Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:57:19 (9728): wrapper (7.7.26015): starting
14:57:19 (9728): 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._045690.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-12 15:10:19,301 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 15:10:19,301 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-12 15:10:19,301 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4443069669
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 29363 s
2019-08-12 15:10:19,302 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 16418
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 16418
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443069669 has completed
2019-08-12 15:10:19,303 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-12 15:10:19,310 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443069669
2019-08-12 15:10:20,312 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [16418]
2019-08-12 15:10:20,312 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 16418
2019-08-12 15:10:20,312 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-12 15:10:21,316 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-12 15:10:21,316 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=16418
2019-08-12 15:10:21,377 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [16418] (in reverse order)
2019-08-12 15:10:21,502 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-12 15:10:21,503 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-12 15:10:21,503 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-12 15:10:21,503 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-12 15:10:22,016 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-12 15:10:32,057 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-12 15:10:32,058 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-12 15:10:32,145 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34535899136 B)
2019-08-12 15:10:32,146 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-12 15:10:32,146 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-12 15:10:32,146 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-12 15:10:32,292 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-12 15:10:32,292 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-12 15:10:32,388 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-12 15:10:32,389 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(job, started 140415304169216)>, <ExcThread(validate_post, started 140414728255232)>, <ExcThread(failed_post, started 140414719862528)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(create_data_payload, started 140415278991104)>, <ExcThread(queue_monitor, started 140414711469824)>, <ExcThread(copytool_in, started 140414736647936)>, <ExcThread(validate, started 140415295776512)>, <ExcThread(execute_payloads, started 140414157846272)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(monitor, started 140415245420288)>, <ExcThread(job_monitor, started 140414745040640)>, <ExcThread(validate_pre, started 140415253812992)>, <ExcThread(payload, started 140415270598400)>]
2019-08-12 15:10:32,650 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-12 15:10:32,763 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-12 15:10:32,793 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-12 15:10:32,793 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(job, started 140415304169216)>, <ExcThread(failed_post, started 140414719862528)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(create_data_payload, started 140415278991104)>, <ExcThread(queue_monitor, started 140414711469824)>, <ExcThread(copytool_in, started 140414736647936)>, <ExcThread(validate, started 140415295776512)>, <ExcThread(execute_payloads, started 140414157846272)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(monitor, started 140415245420288)>, <ExcThread(job_monitor, started 140414745040640)>, <ExcThread(payload, started 140415270598400)>]
2019-08-12 15:10:32,877 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-12 15:10:32,943 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-12 15:10:32,984 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-12 15:10:32,991 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-12 15:10:32,992 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-12 15:10:33,044 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-12 15:10:33,095 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-12 15:10:33,095 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(failed_post, started 140414719862528)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(queue_monitor, started 140414711469824)>, <ExcThread(validate, started 140415295776512)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(job_monitor, started 140414745040640)>, <ExcThread(payload, started 140415270598400)>]
2019-08-12 15:10:33,152 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-12 15:10:33,296 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-12 15:10:33,297 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(queue_monitor, started 140414711469824)>, <ExcThread(validate, started 140415295776512)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(job_monitor, started 140414745040640)>, <ExcThread(payload, started 140415270598400)>]
2019-08-12 15:10:33,325 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-12 15:10:33,326 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-12 15:10:33,346 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-12 15:10:33,398 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-12 15:10:33,398 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(queue_monitor, started 140414711469824)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(job_monitor, started 140414745040640)>]
2019-08-12 15:10:33,539 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-12 15:10:33,805 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-12 15:10:33,805 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-12 15:10:33,902 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-12 15:10:33,902 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(copytool_out, started 140415262205696)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(job_monitor, started 140414745040640)>]
2019-08-12 15:10:34,540 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-12 15:10:34,608 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-12 15:10:34,608 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(queue_monitoring, started 140414761826048)>, <ExcThread(job_monitor, started 140414745040640)>]
2019-08-12 15:10:35,148 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-12 15:10:35,212 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-12 15:10:35,212 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140415520442112)>, <ExcThread(job_monitor, started 140414745040640)>]
2019-08-12 15:11:06,750 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-12 15:11:06,750 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-12 15:11:06,760 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-12 15:11:06,760 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-12 15:11:06,760 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-12 15:11:06 UTC [wrapper] ==== pilot stdout END ====
2019-08-12 15:11:06 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-12 15:11:07 UTC [wrapper] Pilot exit status: 0
2019-08-12 15:11:07 UTC [wrapper] STATUSCODE: 0
2019-08-12 15:11:07 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 12 14:57 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

2019-08-12 15:11:07 UTC [wrapper] Test setup, not cleaning
2019-08-12 15:11:07 UTC [wrapper] ==== wrapper stdout END ====
2019-08-12 15:11:07 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8024.57s
KernelTime=255.51s
UserTime=29262.21s
CPUUsage=367%
MaxResidentMemory=1945164kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=309757
MinorPageFaults=13886623
Swaps=0
ForcedSwitches=3387160
WaitSwitches=6062081
Inputs=75248352
Outputs=519200
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 383168
drwxrwx--x. 7 grid grid      4096 Aug 12 17:11 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 12 17:11 0cgNDmtk4GvnShfckohDCDFpABFKDmABFKDmyHHZDmABFKDmwvgZHm.diag
-rw-------. 1 grid grid   7409065 Aug 12 14:57 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506933 Aug 12 14:57 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 12 14:57 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 12 14:57 APPS
drwxr-xr-x. 2 grid grid         6 Aug 12 14:57 .arc
-rw-------. 1 grid grid       538 Aug 12 14:57 .asetup
-rw-------. 1 grid grid       826 Aug 12 14:58 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 12 14:57 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 17:11 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 12 17:04 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 378366145 Aug 12 14:57 EVNT.17323813._000897.pool.root.1
-rw-------. 1 grid grid     81240 Aug 12 17:10 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 12 14:57 init_data.xml
-rw-rw-r--. 1 grid grid    262337 Aug 12 14:57 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 12 14:57 job.xml
-rw-------. 1 grid grid    483646 Aug 12 17:11 log.18604976._045690.job.log.1
-rw-------. 1 grid grid    827536 Aug 12 17:10 log.18604976._045690.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 12 17:11 output.list
-rw-------. 1 grid grid      2872 Aug 11 17:16 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 16:26 pilot2.tar.gz
-rw-------. 1 grid grid     10394 Aug 12 17:11 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 17:16 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 12 14:57 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 12 14:57 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 17:16 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 17:11 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 17:11 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 17:11 shared
-rw-rw-r--. 1 grid grid      8688 Aug 12 14:57 start_atlas.sh
-rw-rw-r--. 1 grid grid     18532 Aug 12 17:11 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 12 14:57 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 12 17:11 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
17:11:08 (9728): run_atlas exited; CPU time 29262.707006
17:11:08 (9728): called boinc_finish(0)

</stderr_txt>
]]>

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