Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
16:03:53 (2331): wrapper (7.7.26015): starting
16:03:53 (2331): 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.18722495._006931.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 18:26:29,344 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 18:26:29,344 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4441807383
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722495
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 59947 s
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 18:26:29,345 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 9028
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 9028
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441807383 has completed
2019-08-09 18:26:29,346 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 18:26:29,357 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4441807383
2019-08-09 18:26:30,361 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [9028]
2019-08-09 18:26:30,361 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 9028
2019-08-09 18:26:30,361 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 18:26:31,366 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 18:26:31,367 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=9028
2019-08-09 18:26:31,416 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [9028] (in reverse order)
2019-08-09 18:26:31,456 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 18:26:31,457 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 18:26:31,457 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 18:26:31,457 | 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 18:26:31,966 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 18:26:42,006 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 18:26:42,006 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-09 18:26:42,035 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35929456640 B)
2019-08-09 18:26:42,036 | 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 18:26:42,036 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 18:26:42,042 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 18:26:42,086 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 18:26:42,122 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 18:26:42,122 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 18:26:42,279 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-09 18:26:42,279 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job, started 140172160653056)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(execute_payloads, started 140171483801344)>, <ExcThread(copytool_in, started 140171609626368)>, <ExcThread(create_data_payload, started 140172135474944)>, <ExcThread(validate_pre, started 140171492194048)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(validate_post, started 140171601233664)>, <ExcThread(failed_post, started 140171584448256)>, <ExcThread(copytool_out, started 140172118689536)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>, <ExcThread(payload, started 140172127082240)>]
2019-08-09 18:26:42,465 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 18:26:42,466 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 18:26:42,480 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-09 18:26:42,481 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job, started 140172160653056)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(execute_payloads, started 140171483801344)>, <ExcThread(copytool_in, started 140171609626368)>, <ExcThread(create_data_payload, started 140172135474944)>, <ExcThread(validate_pre, started 140171492194048)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(validate_post, started 140171601233664)>, <ExcThread(failed_post, started 140171584448256)>, <ExcThread(copytool_out, started 140172118689536)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:42,677 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 18:26:42,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-09 18:26:42,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job, started 140172160653056)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(execute_payloads, started 140171483801344)>, <ExcThread(copytool_in, started 140171609626368)>, <ExcThread(validate_pre, started 140171492194048)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(validate_post, started 140171601233664)>, <ExcThread(failed_post, started 140171584448256)>, <ExcThread(copytool_out, started 140172118689536)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:42,707 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 18:26:42,717 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 18:26:42,826 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 18:26:42,827 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 18:26:42,839 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 18:26:42,847 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-09 18:26:42,847 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(execute_payloads, started 140171483801344)>, <ExcThread(copytool_in, started 140171609626368)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(copytool_out, started 140172118689536)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:43,087 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 18:26:43,149 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 18:26:43,150 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(execute_payloads, started 140171483801344)>, <ExcThread(copytool_in, started 140171609626368)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:43,270 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 18:26:43,340 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 18:26:43,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 18:26:43,352 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(validate, started 140172152260352)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:43,539 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 18:26:43,553 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-09 18:26:43,553 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(queue_monitoring, started 140171618019072)>, <ExcThread(queue_monitor, started 140171576055552)>]
2019-08-09 18:26:43,850 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 18:26:43,850 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 18:26:43,856 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 18:26:43,856 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job_monitor, started 140171592840960)>, <ExcThread(queue_monitoring, started 140171618019072)>]
2019-08-09 18:26:43,867 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 18:26:46,868 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 18:26:46,880 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 18:26:46,880 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140172376925952)>, <ExcThread(job_monitor, started 140171592840960)>]
2019-08-09 18:27:09,653 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-09 18:27:09,654 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 18:27:09,754 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 18:27:09,755 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 18:27:09,755 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 18:27:09 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 18:27:09 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 18:27:09 UTC [wrapper] Pilot exit status: 0
2019-08-09 18:27:09 UTC [wrapper] STATUSCODE: 0
2019-08-09 18:27:09 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  9 16:04 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 18:27:10 UTC [wrapper] Test setup, not cleaning
2019-08-09 18:27:10 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 18:27:10 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15794.00s
KernelTime=445.66s
UserTime=59705.01s
CPUUsage=380%
MaxResidentMemory=1945264kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=458918
MinorPageFaults=18925162
Swaps=0
ForcedSwitches=6955952
WaitSwitches=9724727
Inputs=110857296
Outputs=963672
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 247576
drwxrwx--x. 7 grid grid      4096 Aug  9 20:27 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409227 Aug  9 16:04 agis_ddmendpoints.json
-rw-------. 1 grid grid   4507257 Aug  9 16:04 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  9 16:03 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  9 16:03 APPS
drwxr-xr-x. 2 grid grid         6 Aug  9 16:04 .arc
-rw-------. 1 grid grid       538 Aug  9 16:03 .asetup
-rw-------. 1 grid grid       826 Aug  9 16:05 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug  9 16:03 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug  9 20:27 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug  9 20:18 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 239249415 Aug  9 16:03 EVNT.18605790._000135.pool.root.1
-rw-------. 1 grid grid     71974 Aug  9 20:26 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug  9 16:03 init_data.xml
-rw-rw-r--. 1 grid grid    262338 Aug  9 16:03 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug  9 16:03 job.xml
-rw-------. 1 grid grid    748931 Aug  9 20:27 log.18722495._006931.job.log.1
-rw-------. 1 grid grid    847231 Aug  9 20:26 log.18722495._006931.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug  9 20:27 output.list
-rw-------. 1 grid grid      2948 Aug  9 09:17 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 08:24 pilot2.tar.gz
-rw-------. 1 grid grid     11277 Aug  9 20:27 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 09:17 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug  9 16:03 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  9 16:03 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 09:17 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug  9 20:27 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug  9 20:27 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug  9 20:27 shared
-rw-rw-r--. 1 grid grid      8688 Aug  9 16:03 start_atlas.sh
-rw-rw-r--. 1 grid grid     19147 Aug  9 20:27 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug  9 16:03 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug  9 20:27 wrapper_checkpoint.txt
-rw-------. 1 grid grid       518 Aug  9 20:27 YiKNDmMKEGvnShfckohDCDFpABFKDmABFKDmYKsXDmABFKDmg8Q8Hm.diag

running start_atlas return value is 0
Parent exit 0
child process exit 0
20:27:11 (2331): run_atlas exited; CPU time 59705.396411
20:27:11 (2331): called boinc_finish(0)

</stderr_txt>
]]>

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