Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
15:43:10 (12141): wrapper (7.7.26015): starting
15:43:10 (12141): wrapper: running run_atlas (--nthreads 4)
2019-08-19 15:43:10,982: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-19 15:43:10,982: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-19 15:43:10,983: THREADS=4

2019-08-19 15:43:10,985: Checking for CVMFS
2019-08-19 15:43:12,340: CVMFS is installed
2019-08-19 15:43:12,344: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-19 15:43:12,345: This is not SLC6, need to run with Singularity....
2019-08-19 15:43:12,345: Checking Singularity...
2019-08-19 15:43:12,348: Singularity is not installed, using version from CVMFS
2019-08-19 15:43:12,348: Testing the function of Singularity...
2019-08-19 15:43:12,348: 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
2019-08-19 15:43:12,564: Singularity Works...
2019-08-19 15:43:12,564: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-19 15:43:13,307: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-19 15:43:13,308: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-19 15:43:13,308: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-19 15:43:13,308: export ATHENA_PROC_NUMBER=4;
2019-08-19 15:43:13,328: start atlas job with PandaID=4454359095
2019-08-19 15:43:13,328: 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
2019-08-19 17:19:28,319: running cmd return value is 0
2019-08-19 17:19:28,322: Moving ./HITS.18605019._052854.pool.root.1 to shared/HITS.pool.root.1
2019-08-19 17:19:28,323: *****************The last 100 lines of the pilot log******************
2019-08-19 17:19:28,334: 2019-08-19 15:18:37,318 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18605019
2019-08-19 15:18:37,318 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-19 15:18:37,318 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-19 15:18:37,318 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 20634 s
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 18833
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 18833
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-19 15:18:37,319 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4454359095 has completed
2019-08-19 15:18:37,320 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-19 15:18:37,327 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4454359095
2019-08-19 15:18:38,331 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [18833]
2019-08-19 15:18:38,332 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 18833
2019-08-19 15:18:38,332 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-19 15:18:39,335 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-19 15:18:39,336 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=18833
2019-08-19 15:18:39,381 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [18833] (in reverse order)
2019-08-19 15:18:39,422 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-19 15:18:39,422 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-19 15:18:39,422 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-19 15:18:39,422 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-19 15:18:39,932 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-19 15:18:49,982 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-19 15:18:49,983 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-19 15:18:50,016 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34900803584 B)
2019-08-19 15:18:50,016 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-19 15:18:50,016 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-19 15:18:50,044 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-19 15:18:50,044 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-19 15:18:50,069 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-19 15:18:50,373 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-19 15:18:50,374 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job, started 140125717653248)>, <ExcThread(payload, started 140125692475136)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(validate, started 140125709260544)>, <ExcThread(copytool_in, started 140125145114368)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(validate_pre, started 140125187077888)>, <ExcThread(execute_payloads, started 140124641814272)>, <ExcThread(monitor, started 140125667297024)>, <ExcThread(copytool_out, started 140125684082432)>, <ExcThread(create_data_payload, started 140125675689728)>]
2019-08-19 15:18:50,468 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-19 15:18:50,608 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-19 15:18:50,775 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-19 15:18:50,776 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job, started 140125717653248)>, <ExcThread(payload, started 140125692475136)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(validate, started 140125709260544)>, <ExcThread(copytool_in, started 140125145114368)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(validate_pre, started 140125187077888)>, <ExcThread(monitor, started 140125667297024)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:50,781 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-19 15:18:50,966 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-19 15:18:50,966 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-19 15:18:50,977 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-19 15:18:50,977 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job, started 140125717653248)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(validate, started 140125709260544)>, <ExcThread(copytool_in, started 140125145114368)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(validate_pre, started 140125187077888)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:50,987 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-19 15:18:50,987 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-19 15:18:51,016 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-19 15:18:51,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-19 15:18:51,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(validate, started 140125709260544)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(validate_pre, started 140125187077888)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:51,203 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-19 15:18:51,280 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-19 15:18:51,280 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(validate, started 140125709260544)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:51,345 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-19 15:18:51,397 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-19 15:18:51,422 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-19 15:18:51,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-19 15:18:51,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(validate_post, started 140125161899776)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(queue_monitor, started 140125136721664)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:51,572 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-19 15:18:51,581 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-19 15:18:51,581 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-19 15:18:51,582 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-19 15:18:51,583 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(queue_monitoring, started 140125170292480)>, <ExcThread(copytool_out, started 140125684082432)>]
2019-08-19 15:18:52,397 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-19 15:18:52,489 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-19 15:18:52,489 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job_monitor, started 140125153507072)>, <ExcThread(queue_monitoring, started 140125170292480)>]
2019-08-19 15:18:54,346 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-19 15:18:54,402 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-19 15:18:54,403 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140125933926144)>, <ExcThread(job_monitor, started 140125153507072)>]
2019-08-19 15:19:27,762 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-19 15:19:27,762 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-19 15:19:27,820 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-19 15:19:27,820 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-19 15:19:27,821 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-19 15:19:28 UTC [wrapper] ==== pilot stdout END ====
2019-08-19 15:19:28 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-19 15:19:28 UTC [wrapper] Pilot exit status: 0
2019-08-19 15:19:28 UTC [wrapper] STATUSCODE: 0
2019-08-19 15:19:28 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 19 15:43 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

2019-08-19 15:19:28 UTC [wrapper] Test setup, not cleaning
2019-08-19 15:19:28 UTC [wrapper] ==== wrapper stdout END ====
2019-08-19 15:19:28 UTC [wrapper] ==== wrapper stderr END ====
2019-08-19 15:19:28 UTC [wrapper] wrapper wrapperexiting ec=0, duration=5775
2019-08-19 15:19:28 UTC [wrapper] apfmon messages muted
2019-08-19 17:19:28,338: ***************diag file************
2019-08-19 17:19:28,339: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5774.56s
KernelTime=195.26s
UserTime=20546.27s
CPUUsage=359%
MaxResidentMemory=1945032kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=264013
MinorPageFaults=12501989
Swaps=0
ForcedSwitches=2413593
WaitSwitches=5223382
Inputs=64310256
Outputs=500792
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-19 17:19:28,350: ******************************WorkDir***********************
2019-08-19 17:19:28,350: total 382640
drwxrwx--x. 6 grid grid      4096 Aug 19 17:19 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7442625 Aug 19 15:43 agis_ddmendpoints.json
-rw-------. 1 grid grid   4371598 Aug 19 15:43 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 19 15:43 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 19 15:43 APPS
-rw-------. 1 grid grid       538 Aug 19 15:43 .asetup
-rw-------. 1 grid grid       826 Aug 19 15:44 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 19 15:43 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 19 17:19 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 19 17:13 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 378054856 Aug 19 15:43 EVNT.17323843._000984.pool.root.1
-rw-------. 1 grid grid     59745 Aug 19 17:18 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 19 15:43 init_data.xml
-rw-rw-r--. 1 grid grid    261623 Aug 19 15:43 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 19 15:43 job.xml
-rw-------. 1 grid grid    386224 Aug 19 17:19 log.18605019._052854.job.log.1
-rw-------. 1 grid grid    819641 Aug 19 17:18 log.18605019._052854.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug 19 17:19 mGHMDmAarJvnShfckohDCDFpABFKDmABFKDmmvCMDmABFKDmk3Ihwn.diag
-rw-------. 1 grid grid       391 Aug 19 17:19 output.list
-rw-------. 1 grid grid      2887 Aug 19 09:48 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 19 09:29 pilot2.tar.gz
-rw-------. 1 grid grid     11146 Aug 19 17:19 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 19 09:45 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 19 15:43 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 19 15:43 run_atlas
-rwx------. 1 grid grid     12641 Aug 19 09:48 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 19 17:19 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 19 17:19 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 19 17:19 shared
-rw-rw-r--. 1 grid grid      8688 Aug 19 15:43 start_atlas.sh
-rw-rw-r--. 1 grid grid     19430 Aug 19 17:19 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 19 15:43 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 19 17:19 wrapper_checkpoint.txt

2019-08-19 17:19:28,350: running start_atlas return value is 0
2019-08-19 17:19:28,350: Parent exit 0
2019-08-19 17:19:28,352: child process exit 0
17:19:29 (12141): run_atlas exited; CPU time 20546.696162
17:19:29 (12141): called boinc_finish(0)

</stderr_txt>
]]>

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