Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
06:09:08 (22689): wrapper (7.7.26015): starting
06:09:08 (22689): wrapper: running run_atlas (--nthreads 4)
2019-08-21 06:09:08,462: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-21 06:09:08,462: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-21 06:09:08,463: THREADS=4

2019-08-21 06:09:08,466: Checking for CVMFS
2019-08-21 06:09:09,894: CVMFS is installed
2019-08-21 06:09:09,898: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-21 06:09:09,898: This is not SLC6, need to run with Singularity....
2019-08-21 06:09:09,898: Checking Singularity...
2019-08-21 06:09:09,901: Singularity is not installed, using version from CVMFS
2019-08-21 06:09:09,901: Testing the function of Singularity...
2019-08-21 06:09:09,901: 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
2019-08-21 06:09:10,122: Singularity Works...
2019-08-21 06:09:10,122: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-21 06:09:10,651: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-21 06:09:10,652: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-21 06:09:10,653: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-21 06:09:10,653: export ATHENA_PROC_NUMBER=4;
2019-08-21 06:09:10,679: start atlas job with PandaID=4451623648
2019-08-21 06:09:10,679: 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
2019-08-21 11:13:03,348: running cmd return value is 0
2019-08-21 11:13:03,352: Moving ./HITS.18722326._013728.pool.root.1 to shared/HITS.pool.root.1
2019-08-21 11:13:03,353: *****************The last 100 lines of the pilot log******************
2019-08-21 11:13:03,363: 2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4451623648
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722326
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-21 09:12:22,557 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 70146 s
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 29489
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 29489
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 09:12:22,558 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 09:12:22,559 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4451623648 has completed
2019-08-21 09:12:22,559 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-21 09:12:22,567 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4451623648
2019-08-21 09:12:23,570 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [29489]
2019-08-21 09:12:23,570 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 29489
2019-08-21 09:12:23,570 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-21 09:12:24,571 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-21 09:12:24,571 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=29489
2019-08-21 09:12:24,621 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [29489] (in reverse order)
2019-08-21 09:12:24,662 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-21 09:12:24,662 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-21 09:12:24,662 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-21 09:12:24,662 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-21 09:12:25,172 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-21 09:12:35,217 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-21 09:12:35,218 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-21 09:12:35,262 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36281778176 B)
2019-08-21 09:12:35,263 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-21 09:12:35,263 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-21 09:12:35,286 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-21 09:12:35,286 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(job, started 140675310839552)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(create_data_payload, started 140675043538688)>, <ExcThread(validate, started 140675294054144)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(data, started 140675302446848)>, <ExcThread(monitor, started 140675051931392)>, <ExcThread(copytool_in, started 140674515060480)>, <ExcThread(copytool_out, started 140675077109504)>, <ExcThread(job_monitor, started 140674523453184)>, <ExcThread(failed_post, started 140674540238592)>, <ExcThread(validate_post, started 140675026753280)>, <ExcThread(validate_pre, started 140675060324096)>, <ExcThread(payload, started 140675068716800)>, <ExcThread(execute_payloads, started 140674506667776)>]
2019-08-21 09:12:35,339 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-21 09:12:35,347 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-21 09:12:35,347 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-21 09:12:35,347 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-21 09:12:35,353 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-21 09:12:35,354 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-21 09:12:35,394 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-21 09:12:35,394 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-21 09:12:35,696 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-21 09:12:35,696 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(data, started 140675302446848)>, <ExcThread(monitor, started 140675051931392)>, <ExcThread(copytool_out, started 140675077109504)>, <ExcThread(job_monitor, started 140674523453184)>, <ExcThread(failed_post, started 140674540238592)>, <ExcThread(validate_post, started 140675026753280)>, <ExcThread(payload, started 140675068716800)>]
2019-08-21 09:12:35,841 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-21 09:12:35,856 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-21 09:12:35,895 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-21 09:12:35,895 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-21 09:12:35,897 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-21 09:12:35,897 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(data, started 140675302446848)>, <ExcThread(copytool_out, started 140675077109504)>, <ExcThread(job_monitor, started 140674523453184)>, <ExcThread(failed_post, started 140674540238592)>, <ExcThread(validate_post, started 140675026753280)>]
2019-08-21 09:12:36,000 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-21 09:12:36,000 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-21 09:12:36,002 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-21 09:12:36,002 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(copytool_out, started 140675077109504)>, <ExcThread(job_monitor, started 140674523453184)>, <ExcThread(failed_post, started 140674540238592)>, <ExcThread(validate_post, started 140675026753280)>]
2019-08-21 09:12:36,371 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-21 09:12:36,373 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-21 09:12:36,405 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-21 09:12:36,405 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(copytool_out, started 140675077109504)>, <ExcThread(job_monitor, started 140674523453184)>]
2019-08-21 09:12:36,841 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-21 09:12:36,909 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-21 09:12:36,909 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitor, started 140674498275072)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(job_monitor, started 140674523453184)>]
2019-08-21 09:12:37,057 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-21 09:12:37,057 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-21 09:12:37,110 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-21 09:12:37,111 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(queue_monitoring, started 140674531845888)>, <ExcThread(job_monitor, started 140674523453184)>]
2019-08-21 09:12:38,340 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-21 09:12:38,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-21 09:12:38,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140675527112448)>, <ExcThread(job_monitor, started 140674523453184)>]
2019-08-21 09:13:02,799 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-21 09:13:02,800 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-21 09:13:02,888 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-21 09:13:02,889 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-21 09:13:02,889 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-21 09:13:03 UTC [wrapper] ==== pilot stdout END ====
2019-08-21 09:13:03 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-21 09:13:03 UTC [wrapper] Pilot exit status: 0
2019-08-21 09:13:03 UTC [wrapper] STATUSCODE: 0
2019-08-21 09:13:03 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 21 06:09 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

2019-08-21 09:13:03 UTC [wrapper] Test setup, not cleaning
2019-08-21 09:13:03 UTC [wrapper] ==== wrapper stdout END ====
2019-08-21 09:13:03 UTC [wrapper] ==== wrapper stderr END ====
2019-08-21 09:13:03 UTC [wrapper] wrapper wrapperexiting ec=0, duration=18233
2019-08-21 09:13:03 UTC [wrapper] apfmon messages muted
2019-08-21 11:13:03,367: ***************diag file************
2019-08-21 11:13:03,368: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=18232.28s
KernelTime=503.96s
UserTime=69853.14s
CPUUsage=385%
MaxResidentMemory=1944564kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=511498
MinorPageFaults=20640065
Swaps=0
ForcedSwitches=8135676
WaitSwitches=10766646
Inputs=123061664
Outputs=1037744
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-21 11:13:03,379: ******************************WorkDir***********************
2019-08-21 11:13:03,379: total 286416
drwxrwx--x. 6 grid grid      4096 Aug 21 11:13 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7474631 Aug 21 06:09 agis_ddmendpoints.json
-rw-------. 1 grid grid   4339667 Aug 21 06:09 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 21 06:09 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 21 06:09 APPS
-rw-------. 1 grid grid       538 Aug 21 06:09 .asetup
-rw-------. 1 grid grid       826 Aug 21 06:10 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 21 06:09 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 21 11:12 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 21 11:05 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 279053531 Aug 21 06:09 EVNT.18605758._000431.pool.root.1
-rw-------. 1 grid grid     63295 Aug 21 11:12 heartbeat.json
-rw-------. 1 grid grid       520 Aug 21 11:13 IA0LDmfNZJvnShfckohDCDFpABFKDmABFKDm8liLDmABFKDmFJ8Csm.diag
-rw-rw-r--. 1 grid grid      5866 Aug 21 06:09 init_data.xml
-rw-rw-r--. 1 grid grid    261618 Aug 21 06:09 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 21 06:09 job.xml
-rw-------. 1 grid grid    827962 Aug 21 11:13 log.18722326._013728.job.log.1
-rw-------. 1 grid grid    847741 Aug 21 11:12 log.18722326._013728.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 21 11:13 output.list
-rw-------. 1 grid grid      2914 Aug 18 14:22 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 18 13:45 pilot2.tar.gz
-rw-------. 1 grid grid     10290 Aug 21 11:13 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 18 14:22 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 21 06:09 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 21 06:09 run_atlas
-rwx------. 1 grid grid     12641 Aug 18 14:22 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 21 11:13 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 21 11:13 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 21 11:13 shared
-rw-rw-r--. 1 grid grid      8688 Aug 21 06:09 start_atlas.sh
-rw-rw-r--. 1 grid grid     18899 Aug 21 11:13 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 21 06:09 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 21 11:12 wrapper_checkpoint.txt

2019-08-21 11:13:03,379: running start_atlas return value is 0
2019-08-21 11:13:03,379: Parent exit 0
2019-08-21 11:13:03,382: child process exit 0
11:13:04 (22689): run_atlas exited; CPU time 69853.566131
11:13:04 (22689): called boinc_finish(0)

</stderr_txt>
]]>

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