Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
18:35:42 (2212884): wrapper (7.7.26015): starting
18:35:42 (2212884): wrapper: running run_atlas (--nthreads 4)
2019-09-30 18:35:42,996: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-30 18:35:42,996: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-30 18:35:42,997: THREADS=4

2019-09-30 18:35:42,997: Checking for CVMFS
2019-09-30 18:35:43,665: CVMFS is installed
2019-09-30 18:35:43,665: Checking Singularity...
2019-09-30 18:35:43,680: Singularity is installed, version singularity version 3.4.0-1.2.el7
2019-09-30 18:35:43,680: Testing the function of Singularity...
2019-09-30 18:35:43,680: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-30 18:35:43,757: Singularity Works...
2019-09-30 18:35:43,757: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-09-30 18:35:44,367: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-09-30 18:35:44,367: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-09-30 18:35:44,368: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-09-30 18:35:44,368: export ATHENA_PROC_NUMBER=4;
2019-09-30 18:35:44,381: start atlas job with PandaID=4484649192
2019-09-30 18:35:44,381: 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 00:04:44,705: running cmd return value is 0
2019-10-01 00:04:44,705: Moving ./HITS.19056259._004297.pool.root.1 to shared/HITS.pool.root.1
2019-10-01 00:04:44,705: HITS result file:
2019-10-01 00:04:44,710: -rw-------. 1 dcameron zp 249260946 Oct  1 00:02 shared/HITS.pool.root.1
2019-10-01 00:04:44,710: *****************The last 100 lines of the pilot log******************
2019-10-01 00:04:44,713: 2019-09-30 22:04:35,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-30 22:04:35,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-30 22:04:35,345 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4484649192 has completed
2019-09-30 22:04:35,345 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-30 22:04:35,349 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4484649192
2019-09-30 22:04:36,351 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2219846]
2019-09-30 22:04:36,351 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2219846
2019-09-30 22:04:36,351 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-30 22:04:37,354 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-30 22:04:37,354 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2219846
2019-09-30 22:04:37,424 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2219846] (in reverse order)
2019-09-30 22:04:37,459 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-30 22:04:37,459 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-30 22:04:37,459 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-30 22:04:37,459 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-30 22:04:37,461 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 22:04:37,462 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-30 22:04:37,462 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 22:04:37,462 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-30 22:04:37,462 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-30 22:04:37,526 | 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
2019-09-30 22:04:37,526 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 22:04:38,029 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-09-30 22:04:38,045 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (70011322368 B)
2019-09-30 22:04:38,046 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-30 22:04:38,046 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-30 22:04:38,129 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-30 22:04:38,129 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-30 22:04:38,257 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-30 22:04:38,341 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-30 22:04:38,379 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-30 22:04:38,379 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job, started 140353167398656)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(create_data_payload, started 140353055209216)>, <ExcThread(validate_post, started 140352535123712)>, <ExcThread(payload, started 140353063601920)>, <ExcThread(monitor, started 140352551909120)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitor, started 140352015038208)>, <ExcThread(execute_payloads, started 140352501552896)>, <ExcThread(queue_monitoring, started 140353046816512)>, <ExcThread(copytool_in, started 140352526731008)>, <ExcThread(validate_pre, started 140353038423808)>]
2019-09-30 22:04:38,463 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-30 22:04:38,539 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-30 22:04:38,539 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-30 22:04:38,549 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-30 22:04:38,552 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-30 22:04:38,655 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-30 22:04:38,703 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-30 22:04:38,707 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-09-30 22:04:38,707 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(create_data_payload, started 140353055209216)>, <ExcThread(payload, started 140353063601920)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitor, started 140352015038208)>, <ExcThread(queue_monitoring, started 140353046816512)>, <ExcThread(copytool_in, started 140352526731008)>]
2019-09-30 22:04:38,778 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-30 22:04:38,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-09-30 22:04:38,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(payload, started 140353063601920)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitor, started 140352015038208)>, <ExcThread(queue_monitoring, started 140353046816512)>, <ExcThread(copytool_in, started 140352526731008)>]
2019-09-30 22:04:39,072 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-30 22:04:39,072 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-30 22:04:39,072 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-30 22:04:39,072 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitor, started 140352015038208)>, <ExcThread(queue_monitoring, started 140353046816512)>, <ExcThread(copytool_in, started 140352526731008)>]
2019-09-30 22:04:39,143 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-30 22:04:39,173 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-30 22:04:39,173 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitor, started 140352015038208)>, <ExcThread(queue_monitoring, started 140353046816512)>]
2019-09-30 22:04:39,312 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-30 22:04:39,312 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-30 22:04:39,329 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-30 22:04:39,374 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-09-30 22:04:39,374 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(copytool_out, started 140353071994624)>, <ExcThread(queue_monitoring, started 140353046816512)>]
2019-09-30 22:04:39,464 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-30 22:04:39,475 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-30 22:04:39,475 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>, <ExcThread(queue_monitoring, started 140353046816512)>]
2019-09-30 22:04:42,329 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-30 22:04:42,393 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-30 22:04:42,393 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140353383671552)>, <ExcThread(job_monitor, started 140352518338304)>]
2019-09-30 22:04:43,949 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-09-30 22:04:43,949 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-30 22:04:44,002 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-30 22:04:44,002 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-30 22:04:44,002 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-30 22:04:44 UTC [wrapper] ==== pilot stdout END ====
2019-09-30 22:04:44 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-30 22:04:44 UTC [wrapper] Pilot exit status: 0
2019-09-30 22:04:44 UTC [wrapper] STATUSCODE: 0
2019-09-30 22:04:44 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 Sep 30 18:35 pandaIDs.out
drwx------. 14 dcameron zp   216 Sep 30 18:35 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

2019-09-30 22:04:44 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 dcameron zp 11 Sep 30 18:35 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
2019-09-30 22:04:44 UTC [wrapper] pandaIDs.out content:
4484649192

2019-09-30 22:04:44 UTC [wrapper] Test setup, not cleaning
2019-09-30 22:04:44 UTC [wrapper] ==== wrapper stdout END ====
2019-09-30 22:04:44 UTC [wrapper] ==== wrapper stderr END ====
2019-09-30 22:04:44 UTC [wrapper] wrapper wrapperexiting ec=0, duration=19740
2019-09-30 22:04:44 UTC [wrapper] apfmon messages muted
2019-10-01 00:04:44,715: ***************diag file************
2019-10-01 00:04:44,715: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=19740.16s
KernelTime=642.36s
UserTime=77003.05s
CPUUsage=393%
MaxResidentMemory=1945276kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=657743
MinorPageFaults=23256618
Swaps=0
ForcedSwitches=4227030
WaitSwitches=13067682
Inputs=152354256
Outputs=1052224
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-10-01 00:04:44,719: ******************************WorkDir***********************
2019-10-01 00:04:44,719: total 281692
drwxrwx--x. 7 dcameron zp      4096 Oct  1 00:04 .
drwxrwx--x. 4 dcameron zp        24 Sep 26 17:13 ..
-rw-------. 1 dcameron zp       517 Oct  1 00:04 6MHNDm8YrVvnShfckohDCDFpABFKDmABFKDmeorNDmABFKDmZGJGXn.diag
-rw-------. 1 dcameron zp   7579780 Sep 30 18:35 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   3948330 Sep 30 18:35 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Sep 30 18:35 .alrb
drwxr-xr-x. 3 dcameron zp        17 Sep 30 18:35 APPS
-rw-------. 1 dcameron zp       548 Sep 30 18:35 .asetup
-rw-------. 1 dcameron zp       826 Sep 30 18:36 .asetup.save
drwx------. 2 dcameron zp         6 Sep 30 18:36 .asetup-sysbin_2217061
-rw-r--r--. 1 dcameron zp         0 Sep 30 18:35 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Oct  1 00:04 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       537 Sep 30 23:56 boinc_task_state.xml
-rw-r--r--. 1 dcameron zp 274260279 Sep 30 18:35 EVNT.18605762._000086.pool.root.1
-rw-------. 1 dcameron zp     80279 Oct  1 00:04 heartbeat.json
-rw-r--r--. 1 dcameron zp      6290 Sep 30 18:35 init_data.xml
-rw-r--r--. 1 dcameron zp    267509 Sep 30 18:35 input.tar.gz
-rw-r--r--. 1 dcameron zp       112 Sep 30 18:35 job.xml
-rw-------. 1 dcameron zp   1037453 Oct  1 00:04 log.19056259._004297.job.log.1
-rw-------. 1 dcameron zp    841255 Oct  1 00:04 log.19056259._004297.job.log.tgz.1
-rw-------. 1 dcameron zp       463 Oct  1 00:04 output.list
-rw-------. 1 dcameron zp      2842 Sep 21 12:13 pandaJobData.out
drwx------. 3 dcameron zp       229 Sep 30 18:35 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 21 11:37 pilot2.tar.gz
-rw-------. 1 dcameron zp     10907 Oct  1 00:04 pilotlog.txt
-rw-r--r--. 1 dcameron zp      4480 Sep 21 12:10 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Sep 30 18:35 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      7941 Sep 30 18:35 run_atlas
-rwx------. 1 dcameron zp     12762 Sep 21 12:13 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       692 Oct  1 00:04 runtime_log
-rw-r--r--. 1 dcameron zp      8044 Oct  1 00:04 runtime_log.err
-rw-------. 1 dcameron zp       240 Sep 30 18:35 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Oct  1 00:04 shared
-rw-r--r--. 1 dcameron zp      8688 Sep 30 18:35 start_atlas.sh
-rw-r--r--. 1 dcameron zp     17306 Oct  1 00:04 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Sep 30 18:35 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        28 Oct  1 00:04 wrapper_checkpoint.txt

2019-10-01 00:04:44,719: running start_atlas return value is 0
2019-10-01 00:04:44,719: Parent exit 0
2019-10-01 00:04:44,719: child process exit 0
00:04:45 (2212884): run_atlas exited; CPU time 77003.390716
00:04:45 (2212884): called boinc_finish(0)

</stderr_txt>
]]>

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