Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
12:31:56 (62204): wrapper (7.7.26015): starting
12:31:56 (62204): wrapper: running run_atlas (--nthreads 4)
2019-09-10 12:31:56,278: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-10 12:31:56,278: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-10 12:31:56,279: THREADS=4

2019-09-10 12:31:56,279: Checking for CVMFS
2019-09-10 12:31:58,224: CVMFS is installed
2019-09-10 12:31:58,227: OS:CentOS Linux release 7.6.1810 (Core) 
2019-09-10 12:31:58,227: This is not SLC6, need to run with Singularity....
2019-09-10 12:31:58,227: Checking Singularity...
2019-09-10 12:31:58,349: Singularity is installed, version singularity version 3.2.1-1.1.el7
2019-09-10 12:31:58,349: Testing the function of Singularity...
2019-09-10 12:31:58,349: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-10 12:31:59,416: Singularity Works...
2019-09-10 12:31:59,416: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-09-10 12:32:01,004: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-09-10 12:32:01,004: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-09-10 12:32:01,004: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-09-10 12:32:01,004: export ATHENA_PROC_NUMBER=4;
2019-09-10 12:32:01,260: start atlas job with PandaID=4002876565
2019-09-10 12:32:01,260: 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
2019-09-10 12:47:03,145: running cmd return value is 0
2019-09-10 12:47:03,146: Moving ./HITS.000649-2007289-20930._078090.pool.root.1 to shared/HITS.pool.root.1
2019-09-10 12:47:03,146: *****************The last 100 lines of the pilot log******************
2019-09-10 12:47:03,150: 2019-09-10 10:46:10,139 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-10 10:46:10,139 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-10 10:46:10,139 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-10 10:46:10,139 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4002876565 has completed
2019-09-10 10:46:10,139 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-10 10:46:10,142 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4002876565
2019-09-10 10:46:11,148 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [69346]
2019-09-10 10:46:11,148 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 69346
2019-09-10 10:46:11,148 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-10 10:46:12,153 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-10 10:46:12,153 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=69346
2019-09-10 10:46:12,211 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [69346] (in reverse order)
2019-09-10 10:46:12,242 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-10 10:46:12,242 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-10 10:46:12,243 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-10 10:46:12,243 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-10 10:46:12,245 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-10 10:46:12,245 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-10 10:46:12,245 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-10 10:46:12,245 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-10 10:46:12,245 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-10 10:46:12,308 | 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
2019-09-10 10:46:12,308 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-10 10:46:12,811 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-09-10 10:46:12,824 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (39811284992 B)
2019-09-10 10:46:12,825 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-10 10:46:12,825 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-10 10:46:12,827 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-10 10:46:12,827 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-10 10:46:12,836 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-10 10:46:12,838 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-09-10 10:46:12,838 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(data, started 140233519544064)>, <ExcThread(validate_post, started 140232754194176)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(create_data_payload, started 140233282672384)>, <ExcThread(failed_post, started 140232737408768)>, <ExcThread(payload, started 140233291065088)>, <ExcThread(execute_payloads, started 140232729016064)>, <ExcThread(queue_monitor, started 140232720623360)>, <ExcThread(validate_pre, started 140233257494272)>, <ExcThread(validate, started 140233511151360)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:12,842 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-10 10:46:12,923 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-10 10:46:13,139 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-09-10 10:46:13,139 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(data, started 140233519544064)>, <ExcThread(validate_post, started 140232754194176)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(failed_post, started 140232737408768)>, <ExcThread(payload, started 140233291065088)>, <ExcThread(execute_payloads, started 140232729016064)>, <ExcThread(queue_monitor, started 140232720623360)>, <ExcThread(validate, started 140233511151360)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:13,464 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-10 10:46:13,501 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-10 10:46:13,501 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-10 10:46:13,544 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-10 10:46:13,544 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-10 10:46:13,544 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-09-10 10:46:13,544 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(validate_post, started 140232754194176)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(failed_post, started 140232737408768)>, <ExcThread(execute_payloads, started 140232729016064)>, <ExcThread(queue_monitor, started 140232720623360)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:13,801 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-10 10:46:13,846 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-09-10 10:46:13,846 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(failed_post, started 140232737408768)>, <ExcThread(execute_payloads, started 140232729016064)>, <ExcThread(queue_monitor, started 140232720623360)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:13,961 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-10 10:46:13,985 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-10 10:46:14,035 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-10 10:46:14,047 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-10 10:46:14,047 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(queue_monitor, started 140232720623360)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:14,093 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-10 10:46:14,093 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-10 10:46:14,148 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-10 10:46:14,148 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(copytool_in, started 140232762586880)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:14,296 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-10 10:46:14,350 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-09-10 10:46:14,350 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>, <ExcThread(copytool_out, started 140233299457792)>]
2019-09-10 10:46:14,821 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-10 10:46:14,986 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-10 10:46:15,054 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-10 10:46:15,054 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(queue_monitoring, started 140233274279680)>, <ExcThread(job_monitor, started 140232745801472)>]
2019-09-10 10:46:17,822 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-10 10:46:17,870 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-10 10:46:17,871 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140233748485888)>, <ExcThread(job_monitor, started 140232745801472)>]
2019-09-10 10:47:02,841 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-09-10 10:47:02,842 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-10 10:47:02,929 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-10 10:47:02,929 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-10 10:47:02,929 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-10 10:47:03 UTC [wrapper] ==== pilot stdout END ====
2019-09-10 10:47:03 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-10 10:47:03 UTC [wrapper] Pilot exit status: 0
2019-09-10 10:47:03 UTC [wrapper] STATUSCODE: 0
2019-09-10 10:47:03 UTC [wrapper] apfmon messages muted
---- find pandaID.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 10 12:32 pandaIDs.out
drwx------. 14 dcameron zp   216 Sep 10 12:32 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
-rw-------. 1 dcameron zp 11 Sep 10 12:32 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
4002876565

2019-09-10 10:47:03 UTC [wrapper] Test setup, not cleaning
2019-09-10 10:47:03 UTC [wrapper] ==== wrapper stdout END ====
2019-09-10 10:47:03 UTC [wrapper] ==== wrapper stderr END ====
2019-09-10 10:47:03 UTC [wrapper] wrapper wrapperexiting ec=0, duration=901
2019-09-10 10:47:03 UTC [wrapper] apfmon messages muted
2019-09-10 12:47:03,152: ***************diag file************
2019-09-10 12:47:03,152: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=900.99s
KernelTime=44.88s
UserTime=1758.96s
CPUUsage=200%
MaxResidentMemory=1955440kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=176397
MinorPageFaults=8966504
Swaps=0
ForcedSwitches=154869
WaitSwitches=3560729
Inputs=41203376
Outputs=84560
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-09-10 12:47:03,158: ******************************WorkDir***********************
2019-09-10 12:47:03,158: total 369608
drwxrwx--x. 7 dcameron zp      4096 Sep 10 12:47 .
drwxrwx--x. 3 dcameron zp        15 Sep 10 11:23 ..
-rw-------. 1 dcameron zp   7536386 Sep 10 12:32 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   4079984 Sep 10 12:32 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Sep 10 12:32 .alrb
drwxr-xr-x. 3 dcameron zp        17 Sep 10 12:32 APPS
-rw-------. 1 dcameron zp       548 Sep 10 12:32 .asetup
-rw-------. 1 dcameron zp       826 Sep 10 12:32 .asetup.save
drwx------. 2 dcameron zp         6 Sep 10 12:32 .asetup-sysbin_66570
-rw-r--r--. 1 dcameron zp         0 Sep 10 12:31 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Sep 10 12:46 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       534 Sep 10 12:41 boinc_task_state.xml
-rw-r--r--. 1 dcameron zp 365251149 Sep 10 12:32 EVNT.14296418._001447.pool.root.1
-rw-------. 1 dcameron zp     14727 Sep 10 12:46 heartbeat.json
-rw-r--r--. 1 dcameron zp      6286 Sep 10 12:31 init_data.xml
-rw-r--r--. 1 dcameron zp    266067 Sep 10 12:32 input.tar.gz
-rw-r--r--. 1 dcameron zp       112 Sep 10 12:31 job.xml
-rw-------. 1 dcameron zp    713939 Sep 10 12:46 log.000649-2007289-20930._078090.job.log.tgz.1
-rw-------. 1 dcameron zp    180886 Sep 10 12:47 log.14568781._078090.job.log.1
-rw-------. 1 dcameron zp       499 Sep 10 12:47 output.list
-rw-------. 1 dcameron zp      2958 Sep 10 12:30 pandaJobData.out
drwx------. 3 dcameron zp       229 Sep 10 12:32 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 10 12:31 pilot2.tar.gz
-rw-------. 1 dcameron zp     11973 Sep 10 12:47 pilotlog.txt
-rw-------. 1 dcameron zp       507 Sep 10 12:47 qq7LDmSbsRvnShfckohDCDFpABFKDmABFKDmQ6FKDm3BFKDm3kQqnn.diag
-rw-------. 1 dcameron zp      5077 Sep 10 12:32 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Sep 10 12:32 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      8466 Sep 10 12:31 run_atlas
-rwx------. 1 dcameron zp     12641 Sep 10 12:30 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       618 Sep 10 12:47 runtime_log
-rw-r--r--. 1 dcameron zp      8100 Sep 10 12:47 runtime_log.err
-rw-------. 1 dcameron zp       240 Sep 10 12:32 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Sep 10 12:47 shared
-rw-r--r--. 1 dcameron zp      8494 Sep 10 12:32 start_atlas.sh
-rw-r--r--. 1 dcameron zp     18392 Sep 10 12:47 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Sep 10 12:31 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        25 Sep 10 12:46 wrapper_checkpoint.txt

2019-09-10 12:47:03,158: running start_atlas return value is 0
2019-09-10 12:47:03,158: Parent exit 0
2019-09-10 12:47:03,158: child process exit 0
12:47:03 (62204): run_atlas exited; CPU time 1759.297731
12:47:03 (62204): called boinc_finish(0)

</stderr_txt>
]]>

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