Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
03:54:12 (16699): wrapper (7.7.26015): starting
03:54:12 (16699): 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._017171.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-12 06:14:11,829 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-12 06:14:11,829 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 59665 s
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 23372
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 23372
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 06:14:11,830 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 06:14:11,831 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443045815 has completed
2019-08-12 06:14:11,831 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-12 06:14:11,838 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443045815
2019-08-12 06:14:12,842 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [23372]
2019-08-12 06:14:12,843 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 23372
2019-08-12 06:14:12,843 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-12 06:14:13,847 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-12 06:14:13,848 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=23372
2019-08-12 06:14:13,902 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [23372] (in reverse order)
2019-08-12 06:14:13,949 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-12 06:14:13,950 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-12 06:14:13,950 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-12 06:14:13,950 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-12 06:14:14,462 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-12 06:14:24,494 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-12 06:14:24,495 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-12 06:14:24,504 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-12 06:14:24,540 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35422994432 B)
2019-08-12 06:14:24,540 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-12 06:14:24,540 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-12 06:14:24,823 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-12 06:14:24,843 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-12 06:14:24,884 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-12 06:14:24,895 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-12 06:14:24,897 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-12 06:14:24,898 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(job, started 140597113280256)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(copytool_out, started 140597004322560)>, <ExcThread(validate_post, started 140596459058944)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(copytool_in, started 140596475844352)>, <ExcThread(failed_post, started 140596450666240)>, <ExcThread(data, started 140597021107968)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>, <ExcThread(payload, started 140597012715264)>]
2019-08-12 06:14:24,998 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-12 06:14:24,998 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-12 06:14:25,008 | WARNING  | job_monitor         | pilot.util.common                | should_abort              | job:job_monitor:received graceful stop - abort after this iteration
2019-08-12 06:14:25,075 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-12 06:14:25,199 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-12 06:14:25,200 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(copytool_out, started 140597004322560)>, <ExcThread(validate_post, started 140596459058944)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(failed_post, started 140596450666240)>, <ExcThread(data, started 140597021107968)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>, <ExcThread(payload, started 140597012715264)>]
2019-08-12 06:14:25,292 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-12 06:14:25,292 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-12 06:14:25,401 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-12 06:14:25,401 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(copytool_out, started 140597004322560)>, <ExcThread(validate_post, started 140596459058944)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(failed_post, started 140596450666240)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>, <ExcThread(payload, started 140597012715264)>]
2019-08-12 06:14:25,401 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-12 06:14:25,419 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-12 06:14:25,602 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-12 06:14:25,603 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(copytool_out, started 140597004322560)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>, <ExcThread(payload, started 140597012715264)>]
2019-08-12 06:14:25,770 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-12 06:14:25,770 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-12 06:14:25,804 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-12 06:14:25,804 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(copytool_out, started 140597004322560)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>]
2019-08-12 06:14:25,844 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-12 06:14:25,905 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-12 06:14:25,906 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(create_data_payload, started 140596995929856)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(execute_payloads, started 140596442273536)>, <ExcThread(queue_monitoring, started 140596987537152)>]
2019-08-12 06:14:25,912 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-12 06:14:25,940 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-12 06:14:26,007 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-12 06:14:26,007 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(queue_monitor, started 140595955758848)>, <ExcThread(queue_monitoring, started 140596987537152)>]
2019-08-12 06:14:26,035 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-12 06:14:26,323 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-12 06:14:26,323 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-12 06:14:26,410 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-12 06:14:26,410 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(job_monitor, started 140596467451648)>, <ExcThread(queue_monitoring, started 140596987537152)>]
2019-08-12 06:14:29,036 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-12 06:14:29,129 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-12 06:14:29,129 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597329553152)>, <ExcThread(job_monitor, started 140596467451648)>]
2019-08-12 06:15:25,035 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-12 06:15:25,035 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-12 06:15:25,122 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-12 06:15:25,122 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-12 06:15:25,123 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-12 06:15:25 UTC [wrapper] ==== pilot stdout END ====
2019-08-12 06:15:25 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-12 06:15:25 UTC [wrapper] Pilot exit status: 0
2019-08-12 06:15:25 UTC [wrapper] STATUSCODE: 0
2019-08-12 06:15:25 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 12 03:54 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

2019-08-12 06:15:25 UTC [wrapper] Test setup, not cleaning
2019-08-12 06:15:25 UTC [wrapper] ==== wrapper stdout END ====
2019-08-12 06:15:25 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15670.41s
KernelTime=439.39s
UserTime=59416.00s
CPUUsage=381%
MaxResidentMemory=1945288kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=458466
MinorPageFaults=18979508
Swaps=0
ForcedSwitches=6945833
WaitSwitches=9555123
Inputs=110556224
Outputs=979128
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 285768
drwxrwx--x. 7 grid grid      4096 Aug 12 08:15 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 12 03:54 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506574 Aug 12 03:54 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 12 03:54 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 12 03:54 APPS
drwxr-xr-x. 2 grid grid         6 Aug 12 03:54 .arc
-rw-------. 1 grid grid       538 Aug 12 03:54 .asetup
-rw-------. 1 grid grid       826 Aug 12 03:55 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 12 03:54 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 08:14 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 12 08:07 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 278308306 Aug 12 03:54 EVNT.18605754._000333.pool.root.1
-rw-------. 1 grid grid     96865 Aug 12 08:14 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 12 03:54 init_data.xml
-rw-rw-r--. 1 grid grid    262340 Aug 12 03:54 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 12 03:54 job.xml
-rw-------. 1 grid grid       518 Aug 12 08:15 kMGMDmG4yGvnShfckohDCDFpABFKDmABFKDmVO8YDmABFKDmwxpVUm.diag
-rw-------. 1 grid grid    768993 Aug 12 08:15 log.18722298._017171.job.log.1
-rw-------. 1 grid grid    850692 Aug 12 08:14 log.18722298._017171.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 12 08:15 output.list
-rw-------. 1 grid grid      2915 Aug 11 11:11 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 10:24 pilot2.tar.gz
-rw-------. 1 grid grid     11488 Aug 12 08:15 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 11:10 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 12 03:54 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 12 03:54 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 11:11 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 08:15 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 08:15 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 08:15 shared
-rw-rw-r--. 1 grid grid      8688 Aug 12 03:54 start_atlas.sh
-rw-rw-r--. 1 grid grid     19046 Aug 12 08:15 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 12 03:54 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 12 08:14 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
08:15:26 (16699): run_atlas exited; CPU time 59416.376547
08:15:26 (16699): called boinc_finish(0)

</stderr_txt>
]]>

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