Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
13:07:37 (2082092): wrapper (7.7.26015): starting
13:07:37 (2082092): wrapper: running run_atlas (--nthreads 4)
2019-09-30 13:07:37,614: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-30 13:07:37,614: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-30 13:07:37,615: THREADS=4

2019-09-30 13:07:37,616: Checking for CVMFS
2019-09-30 13:07:38,284: CVMFS is installed
2019-09-30 13:07:38,284: Checking Singularity...
2019-09-30 13:07:38,298: Singularity is installed, version singularity version 3.4.0-1.2.el7
2019-09-30 13:07:38,299: Testing the function of Singularity...
2019-09-30 13:07:38,299: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-30 13:07:38,370: Singularity Works...
2019-09-30 13:07:38,370: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-09-30 13:07:38,945: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-09-30 13:07:38,945: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-09-30 13:07:38,946: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-09-30 13:07:38,946: export ATHENA_PROC_NUMBER=4;
2019-09-30 13:07:38,960: start atlas job with PandaID=4484522578
2019-09-30 13:07:38,960: 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
2019-09-30 18:35:38,381: running cmd return value is 0
2019-09-30 18:35:38,381: Moving ./HITS.19000468._014779.pool.root.1 to shared/HITS.pool.root.1
2019-09-30 18:35:38,381: HITS result file:
2019-09-30 18:35:38,387: -rw-------. 1 dcameron zp 242903062 Sep 30 18:33 shared/HITS.pool.root.1
2019-09-30 18:35:38,387: *****************The last 100 lines of the pilot log******************
2019-09-30 18:35:38,389: 2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4484522578 has completed
2019-09-30 16:35:25,150 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-30 16:35:25,154 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4484522578
2019-09-30 16:35:26,158 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2088887]
2019-09-30 16:35:26,159 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2088887
2019-09-30 16:35:26,159 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-30 16:35:27,160 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-30 16:35:27,160 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2088887
2019-09-30 16:35:27,227 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2088887] (in reverse order)
2019-09-30 16:35:27,263 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-30 16:35:27,263 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-30 16:35:27,263 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-30 16:35:27,263 | 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 16:35:27,266 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 16:35:27,266 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-30 16:35:27,266 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 16:35:27,266 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-30 16:35:27,266 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-30 16:35:27,329 | 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 16:35:27,330 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 16:35:27,832 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-09-30 16:35:27,849 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (69956796416 B)
2019-09-30 16:35:27,850 | 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 16:35:27,850 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-30 16:35:27,861 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-30 16:35:27,869 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-30 16:35:27,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-09-30 16:35:27,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(job, started 140385223390976)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(validate_pre, started 140384797701888)>, <ExcThread(job_monitor, started 140384822880000)>, <ExcThread(queue_monitor, started 140384789309184)>, <ExcThread(validate_post, started 140384227292928)>, <ExcThread(copytool_in, started 140384780916480)>, <ExcThread(payload, started 140385181427456)>, <ExcThread(failed_post, started 140384218900224)>, <ExcThread(execute_payloads, started 140384210507520)>, <ExcThread(copytool_out, started 140384831272704)>, <ExcThread(create_data_payload, started 140385198212864)>, <ExcThread(data, started 140385206605568)>, <ExcThread(validate, started 140385214998272)>]
2019-09-30 16:35:28,056 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-30 16:35:28,115 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-30 16:35:28,213 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-30 16:35:28,213 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-30 16:35:28,310 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-09-30 16:35:28,310 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(job, started 140385223390976)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(validate_pre, started 140384797701888)>, <ExcThread(job_monitor, started 140384822880000)>, <ExcThread(queue_monitor, started 140384789309184)>, <ExcThread(copytool_in, started 140384780916480)>, <ExcThread(payload, started 140385181427456)>, <ExcThread(failed_post, started 140384218900224)>, <ExcThread(copytool_out, started 140384831272704)>, <ExcThread(create_data_payload, started 140385198212864)>, <ExcThread(validate, started 140385214998272)>]
2019-09-30 16:35:28,361 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-30 16:35:28,362 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-30 16:35:28,464 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-30 16:35:28,477 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-30 16:35:28,511 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-09-30 16:35:28,511 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(job_monitor, started 140384822880000)>, <ExcThread(queue_monitor, started 140384789309184)>, <ExcThread(payload, started 140385181427456)>, <ExcThread(failed_post, started 140384218900224)>, <ExcThread(copytool_out, started 140384831272704)>, <ExcThread(create_data_payload, started 140385198212864)>, <ExcThread(validate, started 140385214998272)>]
2019-09-30 16:35:28,555 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-30 16:35:28,645 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-30 16:35:28,690 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-30 16:35:28,690 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-30 16:35:28,712 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-30 16:35:28,712 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(job_monitor, started 140384822880000)>, <ExcThread(queue_monitor, started 140384789309184)>, <ExcThread(copytool_out, started 140384831272704)>, <ExcThread(create_data_payload, started 140385198212864)>]
2019-09-30 16:35:28,869 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-30 16:35:28,913 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-30 16:35:28,913 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(job_monitor, started 140384822880000)>, <ExcThread(queue_monitor, started 140384789309184)>, <ExcThread(create_data_payload, started 140385198212864)>]
2019-09-30 16:35:29,036 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-30 16:35:29,105 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-30 16:35:29,106 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-30 16:35:29,114 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-30 16:35:29,115 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(queue_monitoring, started 140384806094592)>, <ExcThread(job_monitor, started 140384822880000)>]
2019-09-30 16:35:30,719 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-30 16:35:33,720 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-30 16:35:33,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-30 16:35:33,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140385439663872)>, <ExcThread(job_monitor, started 140384822880000)>]
2019-09-30 16:35:38,065 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-09-30 16:35:38,066 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-30 16:35:38,164 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-30 16:35:38,164 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-30 16:35:38,164 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-30 16:35:38 UTC [wrapper] ==== pilot stdout END ====
2019-09-30 16:35:38 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-30 16:35:38 UTC [wrapper] Pilot exit status: 0
2019-09-30 16:35:38 UTC [wrapper] STATUSCODE: 0
2019-09-30 16:35:38 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 13:07 pandaIDs.out
drwx------. 14 dcameron zp   216 Sep 30 13:07 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 16:35:38 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 dcameron zp 11 Sep 30 13:07 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
2019-09-30 16:35:38 UTC [wrapper] pandaIDs.out content:
4484522578

2019-09-30 16:35:38 UTC [wrapper] Test setup, not cleaning
2019-09-30 16:35:38 UTC [wrapper] ==== wrapper stdout END ====
2019-09-30 16:35:38 UTC [wrapper] ==== wrapper stderr END ====
2019-09-30 16:35:38 UTC [wrapper] wrapper wrapperexiting ec=0, duration=19679
2019-09-30 16:35:38 UTC [wrapper] apfmon messages muted
2019-09-30 18:35:38,392: ***************diag file************
2019-09-30 18:35:38,392: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=19679.25s
KernelTime=640.61s
UserTime=77108.42s
CPUUsage=395%
MaxResidentMemory=1945420kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=659217
MinorPageFaults=23295310
Swaps=0
ForcedSwitches=4300436
WaitSwitches=12987289
Inputs=153297888
Outputs=1027312
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-09-30 18:35:38,395: ******************************WorkDir***********************
2019-09-30 18:35:38,395: total 281480
drwxrwx--x. 7 dcameron zp      4096 Sep 30 18:35 .
drwxrwx--x. 4 dcameron zp        24 Sep 26 17:13 ..
-rw-------. 1 dcameron zp       517 Sep 30 18:35 82IKDmsbOVvnShfckohDCDFpABFKDmABFKDmVx8MDmABFKDmuzM6Ln.diag
-rw-------. 1 dcameron zp   7579780 Sep 30 13:07 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   3948725 Sep 30 13:07 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Sep 30 13:07 .alrb
drwxr-xr-x. 3 dcameron zp        17 Sep 30 13:07 APPS
-rw-------. 1 dcameron zp       548 Sep 30 13:07 .asetup
-rw-------. 1 dcameron zp       826 Sep 30 13:08 .asetup.save
drwx------. 2 dcameron zp         6 Sep 30 13:08 .asetup-sysbin_2086098
-rw-r--r--. 1 dcameron zp         0 Sep 30 13:07 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Sep 30 18:35 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       537 Sep 30 18:29 boinc_task_state.xml
-rw-r--r--. 1 dcameron zp 274049036 Sep 30 13:07 EVNT.18605543._000281.pool.root.1
-rw-------. 1 dcameron zp     77557 Sep 30 18:35 heartbeat.json
-rw-r--r--. 1 dcameron zp      6290 Sep 30 13:07 init_data.xml
-rw-r--r--. 1 dcameron zp    267507 Sep 30 13:07 input.tar.gz
-rw-r--r--. 1 dcameron zp       112 Sep 30 13:07 job.xml
-rw-------. 1 dcameron zp   1033068 Sep 30 18:35 log.19000468._014779.job.log.1
-rw-------. 1 dcameron zp    840918 Sep 30 18:35 log.19000468._014779.job.log.tgz.1
-rw-------. 1 dcameron zp       463 Sep 30 18:35 output.list
-rw-------. 1 dcameron zp      2843 Sep 20 05:17 pandaJobData.out
drwx------. 3 dcameron zp       229 Sep 30 13:07 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 20 04:25 pilot2.tar.gz
-rw-------. 1 dcameron zp     10823 Sep 30 18:35 pilotlog.txt
-rw-r--r--. 1 dcameron zp      4480 Sep 20 05:15 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Sep 30 13:07 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      7941 Sep 30 13:07 run_atlas
-rwx------. 1 dcameron zp     12762 Sep 20 05:17 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       692 Sep 30 18:35 runtime_log
-rw-r--r--. 1 dcameron zp      8044 Sep 30 18:35 runtime_log.err
-rw-------. 1 dcameron zp       240 Sep 30 13:07 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Sep 30 18:35 shared
-rw-r--r--. 1 dcameron zp      8688 Sep 30 13:07 start_atlas.sh
-rw-r--r--. 1 dcameron zp     17500 Sep 30 18:35 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Sep 30 13:07 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        28 Sep 30 18:35 wrapper_checkpoint.txt

2019-09-30 18:35:38,396: running start_atlas return value is 0
2019-09-30 18:35:38,396: Parent exit 0
2019-09-30 18:35:38,396: child process exit 0
18:35:39 (2082092): run_atlas exited; CPU time 77108.728865
18:35:39 (2082092): called boinc_finish(0)

</stderr_txt>
]]>

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