Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
17:11:11 (2811): wrapper (7.7.26015): starting
17:11:11 (2811): 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.18722398._021132.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-12 17:36:14,475 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4443116404
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-12 17:36:14,476 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 32365 s
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 9515
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 9515
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443116404 has completed
2019-08-12 17:36:14,477 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-12 17:36:14,485 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443116404
2019-08-12 17:36:15,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [9515]
2019-08-12 17:36:15,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 9515
2019-08-12 17:36:15,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-12 17:36:16,496 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-12 17:36:16,497 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=9515
2019-08-12 17:36:16,546 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [9515] (in reverse order)
2019-08-12 17:36:16,588 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-12 17:36:16,588 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-12 17:36:16,588 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-12 17:36:16,588 | 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 17:36:17,095 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-12 17:36:27,135 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-12 17:36:27,136 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-12 17:36:27,165 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34700525568 B)
2019-08-12 17:36:27,166 | 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 17:36:27,166 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-12 17:36:27,172 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-12 17:36:27,287 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-12 17:36:27,305 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-12 17:36:27,345 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-12 17:36:27,345 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job, started 140179710863104)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(validate_post, started 140178924492544)>, <ExcThread(data, started 140179694077696)>, <ExcThread(failed_post, started 140178916099840)>, <ExcThread(validate, started 140179702470400)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(copytool_in, started 140178941277952)>, <ExcThread(validate_pre, started 140179452970752)>, <ExcThread(copytool_out, started 140179478148864)>, <ExcThread(queue_monitoring, started 140179436185344)>, <ExcThread(payload, started 140179461363456)>, <ExcThread(create_data_payload, started 140179469756160)>]
2019-08-12 17:36:27,436 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-12 17:36:27,691 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-12 17:36:27,712 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-12 17:36:27,713 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-12 17:36:27,747 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-12 17:36:27,747 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job, started 140179710863104)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(validate_post, started 140178924492544)>, <ExcThread(data, started 140179694077696)>, <ExcThread(failed_post, started 140178916099840)>, <ExcThread(validate, started 140179702470400)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(validate_pre, started 140179452970752)>, <ExcThread(copytool_out, started 140179478148864)>, <ExcThread(queue_monitoring, started 140179436185344)>, <ExcThread(create_data_payload, started 140179469756160)>]
2019-08-12 17:36:27,762 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-12 17:36:27,890 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-12 17:36:28,024 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-12 17:36:28,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-12 17:36:28,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job, started 140179710863104)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(validate_post, started 140178924492544)>, <ExcThread(data, started 140179694077696)>, <ExcThread(validate, started 140179702470400)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(copytool_out, started 140179478148864)>, <ExcThread(queue_monitoring, started 140179436185344)>]
2019-08-12 17:36:28,121 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-12 17:36:28,121 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-12 17:36:28,159 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-12 17:36:28,232 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-12 17:36:28,233 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-12 17:36:28,250 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-12 17:36:28,250 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(validate_post, started 140178924492544)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(copytool_out, started 140179478148864)>, <ExcThread(queue_monitoring, started 140179436185344)>]
2019-08-12 17:36:28,288 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-12 17:36:28,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-12 17:36:28,352 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(validate_post, started 140178924492544)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(queue_monitoring, started 140179436185344)>]
2019-08-12 17:36:28,728 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-12 17:36:28,755 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-12 17:36:28,755 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(queue_monitor, started 140178907707136)>, <ExcThread(queue_monitoring, started 140179436185344)>]
2019-08-12 17:36:28,946 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-12 17:36:28,946 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-12 17:36:28,956 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-12 17:36:28,957 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job_monitor, started 140178932885248)>, <ExcThread(queue_monitoring, started 140179436185344)>]
2019-08-12 17:36:30,693 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-12 17:36:30,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-12 17:36:30,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140179927136000)>, <ExcThread(job_monitor, started 140178932885248)>]
2019-08-12 17:36:42,102 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-12 17:36:42,103 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-12 17:36:42,143 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-12 17:36:42,143 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-12 17:36:42,144 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-12 17:36:42 UTC [wrapper] ==== pilot stdout END ====
2019-08-12 17:36:42 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-12 17:36:42 UTC [wrapper] Pilot exit status: 0
2019-08-12 17:36:42 UTC [wrapper] STATUSCODE: 0
2019-08-12 17:36:42 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 17:11 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 17:36:42 UTC [wrapper] Test setup, not cleaning
2019-08-12 17:36:42 UTC [wrapper] ==== wrapper stdout END ====
2019-08-12 17:36:42 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8727.13s
KernelTime=260.69s
UserTime=32258.51s
CPUUsage=372%
MaxResidentMemory=1945268kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=319545
MinorPageFaults=14380104
Swaps=0
ForcedSwitches=3748718
WaitSwitches=6432579
Inputs=77797080
Outputs=646312
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216472
drwxrwx--x. 7 grid grid      4096 Aug 12 19:36 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 12 19:36 8cXLDmN1CHvnShfckohDCDFpABFKDmABFKDmJXUZDmABFKDmUsdDUm.diag
-rw-------. 1 grid grid   7409065 Aug 12 17:11 agis_ddmendpoints.json
-rw-------. 1 grid grid   4525411 Aug 12 17:11 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 12 17:11 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 12 17:11 APPS
drwxr-xr-x. 2 grid grid         6 Aug 12 17:11 .arc
-rw-------. 1 grid grid       538 Aug 12 17:11 .asetup
-rw-------. 1 grid grid       826 Aug 12 17:12 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 12 17:11 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 19:36 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 12 19:31 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207603020 Aug 12 17:11 EVNT.18605775._000418.pool.root.1
-rw-------. 1 grid grid     93332 Aug 12 19:36 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 12 17:11 init_data.xml
-rw-rw-r--. 1 grid grid    262345 Aug 12 17:11 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 12 17:11 job.xml
-rw-------. 1 grid grid    518142 Aug 12 19:36 log.18722398._021132.job.log.1
-rw-------. 1 grid grid    833086 Aug 12 19:36 log.18722398._021132.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 12 19:36 output.list
-rw-------. 1 grid grid      2954 Aug 12 02:05 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 12 01:30 pilot2.tar.gz
-rw-------. 1 grid grid     10285 Aug 12 19:36 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 12 02:05 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 12 17:11 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 12 17:11 run_atlas
-rwx------. 1 grid grid     15232 Aug 12 02:05 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 19:36 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 19:36 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 19:36 shared
-rw-rw-r--. 1 grid grid      8688 Aug 12 17:11 start_atlas.sh
-rw-rw-r--. 1 grid grid     18417 Aug 12 19:36 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 12 17:11 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 12 19:36 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
19:36:43 (2811): run_atlas exited; CPU time 32258.917245
19:36:43 (2811): called boinc_finish(0)

</stderr_txt>
]]>

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