Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
03:40:07 (883): wrapper (7.7.26015): starting
03:40:07 (883): 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=4449569756
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._051487.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 03:40:33,711 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 03:40:33,711 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4449569756
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 26677 s
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7645
2019-08-16 03:40:33,712 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7645
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4449569756 has completed
2019-08-16 03:40:33,713 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 03:40:33,720 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4449569756
2019-08-16 03:40:34,725 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7645]
2019-08-16 03:40:34,726 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7645
2019-08-16 03:40:34,726 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 03:40:35,731 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 03:40:35,731 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7645
2019-08-16 03:40:35,791 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7645] (in reverse order)
2019-08-16 03:40:35,843 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 03:40:35,843 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 03:40:35,843 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 03:40:35,843 | 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 03:40:36,354 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 03:40:46,384 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 03:40:46,385 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 03:40:46,416 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34787557376 B)
2019-08-16 03:40:46,417 | 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 03:40:46,417 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 03:40:46,418 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 03:40:46,441 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 03:40:46,446 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 03:40:46,481 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-16 03:40:46,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(job, started 140303522490112)>, <ExcThread(copytool_out, started 140303268824832)>, <ExcThread(copytool_in, started 140302748739328)>, <ExcThread(data, started 140303505704704)>, <ExcThread(validate_post, started 140302731953920)>, <ExcThread(validate, started 140303514097408)>, <ExcThread(validate_pre, started 140302757132032)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(payload, started 140303285610240)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(failed_post, started 140302723561216)>, <ExcThread(job_monitor, started 140303252039424)>, <ExcThread(execute_payloads, started 140302715168512)>, <ExcThread(create_data_payload, started 140303294002944)>]
2019-08-16 03:40:46,789 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 03:40:46,790 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 03:40:46,883 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-16 03:40:46,884 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(job, started 140303522490112)>, <ExcThread(copytool_out, started 140303268824832)>, <ExcThread(copytool_in, started 140302748739328)>, <ExcThread(validate_post, started 140302731953920)>, <ExcThread(validate, started 140303514097408)>, <ExcThread(validate_pre, started 140302757132032)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(payload, started 140303285610240)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(failed_post, started 140302723561216)>, <ExcThread(job_monitor, started 140303252039424)>, <ExcThread(execute_payloads, started 140302715168512)>, <ExcThread(create_data_payload, started 140303294002944)>]
2019-08-16 03:40:46,907 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 03:40:46,964 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 03:40:47,185 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 03:40:47,185 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(job, started 140303522490112)>, <ExcThread(copytool_out, started 140303268824832)>, <ExcThread(copytool_in, started 140302748739328)>, <ExcThread(validate_post, started 140302731953920)>, <ExcThread(validate, started 140303514097408)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(payload, started 140303285610240)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(failed_post, started 140302723561216)>, <ExcThread(job_monitor, started 140303252039424)>, <ExcThread(execute_payloads, started 140302715168512)>]
2019-08-16 03:40:47,261 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 03:40:47,412 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 03:40:47,413 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 03:40:47,419 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 03:40:47,438 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 03:40:47,438 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 03:40:47,487 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-16 03:40:47,487 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(validate, started 140303514097408)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(payload, started 140303285610240)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(job_monitor, started 140303252039424)>, <ExcThread(execute_payloads, started 140302715168512)>]
2019-08-16 03:40:47,585 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 03:40:47,585 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 03:40:47,588 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 03:40:47,588 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(validate, started 140303514097408)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(job_monitor, started 140303252039424)>, <ExcThread(execute_payloads, started 140302715168512)>]
2019-08-16 03:40:47,819 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 03:40:47,874 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 03:40:47,890 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 03:40:47,891 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(queue_monitor, started 140302740346624)>, <ExcThread(job_monitor, started 140303252039424)>]
2019-08-16 03:40:48,208 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 03:40:48,208 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 03:40:48,293 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 03:40:48,294 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(queue_monitoring, started 140303243646720)>, <ExcThread(job_monitor, started 140303252039424)>]
2019-08-16 03:40:49,447 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 03:40:49,501 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 03:40:49,502 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140303738763008)>, <ExcThread(job_monitor, started 140303252039424)>]
2019-08-16 03:41:28,101 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 03:41:28,101 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 03:41:28,172 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 03:41:28,173 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 03:41:28,173 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 03:41:28 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 03:41:28 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 03:41:28 UTC [wrapper] Pilot exit status: 0
2019-08-16 03:41:28 UTC [wrapper] STATUSCODE: 0
2019-08-16 03:41:28 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 03:40 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 03:41:28 UTC [wrapper] Test setup, not cleaning
2019-08-16 03:41:28 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 03:41:28 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 03:41:28 UTC [wrapper] wrapper wrapperexiting ec=0, duration=7278
2019-08-16 03:41:28 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7277.90s
KernelTime=220.61s
UserTime=26573.56s
CPUUsage=368%
MaxResidentMemory=1944364kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=292871
MinorPageFaults=13398199
Swaps=0
ForcedSwitches=3099057
WaitSwitches=5908107
Inputs=71198408
Outputs=495456
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 381580
drwxrwx--x. 6 grid grid      4096 Aug 16 05:41 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7413078 Aug 16 03:40 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438095 Aug 16 03:40 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 03:40 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 03:40 APPS
-rw-------. 1 grid grid       538 Aug 16 03:40 .asetup
-rw-------. 1 grid grid       826 Aug 16 03:41 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 03:40 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 05:41 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 16 05:35 boinc_task_state.xml
-rw-------. 1 grid grid       516 Aug 16 05:41 dBSLDmBlSIvnShfckohDCDFpABFKDmABFKDm0lVbDmABFKDmCUb2Tm.diag
-rw-rw-r--. 1 grid grid 376873384 Aug 16 03:40 EVNT.17323813._001003.pool.root.1
-rw-------. 1 grid grid     66991 Aug 16 05:40 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 03:40 init_data.xml
-rw-rw-r--. 1 grid grid    261619 Aug 16 03:40 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 16 03:40 job.xml
-rw-------. 1 grid grid    444531 Aug 16 05:41 log.18604976._051487.job.log.1
-rw-------. 1 grid grid    818629 Aug 16 05:40 log.18604976._051487.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 05:41 output.list
-rw-------. 1 grid grid      2872 Aug 15 13:06 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 15 12:29 pilot2.tar.gz
-rw-------. 1 grid grid     10710 Aug 16 05:41 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 15 13:00 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 03:40 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 03:40 run_atlas
-rwx------. 1 grid grid     12641 Aug 15 13:06 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 05:41 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 05:41 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 05:41 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 03:40 start_atlas.sh
-rw-rw-r--. 1 grid grid     18678 Aug 16 05:41 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 16 03:40 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 16 05:41 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
05:41:28 (883): run_atlas exited; CPU time 26573.940324
05:41:28 (883): called boinc_finish(0)

</stderr_txt>
]]>

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