Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
19:19:56 (31616): wrapper (7.7.26015): starting
19:19:56 (31616): 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 PandaID=4446044730
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.18722326._010361.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4446044730
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722326
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 22:26:43,110 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 71090 s
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 5913
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 5913
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446044730 has completed
2019-08-16 22:26:43,111 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 22:26:43,119 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446044730
2019-08-16 22:26:44,124 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [5913]
2019-08-16 22:26:44,124 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 5913
2019-08-16 22:26:44,124 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 22:26:45,129 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 22:26:45,130 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=5913
2019-08-16 22:26:45,180 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [5913] (in reverse order)
2019-08-16 22:26:45,222 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 22:26:45,222 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 22:26:45,222 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 22:26:45,222 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-16 22:26:45,732 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 22:26:55,771 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 22:26:55,771 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 22:26:55,819 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35553017856 B)
2019-08-16 22:26:55,819 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-16 22:26:55,819 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 22:26:55,856 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-16 22:26:55,856 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(job, started 140018838611712)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(monitor, started 140018718848768)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(validate_pre, started 140018727241472)>, <ExcThread(validate_post, started 140018215548672)>, <ExcThread(create_data_payload, started 140018744026880)>, <ExcThread(job_monitor, started 140018198763264)>, <ExcThread(data, started 140018752419584)>, <ExcThread(execute_payloads, started 140018181977856)>, <ExcThread(copytool_out, started 140018710456064)>, <ExcThread(copytool_in, started 140018173585152)>, <ExcThread(validate, started 140018830219008)>, <ExcThread(payload, started 140018735634176)>, <ExcThread(failed_post, started 140018207155968)>]
2019-08-16 22:26:55,863 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 22:26:55,895 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 22:26:55,917 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 22:26:55,917 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 22:26:55,929 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 22:26:56,034 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 22:26:56,068 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 22:26:56,122 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 22:26:56,158 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 22:26:56,158 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(validate_post, started 140018215548672)>, <ExcThread(job_monitor, started 140018198763264)>, <ExcThread(data, started 140018752419584)>, <ExcThread(copytool_out, started 140018710456064)>, <ExcThread(copytool_in, started 140018173585152)>, <ExcThread(validate, started 140018830219008)>, <ExcThread(payload, started 140018735634176)>, <ExcThread(failed_post, started 140018207155968)>]
2019-08-16 22:26:56,199 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 22:26:56,459 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-16 22:26:56,460 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(validate_post, started 140018215548672)>, <ExcThread(job_monitor, started 140018198763264)>, <ExcThread(data, started 140018752419584)>, <ExcThread(copytool_out, started 140018710456064)>, <ExcThread(validate, started 140018830219008)>, <ExcThread(payload, started 140018735634176)>, <ExcThread(failed_post, started 140018207155968)>]
2019-08-16 22:26:56,805 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 22:26:56,806 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 22:26:56,832 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 22:26:56,876 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 22:26:56,935 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 22:26:56,936 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 22:26:56,962 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 22:26:56,962 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(job_monitor, started 140018198763264)>, <ExcThread(copytool_out, started 140018710456064)>, <ExcThread(failed_post, started 140018207155968)>]
2019-08-16 22:26:57,122 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 22:26:57,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 22:26:57,164 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(job_monitor, started 140018198763264)>, <ExcThread(failed_post, started 140018207155968)>]
2019-08-16 22:26:57,308 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 22:26:57,365 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 22:26:57,366 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitor, started 140018165192448)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(job_monitor, started 140018198763264)>]
2019-08-16 22:26:57,526 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 22:26:57,526 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 22:26:57,567 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 22:26:57,567 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(queue_monitoring, started 140018190370560)>, <ExcThread(job_monitor, started 140018198763264)>]
2019-08-16 22:26:59,069 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 22:26:59,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 22:26:59,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140019054884608)>, <ExcThread(job_monitor, started 140018198763264)>]
2019-08-16 22:27:30,087 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 22:27:30,088 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 22:27:30,189 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 22:27:30,190 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 22:27:30,190 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 22:27:30 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 22:27:30 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 22:27:30 UTC [wrapper] Pilot exit status: 0
2019-08-16 22:27:30 UTC [wrapper] STATUSCODE: 0
2019-08-16 22:27:30 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 16 19:20 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

2019-08-16 22:27:30 UTC [wrapper] Test setup, not cleaning
2019-08-16 22:27:30 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 22:27:30 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 22:27:30 UTC [wrapper] wrapper wrapperexiting ec=0, duration=18451
2019-08-16 22:27:30 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=18451.17s
KernelTime=476.26s
UserTime=70835.84s
CPUUsage=386%
MaxResidentMemory=1945324kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=512868
MinorPageFaults=20609317
Swaps=0
ForcedSwitches=8210504
WaitSwitches=10937854
Inputs=123748112
Outputs=1002304
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 286500
drwxrwx--x. 6 grid grid      4096 Aug 17 00:27 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       520 Aug 17 00:27 5sGKDmdzFIvnShfckohDCDFpABFKDmABFKDmRYBbDmABFKDmt88SOo.diag
-rw-------. 1 grid grid   7411700 Aug 16 19:20 agis_ddmendpoints.json
-rw-------. 1 grid grid   4399652 Aug 16 19:20 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 19:19 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 19:19 APPS
-rw-------. 1 grid grid       538 Aug 16 19:20 .asetup
-rw-------. 1 grid grid       826 Aug 16 19:20 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 19:19 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 17 00:27 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 17 00:22 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 279093940 Aug 16 19:19 EVNT.18605758._000275.pool.root.1
-rw-------. 1 grid grid     79871 Aug 17 00:26 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 19:19 init_data.xml
-rw-rw-r--. 1 grid grid    261624 Aug 16 19:19 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 16 19:19 job.xml
-rw-------. 1 grid grid    845599 Aug 17 00:27 log.18722326._010361.job.log.1
-rw-------. 1 grid grid    856372 Aug 17 00:26 log.18722326._010361.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 17 00:27 output.list
-rw-------. 1 grid grid      2914 Aug 14 23:28 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 14 23:26 pilot2.tar.gz
-rw-------. 1 grid grid     10384 Aug 17 00:27 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 14 23:26 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 19:19 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 19:19 run_atlas
-rwx------. 1 grid grid     12641 Aug 14 23:28 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 17 00:27 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 17 00:27 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 17 00:27 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 19:19 start_atlas.sh
-rw-rw-r--. 1 grid grid     18361 Aug 17 00:27 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 16 19:19 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 17 00:27 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
00:27:30 (31616): run_atlas exited; CPU time 70836.245625
00:27:30 (31616): called boinc_finish(0)

</stderr_txt>
]]>

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