Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
23:44:49 (8803): wrapper (7.7.26015): starting
23:44:49 (8803): wrapper: running run_atlas (--nthreads 4)
2019-08-20 23:44:49,526: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-20 23:44:49,526: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-20 23:44:49,527: THREADS=4

2019-08-20 23:44:49,529: Checking for CVMFS
2019-08-20 23:44:51,077: CVMFS is installed
2019-08-20 23:44:51,081: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-20 23:44:51,081: This is not SLC6, need to run with Singularity....
2019-08-20 23:44:51,081: Checking Singularity...
2019-08-20 23:44:51,084: Singularity is not installed, using version from CVMFS
2019-08-20 23:44:51,084: Testing the function of Singularity...
2019-08-20 23:44:51,084: Checking singularity with cmd:/cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-20 23:44:51,366: Singularity Works...
2019-08-20 23:44:51,366: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-20 23:44:51,884: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-20 23:44:51,885: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-20 23:44:51,886: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-20 23:44:51,886: export ATHENA_PROC_NUMBER=4;
2019-08-20 23:44:51,911: start atlas job with PandaID=4451312897
2019-08-20 23:44:51,911: cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /home/grid/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
2019-08-21 02:56:30,579: running cmd return value is 0
2019-08-21 02:56:30,584: Moving ./HITS.18722222._017160.pool.root.1 to shared/HITS.pool.root.1
2019-08-21 02:56:30,584: *****************The last 100 lines of the pilot log******************
2019-08-21 02:56:30,593: 2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 42899 s
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 15606
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 15606
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-21 00:55:26,836 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-21 00:55:26,837 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 00:55:26,837 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 00:55:26,837 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4451312897 has completed
2019-08-21 00:55:26,837 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-21 00:55:26,844 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4451312897
2019-08-21 00:55:27,850 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [15606]
2019-08-21 00:55:27,850 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 15606
2019-08-21 00:55:27,850 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-21 00:55:28,502 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-21 00:55:28,855 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-21 00:55:28,855 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=15606
2019-08-21 00:55:28,914 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [15606] (in reverse order)
2019-08-21 00:55:28,960 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-21 00:55:28,960 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-21 00:55:28,960 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-21 00:55:28,961 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-21 00:55:29,472 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-21 00:55:39,517 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-21 00:55:39,518 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-21 00:55:39,557 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34980495360 B)
2019-08-21 00:55:39,557 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-21 00:55:39,558 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-21 00:55:39,574 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-21 00:55:39,593 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-21 00:55:39,593 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-21 00:55:39,594 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(job, started 140309444331264)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(copytool_out, started 140309410760448)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(payload, started 140309419153152)>, <ExcThread(execute_payloads, started 140308637533952)>, <ExcThread(data, started 140309427545856)>, <ExcThread(copytool_in, started 140308645926656)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(monitor, started 140309056972544)>, <ExcThread(failed_post, started 140309015009024)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>, <ExcThread(validate, started 140309435938560)>]
2019-08-21 00:55:39,674 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-21 00:55:39,674 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-21 00:55:39,676 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-21 00:55:39,676 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-21 00:55:39,676 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-21 00:55:39,836 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-21 00:55:39,895 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-21 00:55:39,896 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(job, started 140309444331264)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(copytool_out, started 140309410760448)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(execute_payloads, started 140308637533952)>, <ExcThread(copytool_in, started 140308645926656)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(monitor, started 140309056972544)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:40,050 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-21 00:55:40,091 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-21 00:55:40,092 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-21 00:55:40,197 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-21 00:55:40,197 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(copytool_out, started 140309410760448)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(copytool_in, started 140308645926656)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(monitor, started 140309056972544)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:40,244 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-21 00:55:40,398 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-21 00:55:40,399 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(copytool_out, started 140309410760448)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(monitor, started 140309056972544)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:40,402 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-21 00:55:40,499 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-21 00:55:40,500 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(copytool_out, started 140309410760448)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:40,574 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-21 00:55:40,600 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-21 00:55:40,601 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(create_data_payload, started 140309065365248)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(validate_pre, started 140309048579840)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:40,663 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-21 00:55:40,692 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-21 00:55:40,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-21 00:55:40,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(queue_monitor, started 140308654319360)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:41,030 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-21 00:55:41,031 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-21 00:55:41,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-21 00:55:41,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(validate_post, started 140309023401728)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:41,133 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-21 00:55:41,205 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-21 00:55:41,205 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(job_monitor, started 140308662712064)>, <ExcThread(queue_monitoring, started 140309040187136)>]
2019-08-21 00:55:42,595 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-21 00:55:42,615 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-21 00:55:42,615 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140309660604160)>, <ExcThread(job_monitor, started 140308662712064)>]
2019-08-21 00:56:30,074 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-08-21 00:56:30,074 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-21 00:56:30,143 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-21 00:56:30,143 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-21 00:56:30,144 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-21 00:56:30 UTC [wrapper] ==== pilot stdout END ====
2019-08-21 00:56:30 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-21 00:56:30 UTC [wrapper] Pilot exit status: 0
2019-08-21 00:56:30 UTC [wrapper] STATUSCODE: 0
2019-08-21 00:56:30 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 44
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 20 23:45 pilot
-rwx------.  1 grid grid 20463 Jul 25 16:38 pilot.py
-rw-------.  1 grid grid     8 Aug  7 13:02 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-21 00:56:30 UTC [wrapper] Test setup, not cleaning
2019-08-21 00:56:30 UTC [wrapper] ==== wrapper stdout END ====
2019-08-21 00:56:30 UTC [wrapper] ==== wrapper stderr END ====
2019-08-21 00:56:30 UTC [wrapper] wrapper wrapperexiting ec=0, duration=11498
2019-08-21 00:56:30 UTC [wrapper] apfmon messages muted
2019-08-21 02:56:30,597: ***************diag file************
2019-08-21 02:56:30,598: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11498.25s
KernelTime=336.40s
UserTime=42713.92s
CPUUsage=374%
MaxResidentMemory=1944520kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=379632
MinorPageFaults=16300595
Swaps=0
ForcedSwitches=5000547
WaitSwitches=7659724
Inputs=91875488
Outputs=765048
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-21 02:56:30,608: ******************************WorkDir***********************
2019-08-21 02:56:30,608: total 268472
drwxrwx--x. 6 grid grid      4096 Aug 21 02:56 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7474631 Aug 20 23:45 agis_ddmendpoints.json
-rw-------. 1 grid grid   4339734 Aug 20 23:45 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 20 23:44 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 20 23:44 APPS
-rw-------. 1 grid grid       538 Aug 20 23:44 .asetup
-rw-------. 1 grid grid       826 Aug 20 23:45 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 20 23:44 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 21 02:56 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 21 02:47 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 260768185 Aug 20 23:44 EVNT.18605748._000399.pool.root.1
-rw-------. 1 grid grid    137899 Aug 21 02:55 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 20 23:44 init_data.xml
-rw-rw-r--. 1 grid grid    261609 Aug 20 23:44 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 20 23:44 job.xml
-rw-------. 1 grid grid    661056 Aug 21 02:56 log.18722222._017160.job.log.1
-rw-------. 1 grid grid    851452 Aug 21 02:55 log.18722222._017160.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 21 02:56 output.list
-rw-------. 1 grid grid      2921 Aug 18 09:37 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 18 09:30 pilot2.tar.gz
-rw-------. 1 grid grid     12009 Aug 21 02:56 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 18 09:37 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 20 23:44 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 20 23:44 run_atlas
-rwx------. 1 grid grid     12641 Aug 18 09:37 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 21 02:56 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 21 02:56 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 21 02:56 shared
-rw-rw-r--. 1 grid grid      8688 Aug 20 23:44 start_atlas.sh
-rw-rw-r--. 1 grid grid     20046 Aug 21 02:56 stderr.txt
-rw-------. 1 grid grid       517 Aug 21 02:56 uXPKDmGwUJvnShfckohDCDFpABFKDmABFKDmFXbLDmABFKDmYZWCym.diag
-rw-rw-r--. 1 grid grid       107 Aug 20 23:44 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 21 02:56 wrapper_checkpoint.txt

2019-08-21 02:56:30,609: running start_atlas return value is 0
2019-08-21 02:56:30,609: Parent exit 0
2019-08-21 02:56:30,611: child process exit 0
02:56:30 (8803): run_atlas exited; CPU time 42714.303973
02:56:30 (8803): called boinc_finish(0)

</stderr_txt>
]]>

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