Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
00:04:48 (2344011): wrapper (7.7.26015): starting
00:04:48 (2344011): wrapper: running run_atlas (--nthreads 4)
2019-10-01 00:04:48,790: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-10-01 00:04:48,790: sys.argv = ['run_atlas', '--nthreads', '4']
2019-10-01 00:04:48,791: THREADS=4

2019-10-01 00:04:48,792: Checking for CVMFS
2019-10-01 00:04:49,448: CVMFS is installed
2019-10-01 00:04:49,448: Checking Singularity...
2019-10-01 00:04:49,473: Singularity is installed, version singularity version 3.4.0-1.2.el7
2019-10-01 00:04:49,473: Testing the function of Singularity...
2019-10-01 00:04:49,473: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-10-01 00:04:49,559: Singularity Works...
2019-10-01 00:04:49,559: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-10-01 00:04:50,126: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-10-01 00:04:50,126: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-10-01 00:04:50,126: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-10-01 00:04:50,127: export ATHENA_PROC_NUMBER=4;
2019-10-01 00:04:50,140: start atlas job with PandaID=4492440397
2019-10-01 00:04:50,140: cmd = singularity exec --pwd /home/dcameron/boinc/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
2019-10-01 07:22:21,140: running cmd return value is 0
2019-10-01 07:22:21,141: Moving ./HITS.19000509._020357.pool.root.1 to shared/HITS.pool.root.1
2019-10-01 07:22:21,141: HITS result file:
2019-10-01 07:22:21,146: -rw-------. 1 dcameron zp 250021367 Oct  1 07:19 shared/HITS.pool.root.1
2019-10-01 07:22:21,146: *****************The last 100 lines of the pilot log******************
2019-10-01 07:22:21,148: 2019-10-01 05:21:17,700 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4492440397
2019-10-01 05:21:18,706 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2350789]
2019-10-01 05:21:18,706 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2350789
2019-10-01 05:21:18,706 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-10-01 05:21:19,711 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-10-01 05:21:19,711 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2350789
2019-10-01 05:21:19,778 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2350789] (in reverse order)
2019-10-01 05:21:19,813 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-10-01 05:21:19,813 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-10-01 05:21:19,813 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-10-01 05:21:19,813 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-10-01 05:21:19,816 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-10-01 05:21:19,816 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-10-01 05:21:19,816 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-10-01 05:21:19,816 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-10-01 05:21:19,816 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-10-01 05:21:19,881 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | 
LSB Version:	:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch
Distributor ID:	ScientificCERNSLC
Description:	Scientific Linux CERN SLC release 6.10 (Carbon)
Release:	6.10
Codename:	Carbon
2019-10-01 05:21:19,881 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-10-01 05:21:20,263 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-10-01 05:21:20,384 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-10-01 05:21:20,400 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (70104645632 B)
2019-10-01 05:21:20,400 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-10-01 05:21:20,401 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-10-01 05:21:20,423 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-10-01 05:21:20,678 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-10-01 05:21:20,678 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(job, started 139855419492096)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(queue_monitor, started 139855157761792)>, <ExcThread(copytool_out, started 139855333943040)>, <ExcThread(create_data_payload, started 139855317157632)>, <ExcThread(data, started 139855199725312)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(validate, started 139855342335744)>, <ExcThread(copytool_in, started 139855191332608)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(monitor, started 139855300372224)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(validate_pre, started 139855291979520)>, <ExcThread(job_monitor, started 139855174547200)>, <ExcThread(payload, started 139855325550336)>]
2019-10-01 05:21:20,689 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-10-01 05:21:20,689 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-10-01 05:21:20,719 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-10-01 05:21:20,720 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-10-01 05:21:20,766 | WARNING  | job_monitor         | pilot.util.common                | should_abort              | job:job_monitor:received graceful stop - abort after this iteration
2019-10-01 05:21:20,979 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-10-01 05:21:20,980 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(queue_monitor, started 139855157761792)>, <ExcThread(copytool_out, started 139855333943040)>, <ExcThread(create_data_payload, started 139855317157632)>, <ExcThread(data, started 139855199725312)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(validate, started 139855342335744)>, <ExcThread(copytool_in, started 139855191332608)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(monitor, started 139855300372224)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(validate_pre, started 139855291979520)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,020 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-10-01 05:21:21,149 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-10-01 05:21:21,154 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-10-01 05:21:21,160 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-10-01 05:21:21,258 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-10-01 05:21:21,258 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-10-01 05:21:21,281 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-10-01 05:21:21,281 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(queue_monitor, started 139855157761792)>, <ExcThread(copytool_out, started 139855333943040)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(monitor, started 139855300372224)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,300 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-10-01 05:21:21,381 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-10-01 05:21:21,382 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(queue_monitor, started 139855157761792)>, <ExcThread(copytool_out, started 139855333943040)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,423 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-10-01 05:21:21,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-10-01 05:21:21,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(queue_monitor, started 139855157761792)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,601 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-10-01 05:21:21,601 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-10-01 05:21:21,683 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-10-01 05:21:21,683 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(execute_payloads, started 139854268593920)>, <ExcThread(failed_post, started 139855166154496)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,789 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-10-01 05:21:21,864 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-10-01 05:21:21,884 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-10-01 05:21:21,884 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(validate_post, started 139855182939904)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:21,902 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-10-01 05:21:21,984 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-10-01 05:21:21,984 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(queue_monitoring, started 139855308764928)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:21:23,035 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-10-01 05:21:26,036 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-10-01 05:21:26,107 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-10-01 05:21:26,107 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139855635764992)>, <ExcThread(job_monitor, started 139855174547200)>]
2019-10-01 05:22:20,858 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 122 s)
2019-10-01 05:22:20,858 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-10-01 05:22:20,905 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-10-01 05:22:20,905 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-10-01 05:22:20,905 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-10-01 05:22:21 UTC [wrapper] ==== pilot stdout END ====
2019-10-01 05:22:21 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-10-01 05:22:21 UTC [wrapper] Pilot exit status: 0
2019-10-01 05:22:21 UTC [wrapper] STATUSCODE: 0
2019-10-01 05:22:21 UTC [wrapper] apfmon messages muted
---- find pandaIDs.out ----
total 56
-rw-------.  1 dcameron zp 11357 Jul 25 16:38 LICENSE
-rw-------.  1 dcameron zp    20 Sep  9 13:04 MANIFEST.IN
-rw-------.  1 dcameron zp    11 Oct  1 00:05 pandaIDs.out
drwx------. 14 dcameron zp   216 Oct  1 00:04 pilot
-rwx------.  1 dcameron zp 20136 Sep  9 13:04 pilot.py
-rw-------.  1 dcameron zp     9 Sep  9 13:04 PILOTVERSION
-rw-------.  1 dcameron zp  2251 Jul 25 16:38 README.md
-rw-------.  1 dcameron zp   760 Aug 22 11:01 setup.py
-rw-------.  1 dcameron zp   221 Jul 25 16:38 TODO.md

2019-10-01 05:22:21 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 dcameron zp 11 Oct  1 00:05 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
2019-10-01 05:22:21 UTC [wrapper] pandaIDs.out content:
4492440397

2019-10-01 05:22:21 UTC [wrapper] Test setup, not cleaning
2019-10-01 05:22:21 UTC [wrapper] ==== wrapper stdout END ====
2019-10-01 05:22:21 UTC [wrapper] ==== wrapper stderr END ====
2019-10-01 05:22:21 UTC [wrapper] wrapper wrapperexiting ec=0, duration=26251
2019-10-01 05:22:21 UTC [wrapper] apfmon messages muted
2019-10-01 07:22:21,151: ***************diag file************
2019-10-01 07:22:21,151: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=26250.82s
KernelTime=848.30s
UserTime=102161.17s
CPUUsage=392%
MaxResidentMemory=1945300kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=822910
MinorPageFaults=27673514
Swaps=0
ForcedSwitches=6032771
WaitSwitches=16286517
Inputs=190455536
Outputs=1061688
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-10-01 07:22:21,155: ******************************WorkDir***********************
2019-10-01 07:22:21,155: total 253468
drwxrwx--x. 7 dcameron zp      4096 Oct  1 07:22 .
drwxrwx--x. 4 dcameron zp        24 Sep 26 17:13 ..
-rw-------. 1 dcameron zp   7579848 Oct  1 00:04 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   3948515 Oct  1 00:04 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Oct  1 00:04 .alrb
drwxr-xr-x. 3 dcameron zp        17 Oct  1 00:04 APPS
-rw-------. 1 dcameron zp       548 Oct  1 00:04 .asetup
-rw-------. 1 dcameron zp       826 Oct  1 00:05 .asetup.save
drwx------. 2 dcameron zp         6 Oct  1 00:05 .asetup-sysbin_2348004
-rw-r--r--. 1 dcameron zp         0 Oct  1 00:04 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Oct  1 07:21 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       538 Oct  1 07:11 boinc_task_state.xml
-rw-r--r--. 1 dcameron zp 245085724 Oct  1 00:04 EVNT.18605557._000379.pool.root.1
-rw-------. 1 dcameron zp     72349 Oct  1 07:21 heartbeat.json
-rw-r--r--. 1 dcameron zp      6290 Oct  1 00:04 init_data.xml
-rw-r--r--. 1 dcameron zp    267514 Oct  1 00:04 input.tar.gz
-rw-r--r--. 1 dcameron zp       112 Oct  1 00:04 job.xml
-rw-------. 1 dcameron zp       518 Oct  1 07:22 KN5LDmbsBYvnShfckohDCDFpABFKDmABFKDmcvZRDmABFKDmVRNrfm.diag
-rw-------. 1 dcameron zp   1303481 Oct  1 07:22 log.19000509._020357.job.log.1
-rw-------. 1 dcameron zp    853822 Oct  1 07:21 log.19000509._020357.job.log.tgz.1
-rw-------. 1 dcameron zp       463 Oct  1 07:22 output.list
-rw-------. 1 dcameron zp      2863 Sep 27 22:18 pandaJobData.out
drwx------. 3 dcameron zp       229 Oct  1 00:05 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 27 21:34 pilot2.tar.gz
-rw-------. 1 dcameron zp     12659 Oct  1 07:22 pilotlog.txt
-rw-r--r--. 1 dcameron zp      4480 Sep 27 22:15 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Oct  1 00:04 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      7941 Oct  1 00:04 run_atlas
-rwx------. 1 dcameron zp     12762 Sep 27 22:18 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       692 Oct  1 07:22 runtime_log
-rw-r--r--. 1 dcameron zp      8044 Oct  1 07:22 runtime_log.err
-rw-------. 1 dcameron zp       240 Oct  1 00:04 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Oct  1 07:22 shared
-rw-r--r--. 1 dcameron zp      8688 Oct  1 00:04 start_atlas.sh
-rw-r--r--. 1 dcameron zp     18455 Oct  1 07:22 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Oct  1 00:04 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        29 Oct  1 07:21 wrapper_checkpoint.txt

2019-10-01 07:22:21,155: running start_atlas return value is 0
2019-10-01 07:22:21,155: Parent exit 0
2019-10-01 07:22:21,155: child process exit 0
07:22:21 (2344011): run_atlas exited; CPU time 102161.500877
07:22:21 (2344011): called boinc_finish(0)

</stderr_txt>
]]>

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