Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
10:00:52 (29250): wrapper (7.7.26015): starting
10:00:52 (29250): wrapper: running run_atlas (--nthreads 4)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '4']
THREADS=4
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.6.1810 (Core) 

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is not installed, using version from CVMFS
Testing the function of Singularity...
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
Singularity Works...

copy /home/grid/slots/0/shared/ATLAS.root_0
copy /home/grid/slots/0/shared/input.tar.gz
copy /home/grid/slots/0/shared/RTE.tar.gz
copy /home/grid/slots/0/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=4;start atlas job with grep: pandaJobData.out: No such file or directory
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
running cmd return value is 0
Moving ./HITS.18604976._043388.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 10:00:10,678 | DEBUG    | queue_monitor       | pilot.control.job                | send_state                | wrote heartbeat to file /home/grid/slots/0/heartbeat.json
2019-08-10 10:00:10,678 | INFO     | queue_monitor       | pilot.control.job                | queue_monitor             | job 4441022015 was dequeued from the monitored payloads queue
2019-08-10 10:00:11,429 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4441022015
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 10:00:11,430 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26500 s
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 3561
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 3561
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 10:00:11,431 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441022015 has completed
2019-08-10 10:00:11,432 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 10:00:11,444 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4441022015
2019-08-10 10:00:12,449 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [3561]
2019-08-10 10:00:12,449 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 3561
2019-08-10 10:00:12,449 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 10:00:13,455 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 10:00:13,455 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=3561
2019-08-10 10:00:13,509 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [3561] (in reverse order)
2019-08-10 10:00:13,552 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 10:00:13,552 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 10:00:13,552 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 10:00:13,552 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-10 10:00:14,060 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 10:00:24,082 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 10:00:24,083 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 10:00:24,123 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34466693120 B)
2019-08-10 10:00:24,124 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-10 10:00:24,124 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 10:00:24,142 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 10:00:24,142 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 10:00:24,252 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 10:00:24,315 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-10 10:00:24,316 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(job, started 140409443346176)>, <ExcThread(copytool_in, started 140408495523584)>, <ExcThread(copytool_out, started 140409418168064)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(data, started 140409426560768)>, <ExcThread(validate_pre, started 140409040787200)>, <ExcThread(execute_payloads, started 140408503916288)>, <ExcThread(create_data_payload, started 140409057572608)>, <ExcThread(queue_monitoring, started 140409015609088)>, <ExcThread(queue_monitor, started 140408512308992)>, <ExcThread(failed_post, started 140409007216384)>, <ExcThread(payload, started 140409409775360)>, <ExcThread(validate, started 140409434953472)>]
2019-08-10 10:00:24,379 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 10:00:24,666 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 10:00:24,718 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-10 10:00:24,719 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(job, started 140409443346176)>, <ExcThread(copytool_in, started 140408495523584)>, <ExcThread(copytool_out, started 140409418168064)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(data, started 140409426560768)>, <ExcThread(validate_pre, started 140409040787200)>, <ExcThread(execute_payloads, started 140408503916288)>, <ExcThread(create_data_payload, started 140409057572608)>, <ExcThread(queue_monitoring, started 140409015609088)>, <ExcThread(queue_monitor, started 140408512308992)>, <ExcThread(payload, started 140409409775360)>, <ExcThread(validate, started 140409434953472)>]
2019-08-10 10:00:24,795 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 10:00:24,795 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 10:00:24,842 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 10:00:24,898 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 10:00:24,901 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 10:00:24,901 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 10:00:24,953 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 10:00:24,998 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 10:00:24,998 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 10:00:25,021 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 10:00:25,021 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(copytool_in, started 140408495523584)>, <ExcThread(copytool_out, started 140409418168064)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(queue_monitoring, started 140409015609088)>, <ExcThread(queue_monitor, started 140408512308992)>, <ExcThread(validate, started 140409434953472)>]
2019-08-10 10:00:25,142 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 10:00:25,223 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-10 10:00:25,224 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(copytool_in, started 140408495523584)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(queue_monitoring, started 140409015609088)>, <ExcThread(queue_monitor, started 140408512308992)>, <ExcThread(validate, started 140409434953472)>]
2019-08-10 10:00:25,355 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 10:00:25,426 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-10 10:00:25,426 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(copytool_in, started 140408495523584)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(queue_monitoring, started 140409015609088)>, <ExcThread(queue_monitor, started 140408512308992)>]
2019-08-10 10:00:25,546 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 10:00:25,619 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 10:00:25,619 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 10:00:25,628 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 10:00:25,628 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(job_monitor, started 140408520701696)>, <ExcThread(queue_monitoring, started 140409015609088)>]
2019-08-10 10:00:27,380 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 10:00:27,443 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 10:00:27,444 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140409659610880)>, <ExcThread(job_monitor, started 140408520701696)>]
2019-08-10 10:01:11,084 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 10:01:11,084 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 10:01:11,152 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 10:01:11,153 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 10:01:11,153 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 10:01:11 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 10:01:11 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 10:01:11 UTC [wrapper] Pilot exit status: 0
2019-08-10 10:01:11 UTC [wrapper] STATUSCODE: 0
2019-08-10 10:01:11 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 10 10:01 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

2019-08-10 10:01:11 UTC [wrapper] Test setup, not cleaning
2019-08-10 10:01:11 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 10:01:11 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7216.23s
KernelTime=242.51s
UserTime=26378.39s
CPUUsage=368%
MaxResidentMemory=1900476kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=293602
MinorPageFaults=13424337
Swaps=0
ForcedSwitches=3084783
WaitSwitches=5726022
Inputs=71261744
Outputs=513808
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 380064
drwxrwx--x. 7 grid grid      4096 Aug 10 12:01 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408903 Aug 10 10:01 agis_ddmendpoints.json
-rw-------. 1 grid grid   4507141 Aug 10 10:01 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 10:00 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 10:00 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 10:01 .arc
-rw-------. 1 grid grid       538 Aug 10 10:00 .asetup
-rw-------. 1 grid grid       826 Aug 10 10:01 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 10:00 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 12:01 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 10 11:55 boinc_task_state.xml
-rw-------. 1 grid grid       516 Aug 10 12:01 bYXNDmAw5FvnShfckohDCDFpABFKDmABFKDmi7cXDmABFKDmPy06Oo.diag
-rw-rw-r--. 1 grid grid 375232576 Aug 10 10:00 EVNT.17323813._000784.pool.root.1
-rw-------. 1 grid grid     76053 Aug 10 12:00 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 10:00 init_data.xml
-rw-rw-r--. 1 grid grid    262356 Aug 10 10:00 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 10:00 job.xml
-rw-------. 1 grid grid    448439 Aug 10 12:01 log.18604976._043388.job.log.1
-rw-------. 1 grid grid    824742 Aug 10 12:00 log.18604976._043388.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 12:01 output.list
-rw-------. 1 grid grid      2873 Aug  9 00:19 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  8 23:24 pilot2.tar.gz
-rw-------. 1 grid grid      9743 Aug 10 12:01 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 00:15 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 10:00 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 10:00 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 00:19 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 12:01 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 12:01 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 12:01 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 10:00 start_atlas.sh
-rw-rw-r--. 1 grid grid     18241 Aug 10 12:01 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 10:00 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 10 12:01 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
12:01:12 (29250): run_atlas exited; CPU time 26378.771975
12:01:12 (29250): called boinc_finish(0)

</stderr_txt>
]]>

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