Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
09:59:43 (19949): wrapper (7.7.26015): starting
09:59:43 (19949): wrapper: running run_atlas (--nthreads 4)
2019-09-26 09:59:43,446: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-26 09:59:43,446: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-26 09:59:43,447: THREADS=4

2019-09-26 09:59:43,449: Checking for CVMFS
2019-09-26 09:59:44,239: CVMFS is installed
2019-09-26 09:59:44,240: Checking Singularity...
2019-09-26 09:59:44,349: Singularity is installed, version singularity version 3.2.1-1
2019-09-26 09:59:44,349: Testing the function of Singularity...
2019-09-26 09:59:44,349: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-26 09:59:44,812: Singularity Works...
2019-09-26 09:59:44,813: copy /home/grid/slots/3/shared/ATLAS.root_0
2019-09-26 09:59:45,483: copy /home/grid/slots/3/shared/input.tar.gz
2019-09-26 09:59:45,484: copy /home/grid/slots/3/shared/RTE.tar.gz
2019-09-26 09:59:45,485: copy /home/grid/slots/3/shared/start_atlas.sh
2019-09-26 09:59:45,485: export ATHENA_PROC_NUMBER=4;
2019-09-26 09:59:45,670: start atlas job with PandaID=4490264969
2019-09-26 09:59:45,671: cmd = singularity exec --pwd /home/grid/slots/3 -B /cvmfs,/home /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-09-26 12:54:45,401: running cmd return value is 0
2019-09-26 12:54:45,406: *****************The last 100 lines of the pilot log******************
2019-09-26 12:54:45,437: 2019-09-26 10:54:35,789 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-26 10:54:35,789 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-26 10:54:35,789 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-26 10:54:35,789 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4490264969 has completed
2019-09-26 10:54:35,789 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-26 10:54:35,798 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/3/PanDA_Pilot-4490264969
2019-09-26 10:54:36,803 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2862]
2019-09-26 10:54:36,804 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2862
2019-09-26 10:54:36,804 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-26 10:54:37,809 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-26 10:54:37,809 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2862
2019-09-26 10:54:37,902 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2862] (in reverse order)
2019-09-26 10:54:37,959 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-26 10:54:37,960 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-26 10:54:37,960 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-26 10:54:37,960 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-26 10:54:37,975 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:54:37,975 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-26 10:54:37,975 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:54:37,975 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-26 10:54:37,975 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | pilot is running in a VM
2019-09-26 10:54:37,976 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-26 10:54:38,149 | 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
2019-09-26 10:54:38,149 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:54:38,652 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/3
2019-09-26 10:54:38,688 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (8080326656 B)
2019-09-26 10:54:38,688 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-26 10:54:38,688 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-26 10:54:38,899 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-26 10:54:38,911 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-26 10:54:38,922 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-26 10:54:38,922 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-26 10:54:38,945 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-26 10:54:39,025 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-26 10:54:39,026 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(job, started 140077307672320)>, <ExcThread(validate_pre, started 140077036451584)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(copytool_in, started 140076466042624)>, <ExcThread(create_data_payload, started 140077061629696)>, <ExcThread(validate_post, started 140076449257216)>, <ExcThread(validate, started 140077299279616)>, <ExcThread(monitor, started 140077028058880)>, <ExcThread(job_monitor, started 140077019666176)>, <ExcThread(data, started 140077290886912)>, <ExcThread(queue_monitor, started 140076457649920)>, <ExcThread(copytool_out, started 140077282494208)>]
2019-09-26 10:54:39,114 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-26 10:54:39,115 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-26 10:54:39,162 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-26 10:54:39,177 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-26 10:54:39,179 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-26 10:54:39,243 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-26 10:54:39,259 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-09-26 10:54:39,259 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(validate_pre, started 140077036451584)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(validate_post, started 140076449257216)>, <ExcThread(job_monitor, started 140077019666176)>, <ExcThread(data, started 140077290886912)>, <ExcThread(queue_monitor, started 140076457649920)>, <ExcThread(copytool_out, started 140077282494208)>]
2019-09-26 10:54:39,321 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-26 10:54:39,321 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-26 10:54:39,360 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-09-26 10:54:39,360 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(validate_pre, started 140077036451584)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(validate_post, started 140076449257216)>, <ExcThread(job_monitor, started 140077019666176)>, <ExcThread(queue_monitor, started 140076457649920)>, <ExcThread(copytool_out, started 140077282494208)>]
2019-09-26 10:54:39,716 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-26 10:54:39,717 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-26 10:54:39,763 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-26 10:54:39,763 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(validate_pre, started 140077036451584)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(validate_post, started 140076449257216)>, <ExcThread(job_monitor, started 140077019666176)>, <ExcThread(copytool_out, started 140077282494208)>]
2019-09-26 10:54:39,777 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-26 10:54:39,864 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-26 10:54:39,864 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(validate_post, started 140076449257216)>, <ExcThread(job_monitor, started 140077019666176)>, <ExcThread(copytool_out, started 140077282494208)>]
2019-09-26 10:54:39,912 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-26 10:54:39,960 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-26 10:54:39,965 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-26 10:54:39,965 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(queue_monitoring, started 140077044844288)>, <ExcThread(job_monitor, started 140077019666176)>]
2019-09-26 10:54:40,085 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-26 10:54:43,087 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-26 10:54:43,187 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-26 10:54:43,188 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140077523945216)>, <ExcThread(job_monitor, started 140077019666176)>]
2019-09-26 10:54:44,715 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-09-26 10:54:44,715 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-26 10:54:44,798 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-26 10:54:44,798 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-26 10:54:44,798 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-26 10:54:45 UTC [wrapper] ==== pilot stdout END ====
2019-09-26 10:54:45 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-26 10:54:45 UTC [wrapper] Pilot exit status: 0
2019-09-26 10:54:45 UTC [wrapper] STATUSCODE: 0
2019-09-26 10:54:45 UTC [wrapper] apfmon messages muted
---- find pandaIDs.out ----
total 56
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
-rw-------.  1 grid grid    20 Sep  9 13:04 MANIFEST.IN
-rw-------.  1 grid grid    11 Sep 26 10:00 pandaIDs.out
drwx------. 14 grid grid   216 Sep 26 10:00 pilot
-rwx------.  1 grid grid 20136 Sep  9 13:04 pilot.py
-rw-------.  1 grid grid     9 Sep  9 13:04 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   760 Aug 22 11:01 setup.py
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-09-26 10:54:45 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 grid grid 11 Sep 26 10:00 /home/grid/slots/3/pilot2/pandaIDs.out
2019-09-26 10:54:45 UTC [wrapper] pandaIDs.out content:
4490264969

2019-09-26 10:54:45 UTC [wrapper] Test setup, not cleaning
2019-09-26 10:54:45 UTC [wrapper] ==== wrapper stdout END ====
2019-09-26 10:54:45 UTC [wrapper] ==== wrapper stderr END ====
2019-09-26 10:54:45 UTC [wrapper] wrapper wrapperexiting ec=0, duration=10498
2019-09-26 10:54:45 UTC [wrapper] apfmon messages muted
2019-09-26 12:54:45,449: ***************diag file************
2019-09-26 12:54:45,450: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=10498.19s
KernelTime=352.47s
UserTime=9239.92s
CPUUsage=91%
MaxResidentMemory=1904432kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=392914
MinorPageFaults=12828378
Swaps=0
ForcedSwitches=1444998
WaitSwitches=6139408
Inputs=82358346
Outputs=95704
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-09-26 12:54:45,466: ******************************WorkDir***********************
2019-09-26 12:54:45,467: total 280312
drwxrwx--x. 7 grid grid      4096 Sep 26 12:54 .
drwxr-x--x. 7 grid grid        51 Sep 26 11:56 ..
-rw-------. 1 grid grid   7579510 Sep 26 10:00 agis_ddmendpoints.json
-rw-------. 1 grid grid   4044851 Sep 26 10:00 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Sep 26 09:59 .alrb
drwxr-xr-x. 3 grid grid        17 Sep 26 09:59 APPS
-rw-------. 1 grid grid       538 Sep 26 09:59 .asetup
-rw-------. 1 grid grid       826 Sep 26 10:01 .asetup.save
drwx------. 2 grid grid         6 Sep 26 10:00 .asetup-sysbin_32489
-rw-r--r--. 1 grid grid         0 Sep 26 09:59 boinc_lockfile
-rw-r--r--. 1 grid grid      8192 Sep 26 12:54 boinc_mmap_file
-rw-r--r--. 1 grid grid       537 Sep 26 12:52 boinc_task_state.xml
-rw-r--r--. 1 grid grid 273789384 Sep 26 09:59 EVNT.18605543._000339.pool.root.1
-rw-------. 1 grid grid     32487 Sep 26 12:54 heartbeat.json
-rw-r--r--. 1 grid grid      5872 Sep 26 11:56 init_data.xml
-rw-r--r--. 1 grid grid    267504 Sep 26 09:59 input.tar.gz
-rw-r--r--. 1 grid grid       112 Sep 26 09:59 job.xml
-rw-------. 1 grid grid    496205 Sep 26 12:54 log.19000468._018038.job.log.1
-rw-------. 1 grid grid    401143 Sep 26 12:54 log.19000468._018038.job.log.tgz.1
-rw-------. 1 grid grid       241 Sep 26 12:54 output.list
-rw-------. 1 grid grid      2842 Sep 26 07:39 pandaJobData.out
drwx------. 3 grid grid       229 Sep 26 10:00 pilot2
-rw-r--r--. 1 grid grid    259319 Sep 26 07:39 pilot2.tar.gz
-rw-------. 1 grid grid     10535 Sep 26 12:54 pilotlog.txt
-rw-r--r--. 1 grid grid      4480 Sep 26 07:39 queuedata.json
-rw-r--r--. 1 grid grid       815 Sep 26 09:59 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      7941 Sep 26 09:59 run_atlas
-rwx------. 1 grid grid     12762 Sep 26 07:39 runpilot2-wrapper.sh
-rw-r--r--. 1 grid grid       692 Sep 26 12:54 runtime_log
-rw-r--r--. 1 grid grid      6655 Sep 26 12:54 runtime_log.err
drwxrwx--x. 2 grid grid       107 Sep 26 12:54 shared
-rw-r--r--. 1 grid grid      8688 Sep 26 09:59 start_atlas.sh
-rw-r--r--. 1 grid grid     16726 Sep 26 12:54 stderr.txt
-rw-r--r--. 1 grid grid       107 Sep 26 09:59 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 grid grid        28 Sep 26 12:54 wrapper_checkpoint.txt
-rw-------. 1 grid grid       514 Sep 26 12:54 zdCNDm7fbXvnShfckohDCDFpABFKDmABFKDmtJeQDmABFKDmbDQRwn.diag

2019-09-26 12:54:45,467: running start_atlas return value is 0
2019-09-26 12:54:45,467: Parent exit 0
2019-09-26 12:54:45,470: child process exit 0
12:54:46 (19949): run_atlas exited; CPU time 9240.365288
12:54:46 (19949): called boinc_finish(0)

</stderr_txt>
]]>

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