Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
04:49:26 (14303): wrapper (7.7.26015): starting
04:49:26 (14303): 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 installed, version singularity version 3.2.1-1
Testing the function of Singularity...
Checking singularity with cmd: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 = 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.18605019._038947.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 04:23:48,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 04:23:48,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-09 04:23:48,524 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4437694891
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18605019
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 20297 s
2019-08-09 04:23:48,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 20974
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 20974
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4437694891 has completed
2019-08-09 04:23:48,526 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 04:23:48,534 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4437694891
2019-08-09 04:23:49,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [20974]
2019-08-09 04:23:49,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 20974
2019-08-09 04:23:49,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 04:23:50,545 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 04:23:50,545 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=20974
2019-08-09 04:23:50,601 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [20974] (in reverse order)
2019-08-09 04:23:50,643 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 04:23:50,643 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 04:23:50,644 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 04:23:50,644 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-09 04:23:51,155 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 04:24:01,205 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 04:24:01,205 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-09 04:24:01,246 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34531704832 B)
2019-08-09 04:24:01,247 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-09 04:24:01,247 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 04:24:01,375 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-09 04:24:01,375 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(job, started 139731473192704)>, <ExcThread(validate_pre, started 139730838607616)>, <ExcThread(validate_post, started 139730821822208)>, <ExcThread(queue_monitor, started 139730813429504)>, <ExcThread(create_data_payload, started 139731367085824)>, <ExcThread(execute_payloads, started 139730318522112)>, <ExcThread(failed_post, started 139730805036800)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(copytool_in, started 139730847000320)>, <ExcThread(data, started 139731383871232)>, <ExcThread(validate, started 139731392263936)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(payload, started 139731350300416)>, <ExcThread(monitor, started 139731341907712)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:01,449 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 04:24:01,788 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 04:24:01,789 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 04:24:01,792 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 04:24:01,792 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 04:24:01,793 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 04:24:01,793 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 04:24:01,853 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 04:24:01,878 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-09 04:24:01,878 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(validate_pre, started 139730838607616)>, <ExcThread(queue_monitor, started 139730813429504)>, <ExcThread(create_data_payload, started 139731367085824)>, <ExcThread(execute_payloads, started 139730318522112)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(copytool_in, started 139730847000320)>, <ExcThread(validate, started 139731392263936)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(monitor, started 139731341907712)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:01,881 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 04:24:01,938 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 04:24:01,986 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 04:24:02,064 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 04:24:02,079 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 04:24:02,079 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(queue_monitor, started 139730813429504)>, <ExcThread(create_data_payload, started 139731367085824)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(monitor, started 139731341907712)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:02,122 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 04:24:02,140 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 04:24:02,180 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-09 04:24:02,181 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(queue_monitor, started 139730813429504)>, <ExcThread(create_data_payload, started 139731367085824)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:02,313 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 04:24:02,383 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 04:24:02,383 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(queue_monitor, started 139730813429504)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:02,522 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 04:24:02,998 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 04:24:02,999 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 04:24:03,088 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-09 04:24:03,089 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(copytool_out, started 139731375478528)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:03,141 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 04:24:03,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 04:24:03,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(job_monitor, started 139730830214912)>, <ExcThread(queue_monitoring, started 139731358693120)>]
2019-08-09 04:24:05,524 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 04:24:05,608 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 04:24:05,609 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139731689465600)>, <ExcThread(job_monitor, started 139730830214912)>]
2019-08-09 04:24:47,743 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-09 04:24:47,743 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 04:24:47,817 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 04:24:47,818 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 04:24:47,818 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 04:24:48 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 04:24:48 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 04:24:48 UTC [wrapper] Pilot exit status: 0
2019-08-09 04:24:48 UTC [wrapper] STATUSCODE: 0
2019-08-09 04:24:48 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  9 04:49 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

2019-08-09 04:24:48 UTC [wrapper] Test setup, not cleaning
2019-08-09 04:24:48 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 04:24:48 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5718.52s
KernelTime=209.00s
UserTime=20196.70s
CPUUsage=356%
MaxResidentMemory=1944440kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=262029
MinorPageFaults=12429781
Swaps=0
ForcedSwitches=2358120
WaitSwitches=4990254
Inputs=63823000
Outputs=494656
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 381684
drwxrwx--x. 7 grid grid      4096 Aug  9 06:24 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug  9 06:24 80lLDmuT0FvnShfckohDCDFpABFKDmABFKDmGnTXDmABFKDmkzok2m.diag
-rw-------. 1 grid grid   7409227 Aug  9 04:49 agis_ddmendpoints.json
-rw-------. 1 grid grid   4533755 Aug  9 04:49 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  9 04:49 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  9 04:49 APPS
drwxr-xr-x. 2 grid grid         6 Aug  9 04:49 .arc
-rw-------. 1 grid grid       538 Aug  9 04:49 .asetup
-rw-------. 1 grid grid       826 Aug  9 04:50 .asetup.save
-rw-r--r--. 1 grid grid         0 Aug  9 04:49 boinc_lockfile
-rw-r--r--. 1 grid grid      8192 Aug  9 06:24 boinc_mmap_file
-rw-r--r--. 1 grid grid       536 Aug  9 06:17 boinc_task_state.xml
-rw-r--r--. 1 grid grid 376976526 Aug  9 04:49 EVNT.17323843._000781.pool.root.1
-rw-------. 1 grid grid     50622 Aug  9 06:23 heartbeat.json
-rw-r--r--. 1 grid grid      5857 Aug  9 04:49 init_data.xml
-rw-r--r--. 1 grid grid    262333 Aug  9 04:49 input.tar.gz
-rw-r--r--. 1 grid grid       112 Aug  9 04:49 job.xml
-rw-------. 1 grid grid    377068 Aug  9 06:24 log.18605019._038947.job.log.1
-rw-------. 1 grid grid    808632 Aug  9 06:23 log.18605019._038947.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug  9 06:24 output.list
-rw-------. 1 grid grid      2886 Aug  8 18:30 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  8 18:30 pilot2.tar.gz
-rw-------. 1 grid grid     10273 Aug  9 06:24 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  8 18:30 queuedata.json
-rw-r--r--. 1 grid grid       815 Aug  9 04:49 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  9 04:49 run_atlas
-rwx------. 1 grid grid     15232 Aug  8 18:30 runpilot2-wrapper.sh
-rw-r--r--. 1 grid grid       692 Aug  9 06:24 runtime_log
-rw-r--r--. 1 grid grid      6807 Aug  9 06:24 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug  9 06:24 shared
-rw-r--r--. 1 grid grid      8688 Aug  9 04:49 start_atlas.sh
-rw-r--r--. 1 grid grid     18270 Aug  9 06:24 stderr.txt
-rw-r--r--. 1 grid grid       107 Aug  9 04:49 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 grid grid        27 Aug  9 06:24 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
06:24:48 (14303): run_atlas exited; CPU time 20197.099515
06:24:48 (14303): called boinc_finish(0)

</stderr_txt>
]]>

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