Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
07:12:21 (758): wrapper (7.7.26015): starting
07:12:21 (758): 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=4446451534
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._047327.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 28637 s
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-14 07:21:41,141 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7525
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7525
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446451534 has completed
2019-08-14 07:21:41,142 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-14 07:21:41,149 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446451534
2019-08-14 07:21:42,154 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7525]
2019-08-14 07:21:42,154 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7525
2019-08-14 07:21:42,154 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-14 07:21:43,157 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-14 07:21:43,158 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7525
2019-08-14 07:21:43,204 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7525] (in reverse order)
2019-08-14 07:21:43,242 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-14 07:21:43,243 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-14 07:21:43,243 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-14 07:21:43,243 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-14 07:21:43,752 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-14 07:21:53,049 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-14 07:21:53,793 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-14 07:21:53,793 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-14 07:21:53,824 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35832987648 B)
2019-08-14 07:21:53,824 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-14 07:21:53,824 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-14 07:21:53,834 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-14 07:21:53,868 | WARNING  | job_monitor         | pilot.util.common                | should_abort              | job:job_monitor:received graceful stop - abort after this iteration
2019-08-14 07:21:54,003 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-14 07:21:54,003 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-14 07:21:54,009 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-14 07:21:54,201 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-14 07:21:54,202 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(job, started 139895974909696)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(execute_payloads, started 139895163037440)>, <ExcThread(payload, started 139895725086464)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(create_data_payload, started 139895741871872)>, <ExcThread(validate_post, started 139895205000960)>, <ExcThread(validate_pre, started 139895699908352)>, <ExcThread(monitor, started 139895691515648)>, <ExcThread(copytool_out, started 139895733479168)>]
2019-08-14 07:21:54,277 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-14 07:21:54,277 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-14 07:21:54,290 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-14 07:21:54,386 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-14 07:21:54,403 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-14 07:21:54,403 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(execute_payloads, started 139895163037440)>, <ExcThread(payload, started 139895725086464)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(create_data_payload, started 139895741871872)>, <ExcThread(validate_pre, started 139895699908352)>, <ExcThread(copytool_out, started 139895733479168)>]
2019-08-14 07:21:54,447 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-14 07:21:54,447 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-14 07:21:54,504 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-14 07:21:54,504 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(execute_payloads, started 139895163037440)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(create_data_payload, started 139895741871872)>, <ExcThread(validate_pre, started 139895699908352)>, <ExcThread(copytool_out, started 139895733479168)>]
2019-08-14 07:21:54,596 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-14 07:21:54,605 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-14 07:21:54,605 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(create_data_payload, started 139895741871872)>, <ExcThread(validate_pre, started 139895699908352)>, <ExcThread(copytool_out, started 139895733479168)>]
2019-08-14 07:21:54,834 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-14 07:21:54,907 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-14 07:21:54,908 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(create_data_payload, started 139895741871872)>, <ExcThread(validate_pre, started 139895699908352)>]
2019-08-14 07:21:55,040 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-14 07:21:55,109 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-14 07:21:55,109 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(failed_post, started 139895179822848)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(queue_monitoring, started 139895716693760)>, <ExcThread(validate_pre, started 139895699908352)>]
2019-08-14 07:21:55,129 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-14 07:21:55,176 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-14 07:21:55,210 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-14 07:21:55,210 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(validate, started 139895966516992)>, <ExcThread(queue_monitoring, started 139895716693760)>]
2019-08-14 07:21:55,237 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-14 07:21:55,311 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-14 07:21:55,312 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(queue_monitor, started 139895171430144)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(queue_monitoring, started 139895716693760)>]
2019-08-14 07:21:55,615 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-14 07:21:55,629 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-14 07:21:55,629 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-14 07:21:55,715 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-14 07:21:55,715 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(job_monitor, started 139895188215552)>, <ExcThread(queue_monitoring, started 139895716693760)>]
2019-08-14 07:21:58,616 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-14 07:21:58,634 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-14 07:21:58,635 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896191182592)>, <ExcThread(job_monitor, started 139895188215552)>]
2019-08-14 07:22:53,933 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 122 s)
2019-08-14 07:22:53,933 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-14 07:22:54,004 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-14 07:22:54,005 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-14 07:22:54,005 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-14 07:22:54 UTC [wrapper] ==== pilot stdout END ====
2019-08-14 07:22:54 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-14 07:22:54 UTC [wrapper] Pilot exit status: 0
2019-08-14 07:22:54 UTC [wrapper] STATUSCODE: 0
2019-08-14 07:22:54 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 14 07:12 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

2019-08-14 07:22:54 UTC [wrapper] Test setup, not cleaning
2019-08-14 07:22:54 UTC [wrapper] ==== wrapper stdout END ====
2019-08-14 07:22:54 UTC [wrapper] ==== wrapper stderr END ====
2019-08-14 07:22:54 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7830
2019-08-14 07:22:54 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7830.21s
KernelTime=238.27s
UserTime=28520.82s
CPUUsage=367%
MaxResidentMemory=1944376kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=304896
MinorPageFaults=13762469
Swaps=0
ForcedSwitches=3286212
WaitSwitches=6139827
Inputs=74047848
Outputs=533440
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 382660
drwxrwx--x. 6 grid grid      4096 Aug 14 09:22 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409110 Aug 14 07:12 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517511 Aug 14 07:12 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 14 07:12 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 14 07:12 APPS
-rw-------. 1 grid grid       538 Aug 14 07:12 .asetup
-rw-------. 1 grid grid       826 Aug 14 07:13 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 14 07:12 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 09:22 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 14 09:15 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 377874450 Aug 14 07:12 EVNT.17323813._000923.pool.root.1
-rw-------. 1 grid grid     71383 Aug 14 09:21 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 14 07:12 init_data.xml
-rw-rw-r--. 1 grid grid    261620 Aug 14 07:12 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 14 07:12 job.xml
-rw-------. 1 grid grid    469734 Aug 14 09:22 log.18604976._047327.job.log.1
-rw-------. 1 grid grid    823024 Aug 14 09:21 log.18604976._047327.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 14 09:22 output.list
-rw-------. 1 grid grid      2872 Aug 13 07:43 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 07:28 pilot2.tar.gz
-rw-------. 1 grid grid     12216 Aug 14 09:22 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 07:42 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 14 07:12 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 14 07:12 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 07:43 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 09:22 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 09:22 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 09:22 shared
-rw-rw-r--. 1 grid grid      8688 Aug 14 07:12 start_atlas.sh
-rw-rw-r--. 1 grid grid     19291 Aug 14 09:22 stderr.txt
-rw-------. 1 grid grid       516 Aug 14 09:22 TZJODmJmeHvnShfckohDCDFpABFKDmABFKDmnkDaDmABFKDmkr1ean.diag
-rw-rw-r--. 1 grid grid       107 Aug 14 07:12 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 14 09:22 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
09:22:55 (758): run_atlas exited; CPU time 28521.238043
09:22:55 (758): called boinc_finish(0)

</stderr_txt>
]]>

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