Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
21:14:03 (4643): wrapper (7.7.26015): starting
21:14:03 (4643): 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=4446890719
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.18604976._047758.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 21:09:20,679 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 25518 s
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 11317
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 11317
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446890719 has completed
2019-08-13 21:09:20,680 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 21:09:20,689 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446890719
2019-08-13 21:09:21,695 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11317]
2019-08-13 21:09:21,695 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11317
2019-08-13 21:09:21,695 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 21:09:22,700 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 21:09:22,700 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11317
2019-08-13 21:09:22,757 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11317] (in reverse order)
2019-08-13 21:09:22,800 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 21:09:22,800 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 21:09:22,800 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 21:09:22,800 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 21:09:23,308 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 21:09:33,351 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 21:09:33,351 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 21:09:33,389 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34233909248 B)
2019-08-13 21:09:33,390 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 21:09:33,390 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 21:09:33,393 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 21:09:33,396 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 21:09:33,424 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-13 21:09:33,425 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(job, started 140392697816832)>, <ExcThread(copytool_out, started 140392582330112)>, <ExcThread(copytool_in, started 140392171284224)>, <ExcThread(payload, started 140392590722816)>, <ExcThread(failed_post, started 140392162891520)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(execute_payloads, started 140391609267968)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate, started 140392615900928)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>, <ExcThread(data, started 140392607508224)>]
2019-08-13 21:09:33,563 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 21:09:33,582 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 21:09:33,618 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 21:09:33,618 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 21:09:33,710 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 21:09:33,710 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 21:09:33,726 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-13 21:09:33,727 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(copytool_out, started 140392582330112)>, <ExcThread(copytool_in, started 140392171284224)>, <ExcThread(failed_post, started 140392162891520)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>, <ExcThread(data, started 140392607508224)>]
2019-08-13 21:09:34,125 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 21:09:34,125 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 21:09:34,129 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-13 21:09:34,130 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(copytool_out, started 140392582330112)>, <ExcThread(copytool_in, started 140392171284224)>, <ExcThread(failed_post, started 140392162891520)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,161 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 21:09:34,230 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 21:09:34,231 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(copytool_out, started 140392582330112)>, <ExcThread(failed_post, started 140392162891520)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,394 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 21:09:34,432 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 21:09:34,433 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(failed_post, started 140392162891520)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,489 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 21:09:34,534 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 21:09:34,534 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(create_data_payload, started 140392599115520)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(validate_post, started 140392188069632)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,556 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 21:09:34,562 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 21:09:34,635 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 21:09:34,635 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(validate_pre, started 140392213247744)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,704 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 21:09:34,736 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 21:09:34,736 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(queue_monitor, started 140392179676928)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:34,871 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 21:09:34,907 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 21:09:34,907 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 21:09:34,938 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 21:09:34,938 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(job_monitor, started 140392204855040)>, <ExcThread(queue_monitoring, started 140392196462336)>]
2019-08-13 21:09:37,873 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 21:09:37,959 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 21:09:37,959 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140392914089728)>, <ExcThread(job_monitor, started 140392204855040)>]
2019-08-13 21:09:54,961 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 21:09:54,961 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 21:09:54,975 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 21:09:54,975 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 21:09:54,975 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 21:09:55 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 21:09:55 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 21:09:55 UTC [wrapper] Pilot exit status: 0
2019-08-13 21:09:55 UTC [wrapper] STATUSCODE: 0
2019-08-13 21:09:55 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 13 21:14 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

2019-08-13 21:09:55 UTC [wrapper] Test setup, not cleaning
2019-08-13 21:09:55 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 21:09:55 UTC [wrapper] ==== wrapper stderr END ====
2019-08-13 21:09:55 UTC [wrapper] wrapper wrapperexiting ec=0, duration=6949
2019-08-13 21:09:55 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6948.47s
KernelTime=225.87s
UserTime=25400.83s
CPUUsage=368%
MaxResidentMemory=1945212kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=286989
MinorPageFaults=13217377
Swaps=0
ForcedSwitches=2955339
WaitSwitches=5552978
Inputs=70053296
Outputs=503768
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 382252
drwxrwx--x. 6 grid grid      4096 Aug 13 23:09 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409110 Aug 13 21:14 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517750 Aug 13 21:14 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 21:14 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 21:14 APPS
-rw-------. 1 grid grid       538 Aug 13 21:14 .asetup
-rw-------. 1 grid grid       826 Aug 13 21:15 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 21:14 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 23:09 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 13 23:04 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 377441982 Aug 13 21:14 EVNT.17323813._000931.pool.root.1
-rw-------. 1 grid grid     93602 Aug 13 23:09 heartbeat.json
-rw-rw-r--. 1 grid grid      5864 Aug 13 21:14 init_data.xml
-rw-rw-r--. 1 grid grid    261612 Aug 13 21:14 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 13 21:14 job.xml
-rw-------. 1 grid grid    462350 Aug 13 23:09 log.18604976._047758.job.log.1
-rw-------. 1 grid grid    825328 Aug 13 23:09 log.18604976._047758.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 13 23:09 output.list
-rw-------. 1 grid grid      2872 Aug 13 13:50 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 13:29 pilot2.tar.gz
-rw-------. 1 grid grid     11916 Aug 13 23:09 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 13:50 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 21:14 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 21:14 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 13:50 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 23:09 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 23:09 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 23:09 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 21:14 start_atlas.sh
-rw-rw-r--. 1 grid grid     19295 Aug 13 23:09 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 21:14 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 13 23:09 wrapper_checkpoint.txt
-rw-------. 1 grid grid       516 Aug 13 23:09 zWJKDmyUkHvnShfckohDCDFpABFKDmABFKDmKONaDmABFKDmJbPkSo.diag

running start_atlas return value is 0
Parent exit 0
child process exit 0
23:09:55 (4643): run_atlas exited; CPU time 25401.233748
23:09:55 (4643): called boinc_finish(0)

</stderr_txt>
]]>

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