Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
11:52:13 (4765): wrapper (7.7.26015): starting
11:52:13 (4765): 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=4445902326
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.18722183._012878.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 30725 s
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-15 12:10:08,199 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 11519
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 11519
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4445902326 has completed
2019-08-15 12:10:08,200 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-15 12:10:08,210 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4445902326
2019-08-15 12:10:08,353 | INFO     | monitor             | pilot.control.monitor            | control                   | 8248 s have passed since pilot start
2019-08-15 12:10:09,215 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11519]
2019-08-15 12:10:09,216 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11519
2019-08-15 12:10:09,216 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-15 12:10:10,221 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-15 12:10:10,221 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11519
2019-08-15 12:10:10,268 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11519] (in reverse order)
2019-08-15 12:10:10,304 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-15 12:10:10,304 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-15 12:10:10,305 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-15 12:10:10,305 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-15 12:10:10,813 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-15 12:10:20,853 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-15 12:10:20,853 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-15 12:10:20,896 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36225155072 B)
2019-08-15 12:10:20,896 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-15 12:10:20,896 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-15 12:10:21,114 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-15 12:10:21,114 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-15 12:10:21,186 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-15 12:10:21,186 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(job, started 140402940040960)>, <ExcThread(data, started 140402923255552)>, <ExcThread(validate, started 140402931648256)>, <ExcThread(copytool_in, started 140402531227392)>, <ExcThread(validate_pre, started 140402522834688)>, <ExcThread(validate_post, started 140401944033024)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(monitor, started 140402514441984)>, <ExcThread(failed_post, started 140401935640320)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(execute_payloads, started 140401927247616)>, <ExcThread(create_data_payload, started 140402914862848)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:21,218 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-15 12:10:21,222 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-15 12:10:21,316 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-15 12:10:21,316 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-15 12:10:21,387 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-15 12:10:21,388 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-15 12:10:21,408 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-15 12:10:21,408 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-15 12:10:21,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-15 12:10:21,420 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(validate, started 140402931648256)>, <ExcThread(validate_post, started 140401944033024)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(failed_post, started 140401935640320)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(execute_payloads, started 140401927247616)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:21,480 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-15 12:10:21,582 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-15 12:10:21,621 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-15 12:10:21,622 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(validate, started 140402931648256)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(failed_post, started 140401935640320)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(execute_payloads, started 140401927247616)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:21,731 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-15 12:10:21,823 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-15 12:10:21,824 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(failed_post, started 140401935640320)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(execute_payloads, started 140401927247616)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:22,118 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-15 12:10:22,126 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-15 12:10:22,126 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(execute_payloads, started 140401927247616)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:22,152 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-15 12:10:22,227 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-15 12:10:22,227 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(queue_monitor, started 140402497656576)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:22,417 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-15 12:10:22,417 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-15 12:10:22,429 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-15 12:10:22,429 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(job_monitor, started 140402506049280)>, <ExcThread(copytool_out, started 140402898077440)>]
2019-08-15 12:10:22,436 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-15 12:10:22,481 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-15 12:10:22,530 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-15 12:10:22,531 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(queue_monitoring, started 140402548012800)>, <ExcThread(job_monitor, started 140402506049280)>]
2019-08-15 12:10:25,437 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-15 12:10:25,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-15 12:10:25,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140403156313856)>, <ExcThread(job_monitor, started 140402506049280)>]
2019-08-15 12:10:51,862 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-15 12:10:51,863 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-15 12:10:51,941 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-15 12:10:51,942 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-15 12:10:51,942 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-15 12:10:52 UTC [wrapper] ==== pilot stdout END ====
2019-08-15 12:10:52 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-15 12:10:52 UTC [wrapper] Pilot exit status: 0
2019-08-15 12:10:52 UTC [wrapper] STATUSCODE: 0
2019-08-15 12:10:52 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 15 11:52 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

2019-08-15 12:10:52 UTC [wrapper] Test setup, not cleaning
2019-08-15 12:10:52 UTC [wrapper] ==== wrapper stdout END ====
2019-08-15 12:10:52 UTC [wrapper] ==== wrapper stderr END ====
2019-08-15 12:10:52 UTC [wrapper] wrapper wrapperexiting ec=0, duration=8315
2019-08-15 12:10:52 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8315.30s
KernelTime=251.85s
UserTime=30607.95s
CPUUsage=371%
MaxResidentMemory=1945296kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=313995
MinorPageFaults=14171355
Swaps=0
ForcedSwitches=3561812
WaitSwitches=6378363
Inputs=76573656
Outputs=628208
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 251248
drwxrwx--x. 6 grid grid      4096 Aug 15 14:10 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409162 Aug 15 11:52 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438522 Aug 15 11:52 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 11:52 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 11:52 APPS
-rw-------. 1 grid grid       538 Aug 15 11:52 .asetup
-rw-------. 1 grid grid       826 Aug 15 11:53 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 11:52 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 15 14:10 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 15 14:04 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 243346763 Aug 15 11:52 EVNT.18605745._000279.pool.root.1
-rw-------. 1 grid grid     79196 Aug 15 14:10 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 11:52 init_data.xml
-rw-rw-r--. 1 grid grid    261620 Aug 15 11:52 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 11:52 job.xml
-rw-------. 1 grid grid    493846 Aug 15 14:10 log.18722183._012878.job.log.1
-rw-------. 1 grid grid    830128 Aug 15 14:09 log.18722183._012878.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 15 14:10 output.list
-rw-------. 1 grid grid      2921 Aug 14 19:04 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 14 18:26 pilot2.tar.gz
-rw-------. 1 grid grid     10823 Aug 15 14:10 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 14 19:02 queuedata.json
-rw-------. 1 grid grid       516 Aug 15 14:10 qzULDmEsBIvnShfckohDCDFpABFKDmABFKDmPA5aDmABFKDm7WmQem.diag
-rw-rw-r--. 1 grid grid       815 Aug 15 11:52 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 11:52 run_atlas
-rwx------. 1 grid grid     12641 Aug 14 19:04 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 15 14:10 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 15 14:10 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 15 14:10 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 11:52 start_atlas.sh
-rw-rw-r--. 1 grid grid     18498 Aug 15 14:10 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 11:52 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 15 14:10 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
14:10:52 (4765): run_atlas exited; CPU time 30608.339814
14:10:52 (4765): called boinc_finish(0)

</stderr_txt>
]]>

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