Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
17:16:09 (10286): wrapper (7.7.26015): starting
17:16:09 (10286): 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 grep: pandaJobData.out: No such file or directory
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.18722298._014046.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 19:40:24,941 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442733335
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 19:40:24,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 60212 s
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 16978
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 16978
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442733335 has completed
2019-08-10 19:40:24,943 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 19:40:24,953 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442733335
2019-08-10 19:40:25,957 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [16978]
2019-08-10 19:40:25,958 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 16978
2019-08-10 19:40:25,958 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 19:40:26,963 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 19:40:26,963 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=16978
2019-08-10 19:40:27,021 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [16978] (in reverse order)
2019-08-10 19:40:27,069 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 19:40:27,069 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 19:40:27,069 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 19:40:27,070 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-10 19:40:27,583 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 19:40:37,632 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 19:40:37,632 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 19:40:37,674 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36010196992 B)
2019-08-10 19:40:37,675 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-10 19:40:37,675 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 19:40:37,698 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 19:40:37,742 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-10 19:40:37,742 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job, started 140419935213312)>, <ExcThread(failed_post, started 140419350374144)>, <ExcThread(validate_pre, started 140419884857088)>, <ExcThread(create_data_payload, started 140419893249792)>, <ExcThread(queue_monitor, started 140419341981440)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>, <ExcThread(payload, started 140419910035200)>, <ExcThread(validate_post, started 140419367159552)>, <ExcThread(data, started 140419926820608)>, <ExcThread(execute_payloads, started 140418855466752)>, <ExcThread(copytool_in, started 140419375552256)>, <ExcThread(validate, started 140419918427904)>]
2019-08-10 19:40:37,780 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 19:40:38,145 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-10 19:40:38,145 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job, started 140419935213312)>, <ExcThread(failed_post, started 140419350374144)>, <ExcThread(validate_pre, started 140419884857088)>, <ExcThread(create_data_payload, started 140419893249792)>, <ExcThread(queue_monitor, started 140419341981440)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>, <ExcThread(payload, started 140419910035200)>, <ExcThread(validate_post, started 140419367159552)>, <ExcThread(data, started 140419926820608)>, <ExcThread(execute_payloads, started 140418855466752)>, <ExcThread(validate, started 140419918427904)>]
2019-08-10 19:40:38,360 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 19:40:38,431 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 19:40:38,436 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 19:40:38,438 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 19:40:38,444 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 19:40:38,445 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 19:40:38,519 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 19:40:38,520 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 19:40:38,547 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-10 19:40:38,548 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job, started 140419935213312)>, <ExcThread(validate_pre, started 140419884857088)>, <ExcThread(queue_monitor, started 140419341981440)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>, <ExcThread(validate_post, started 140419367159552)>]
2019-08-10 19:40:38,660 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 19:40:38,660 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 19:40:38,665 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 19:40:38,665 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(validate_pre, started 140419884857088)>, <ExcThread(queue_monitor, started 140419341981440)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>, <ExcThread(validate_post, started 140419367159552)>]
2019-08-10 19:40:38,894 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 19:40:38,998 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 19:40:39,103 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 19:40:39,139 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 19:40:39,169 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-10 19:40:39,170 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(queue_monitor, started 140419341981440)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>]
2019-08-10 19:40:39,363 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 19:40:39,364 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 19:40:39,372 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 19:40:39,372 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(copytool_out, started 140419901642496)>, <ExcThread(queue_monitoring, started 140419383944960)>]
2019-08-10 19:40:39,999 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 19:40:40,077 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 19:40:40,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job_monitor, started 140419358766848)>, <ExcThread(queue_monitoring, started 140419383944960)>]
2019-08-10 19:40:41,895 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 19:40:41,992 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 19:40:41,993 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140420151486208)>, <ExcThread(job_monitor, started 140419358766848)>]
2019-08-10 19:41:09,336 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 19:41:09,336 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 19:41:09,402 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 19:41:09,403 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 19:41:09,403 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 19:41:09 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 19:41:09 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 19:41:09 UTC [wrapper] Pilot exit status: 0
2019-08-10 19:41:09 UTC [wrapper] STATUSCODE: 0
2019-08-10 19:41:09 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 10 17:16 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

2019-08-10 19:41:09 UTC [wrapper] Test setup, not cleaning
2019-08-10 19:41:09 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 19:41:09 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15897.55s
KernelTime=449.22s
UserTime=59964.55s
CPUUsage=380%
MaxResidentMemory=1945196kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=459843
MinorPageFaults=18929140
Swaps=0
ForcedSwitches=6950309
WaitSwitches=9634932
Inputs=111316072
Outputs=979040
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 285300
drwxrwx--x. 7 grid grid      4096 Aug 10 21:41 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 10 17:16 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506428 Aug 10 17:16 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 17:16 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 17:16 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 17:16 .arc
-rw-------. 1 grid grid       538 Aug 10 17:16 .asetup
-rw-------. 1 grid grid       826 Aug 10 17:17 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 10 17:16 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 21:41 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 10 21:31 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 277831214 Aug 10 17:16 EVNT.18605754._000271.pool.root.1
-rw-------. 1 grid grid     92455 Aug 10 21:40 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 17:16 init_data.xml
-rw-rw-r--. 1 grid grid    262336 Aug 10 17:16 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 17:16 job.xml
-rw-------. 1 grid grid    770679 Aug 10 21:41 log.18722298._014046.job.log.1
-rw-------. 1 grid grid    851494 Aug 10 21:40 log.18722298._014046.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 21:41 output.list
-rw-------. 1 grid grid      2915 Aug 10 08:15 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 07:29 pilot2.tar.gz
-rw-------. 1 grid grid     10454 Aug 10 21:41 pilotlog.txt
-rw-------. 1 grid grid       518 Aug 10 21:41 pZALDmfqZGvnShfckohDCDFpABFKDmABFKDmtwSYDmABFKDmtFzlbm.diag
-rw-r--r--. 1 grid grid      4468 Aug 10 08:15 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 17:16 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 17:16 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 08:15 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 21:41 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 21:41 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 21:41 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 17:16 start_atlas.sh
-rw-rw-r--. 1 grid grid     18596 Aug 10 21:41 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 17:16 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 10 21:41 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
21:41:10 (10286): run_atlas exited; CPU time 59964.954636
21:41:10 (10286): called boinc_finish(0)

</stderr_txt>
]]>

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