Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
20:32:16 (19419): wrapper (7.7.26015): starting
20:32:16 (19419): 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._016623.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-11 22:56:05,801 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 22:56:05,801 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-11 22:56:05,801 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 22:56:05,801 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4443004775
2019-08-11 22:56:05,801 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 60437 s
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 26089
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 26089
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-11 22:56:05,802 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-11 22:56:05,803 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-11 22:56:05,803 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-11 22:56:05,803 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443004775 has completed
2019-08-11 22:56:05,803 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-11 22:56:05,810 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443004775
2019-08-11 22:56:06,815 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [26089]
2019-08-11 22:56:06,816 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 26089
2019-08-11 22:56:06,816 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-11 22:56:07,817 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-11 22:56:07,818 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=26089
2019-08-11 22:56:07,885 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [26089] (in reverse order)
2019-08-11 22:56:07,930 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-11 22:56:07,931 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-11 22:56:07,931 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-11 22:56:07,931 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-11 22:56:08,444 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-11 22:56:18,491 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-11 22:56:18,491 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-11 22:56:18,539 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36045848576 B)
2019-08-11 22:56:18,539 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-11 22:56:18,539 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-11 22:56:18,541 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-11 22:56:18,650 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-11 22:56:18,661 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-11 22:56:18,783 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-11 22:56:18,820 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-11 22:56:18,820 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-11 22:56:18,922 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-11 22:56:18,923 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(job, started 140079786616576)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(failed_post, started 140078982608640)>, <ExcThread(validate, started 140079778223872)>, <ExcThread(copytool_out, started 140079544657664)>, <ExcThread(validate_pre, started 140079016179456)>, <ExcThread(execute_payloads, started 140078974215936)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(payload, started 140079536264960)>, <ExcThread(create_data_payload, started 140079553050368)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:18,930 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-11 22:56:19,036 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-11 22:56:19,036 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-11 22:56:19,054 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-11 22:56:19,054 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-11 22:56:19,056 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-11 22:56:19,056 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(validate, started 140079778223872)>, <ExcThread(copytool_out, started 140079544657664)>, <ExcThread(validate_pre, started 140079016179456)>, <ExcThread(execute_payloads, started 140078974215936)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(create_data_payload, started 140079553050368)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:19,210 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-11 22:56:19,258 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-11 22:56:19,258 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(copytool_out, started 140079544657664)>, <ExcThread(validate_pre, started 140079016179456)>, <ExcThread(execute_payloads, started 140078974215936)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(create_data_payload, started 140079553050368)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:19,460 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-11 22:56:19,542 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-11 22:56:19,561 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-11 22:56:19,561 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(validate_pre, started 140079016179456)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(create_data_payload, started 140079553050368)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:19,614 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-11 22:56:19,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-11 22:56:19,663 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(validate_pre, started 140079016179456)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:19,770 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-11 22:56:19,865 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-11 22:56:19,865 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(queue_monitor, started 140079007786752)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:20,296 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-11 22:56:20,296 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-11 22:56:20,339 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-11 22:56:20,369 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-11 22:56:20,370 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(queue_monitoring, started 140079519479552)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:56:23,340 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-11 22:56:23,395 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-11 22:56:23,395 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140080002889472)>, <ExcThread(job_monitor, started 140079511086848)>]
2019-08-11 22:57:03,963 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-11 22:57:03,963 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-11 22:57:04,019 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-11 22:57:04,019 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-11 22:57:04,020 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-11 22:57:04 UTC [wrapper] ==== pilot stdout END ====
2019-08-11 22:57:04 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-11 22:57:04 UTC [wrapper] Pilot exit status: 0
2019-08-11 22:57:04 UTC [wrapper] STATUSCODE: 0
2019-08-11 22:57:04 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 11 20:32 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

2019-08-11 22:57:04 UTC [wrapper] Test setup, not cleaning
2019-08-11 22:57:04 UTC [wrapper] ==== wrapper stdout END ====
2019-08-11 22:57:04 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=15885.47s
KernelTime=450.76s
UserTime=60194.67s
CPUUsage=381%
MaxResidentMemory=1944660kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=460724
MinorPageFaults=18971587
Swaps=0
ForcedSwitches=6985090
WaitSwitches=9684884
Inputs=111157416
Outputs=987824
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 286708
drwxrwx--x. 7 grid grid      4096 Aug 12 00:57 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 11 20:32 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506392 Aug 11 20:32 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 11 20:32 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 11 20:32 APPS
drwxr-xr-x. 2 grid grid         6 Aug 11 20:32 .arc
-rw-------. 1 grid grid       538 Aug 11 20:32 .asetup
-rw-------. 1 grid grid       826 Aug 11 20:33 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 11 20:32 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 00:57 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 12 00:48 boinc_task_state.xml
-rw-------. 1 grid grid       518 Aug 12 00:57 cDuNDmVQwGvnShfckohDCDFpABFKDmABFKDmwC4YDmABFKDmdnDo2m.diag
-rw-rw-r--. 1 grid grid 279302079 Aug 11 20:32 EVNT.18605754._000322.pool.root.1
-rw-------. 1 grid grid     78535 Aug 12 00:56 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 11 20:32 init_data.xml
-rw-rw-r--. 1 grid grid    262345 Aug 11 20:32 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 11 20:32 job.xml
-rw-------. 1 grid grid    756862 Aug 12 00:57 log.18722298._016623.job.log.1
-rw-------. 1 grid grid    848540 Aug 12 00:55 log.18722298._016623.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 12 00:57 output.list
-rw-------. 1 grid grid      2915 Aug 11 08:22 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 07:37 pilot2.tar.gz
-rw-------. 1 grid grid     10041 Aug 12 00:57 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 08:21 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 11 20:32 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 11 20:32 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 08:22 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 00:57 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 00:57 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 00:57 shared
-rw-rw-r--. 1 grid grid      8688 Aug 11 20:32 start_atlas.sh
-rw-rw-r--. 1 grid grid     18183 Aug 12 00:57 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 11 20:32 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 12 00:57 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
00:57:04 (19419): run_atlas exited; CPU time 60195.060607
00:57:04 (19419): called boinc_finish(0)

</stderr_txt>
]]>

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