-08-11 02:07:55,581 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [10196]
2019-08-11 02:07:55,581 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 10196
2019-08-11 02:07:55,581 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 02:07:56,586 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 02:07:56,587 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=10196
2019-08-11 02:07:56,644 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [10196] (in reverse order)
2019-08-11 02:07:56,687 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 02:07:56,687 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 02:07:56,687 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 02:07:56,688 | 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 02:07:57,198 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 02:08:07,246 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 02:08:07,247 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 02:08:07,287 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35558260736 B)
2019-08-11 02:08:07,287 | 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 02:08:07,288 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 02:08:07,293 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 02:08:07,296 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 02:08:07,306 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 02:08:07,376 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 02:08:07,438 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 02:08:07,439 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 02:08:07,460 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-11 02:08:07,460 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(copytool_out, started 140647375763200)>, <ExcThread(data, started 140647409334016)>, <ExcThread(failed_post, started 140646857815808)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>, <ExcThread(copytool_in, started 140646841030400)>, <ExcThread(validate_post, started 140646882993920)>, <ExcThread(create_data_payload, started 140647384155904)>, <ExcThread(validate, started 140647417726720)>]
2019-08-11 02:08:07,592 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 02:08:07,609 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 02:08:07,609 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 02:08:07,661 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-11 02:08:07,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(copytool_out, started 140647375763200)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>, <ExcThread(copytool_in, started 140646841030400)>, <ExcThread(validate_post, started 140646882993920)>, <ExcThread(create_data_payload, started 140647384155904)>, <ExcThread(validate, started 140647417726720)>]
2019-08-11 02:08:07,692 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 02:08:07,863 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-11 02:08:07,863 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(copytool_out, started 140647375763200)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>, <ExcThread(copytool_in, started 140646841030400)>, <ExcThread(validate_post, started 140646882993920)>, <ExcThread(validate, started 140647417726720)>]
2019-08-11 02:08:08,028 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 02:08:08,064 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-11 02:08:08,065 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(copytool_out, started 140647375763200)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>, <ExcThread(copytool_in, started 140646841030400)>, <ExcThread(validate_post, started 140646882993920)>]
2019-08-11 02:08:08,216 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 02:08:08,263 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 02:08:08,266 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-11 02:08:08,266 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(copytool_out, started 140647375763200)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>]
2019-08-11 02:08:08,306 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 02:08:08,467 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-11 02:08:08,467 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job, started 140647426119424)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>]
2019-08-11 02:08:08,562 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 02:08:08,563 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 02:08:08,568 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 02:08:08,568 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(queue_monitor, started 140646354515712)>, <ExcThread(job_monitor, started 140646849423104)>]
2019-08-11 02:08:08,717 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 02:08:08,718 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 02:08:08,749 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 02:08:08,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 02:08:08,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(queue_monitoring, started 140646866208512)>, <ExcThread(job_monitor, started 140646849423104)>]
2019-08-11 02:08:11,750 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 02:08:11,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 02:08:11,791 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140647642392320)>, <ExcThread(job_monitor, started 140646849423104)>]
2019-08-11 02:08:47,366 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-11 02:08:47,368 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 02:08:47,448 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 02:08:47,449 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 02:08:47,449 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 02:08:50 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 02:08:50 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 02:08:50 UTC [wrapper] Pilot exit status: 0
2019-08-11 02:08:50 UTC [wrapper] STATUSCODE: 0
2019-08-11 02:08:50 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 23:59 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

2019-08-11 02:08:50 UTC [wrapper] Test setup, not cleaning
2019-08-11 02:08:50 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 02:08:50 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=14991.72s
KernelTime=438.84s
UserTime=56873.96s
CPUUsage=382%
MaxResidentMemory=1944544kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=447396
MinorPageFaults=18524500
Swaps=0
ForcedSwitches=6663285
WaitSwitches=9269304
Inputs=107975048
Outputs=946264
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 285004
drwxrwx--x. 7 grid grid      4096 Aug 11 04:08 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 10 23:59 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506467 Aug 10 23:59 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 23:58 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 23:58 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 23:59 .arc
-rw-------. 1 grid grid       538 Aug 10 23:59 .asetup
-rw-------. 1 grid grid       826 Aug 10 23:59 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 23:58 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 11 04:08 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 11 04:02 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 277539696 Aug 10 23:58 EVNT.18605754._000267.pool.root.1
-rw-------. 1 grid grid     97848 Aug 11 04:07 heartbeat.json
-rw-------. 1 grid grid       518 Aug 11 04:08 InhNDm1wVGvnShfckohDCDFpABFKDmABFKDmcUMYDmABFKDm0GU4Tm.diag
-rw-rw-r--. 1 grid grid      5862 Aug 10 23:58 init_data.xml
-rw-rw-r--. 1 grid grid    262342 Aug 10 23:58 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 23:58 job.xml
-rw-------. 1 grid grid    747194 Aug 11 04:08 log.18722298._013837.job.log.1
-rw-------. 1 grid grid    857353 Aug 11 04:07 log.18722298._013837.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 11 04:08 output.list
-rw-------. 1 grid grid      2915 Aug 10 04:06 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 03:23 pilot2.tar.gz
-rw-------. 1 grid grid     10774 Aug 11 04:08 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 10 04:06 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 23:58 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 23:58 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 04:06 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 11 04:08 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 11 04:08 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 11 04:08 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 23:58 start_atlas.sh
-rw-rw-r--. 1 grid grid     18650 Aug 11 04:08 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 23:58 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 11 04:08 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
04:08:51 (3516): run_atlas exited; CPU time 56874.354180
04:08:51 (3516): called boinc_finish(0)

</stderr_txt>
]]>

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