Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
21:41:14 (10281): wrapper (7.7.26015): starting
21:41:14 (10281): 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.18722398._016211.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442745580
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 21:57:48,942 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 30534 s
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 16972
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 16972
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442745580 has completed
2019-08-10 21:57:48,943 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 21:57:48,950 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442745580
2019-08-10 21:57:49,955 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [16972]
2019-08-10 21:57:49,956 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 16972
2019-08-10 21:57:49,956 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 21:57:50,459 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 21:57:50,959 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 21:57:50,960 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=16972
2019-08-10 21:57:51,006 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [16972] (in reverse order)
2019-08-10 21:57:51,047 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 21:57:51,047 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 21:57:51,047 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 21:57:51,047 | 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 21:57:51,559 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 21:58:01,606 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 21:58:01,607 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-10 21:58:01,639 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36148609024 B)
2019-08-10 21:58:01,640 | 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 21:58:01,640 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 21:58:01,645 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 21:58:01,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-10 21:58:01,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job, started 139964167546624)>, <ExcThread(payload, started 139964142368512)>, <ExcThread(create_data_payload, started 139963890906880)>, <ExcThread(validate_pre, started 139963899299584)>, <ExcThread(failed_post, started 139963303712512)>, <ExcThread(data, started 139964159153920)>, <ExcThread(validate_post, started 139963874121472)>, <ExcThread(queue_monitor, started 139963286927104)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(copytool_in, started 139963882514176)>, <ExcThread(queue_monitoring, started 139963907692288)>, <ExcThread(validate, started 139964150761216)>, <ExcThread(execute_payloads, started 139963295319808)>]
2019-08-10 21:58:01,813 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 21:58:02,077 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-10 21:58:02,078 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job, started 139964167546624)>, <ExcThread(payload, started 139964142368512)>, <ExcThread(validate_pre, started 139963899299584)>, <ExcThread(failed_post, started 139963303712512)>, <ExcThread(data, started 139964159153920)>, <ExcThread(validate_post, started 139963874121472)>, <ExcThread(queue_monitor, started 139963286927104)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(copytool_in, started 139963882514176)>, <ExcThread(queue_monitoring, started 139963907692288)>, <ExcThread(validate, started 139964150761216)>, <ExcThread(execute_payloads, started 139963295319808)>]
2019-08-10 21:58:02,108 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 21:58:02,108 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 21:58:02,269 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 21:58:02,269 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 21:58:02,316 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 21:58:02,330 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 21:58:02,379 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-10 21:58:02,380 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job, started 139964167546624)>, <ExcThread(data, started 139964159153920)>, <ExcThread(queue_monitor, started 139963286927104)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(copytool_in, started 139963882514176)>, <ExcThread(queue_monitoring, started 139963907692288)>, <ExcThread(execute_payloads, started 139963295319808)>]
2019-08-10 21:58:02,389 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 21:58:02,484 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 21:58:02,570 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 21:58:02,580 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 21:58:02,581 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 21:58:02,581 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 21:58:02,581 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job, started 139964167546624)>, <ExcThread(queue_monitor, started 139963286927104)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(copytool_in, started 139963882514176)>, <ExcThread(queue_monitoring, started 139963907692288)>]
2019-08-10 21:58:02,626 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 21:58:02,663 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 21:58:02,663 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 21:58:02,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-10 21:58:02,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(queue_monitor, started 139963286927104)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(queue_monitoring, started 139963907692288)>]
2019-08-10 21:58:03,429 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 21:58:03,429 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 21:58:03,489 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 21:58:03,489 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(copytool_out, started 139963924477696)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(queue_monitoring, started 139963907692288)>]
2019-08-10 21:58:03,571 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 21:58:03,590 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 21:58:03,590 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job_monitor, started 139963312105216)>, <ExcThread(queue_monitoring, started 139963907692288)>]
2019-08-10 21:58:05,485 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 21:58:05,503 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 21:58:05,503 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139964383819520)>, <ExcThread(job_monitor, started 139963312105216)>]
2019-08-10 21:58:52,037 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-08-10 21:58:52,038 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 21:58:52,138 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 21:58:52,139 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 21:58:52,139 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 21:58:52 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 21:58:52 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 21:58:52 UTC [wrapper] Pilot exit status: 0
2019-08-10 21:58:52 UTC [wrapper] STATUSCODE: 0
2019-08-10 21:58:52 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 10 21:41 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 21:58:52 UTC [wrapper] Test setup, not cleaning
2019-08-10 21:58:52 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 21:58:52 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8255.81s
KernelTime=266.58s
UserTime=30400.36s
CPUUsage=371%
MaxResidentMemory=1944612kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=312033
MinorPageFaults=14097766
Swaps=0
ForcedSwitches=3581853
WaitSwitches=6125766
Inputs=75767864
Outputs=632896
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216072
drwxrwx--x. 7 grid grid      4096 Aug 10 23:58 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 10 21:41 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506428 Aug 10 21:41 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 10 21:41 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 10 21:41 APPS
drwxr-xr-x. 2 grid grid         6 Aug 10 21:41 .arc
-rw-------. 1 grid grid       538 Aug 10 21:41 .asetup
-rw-------. 1 grid grid       826 Aug 10 21:42 .asetup.save
-rw-------. 1 grid grid       516 Aug 10 23:58 aXOLDmYbcGvnShfckohDCDFpABFKDmABFKDmQrXYDmABFKDmVJ6k6n.diag
-rw-rw-r--. 1 grid grid         0 Aug 10 21:41 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 23:58 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 10 23:52 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207233352 Aug 10 21:41 EVNT.18605775._000318.pool.root.1
-rw-------. 1 grid grid     89419 Aug 10 23:57 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 10 21:41 init_data.xml
-rw-rw-r--. 1 grid grid    262341 Aug 10 21:41 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 10 21:41 job.xml
-rw-------. 1 grid grid    498100 Aug 10 23:58 log.18722398._016211.job.log.1
-rw-------. 1 grid grid    832908 Aug 10 23:57 log.18722398._016211.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 23:58 output.list
-rw-------. 1 grid grid      2957 Aug 10 11:12 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 10:36 pilot2.tar.gz
-rw-------. 1 grid grid     10482 Aug 10 23:58 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 10 11:12 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 10 21:41 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 10 21:41 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 11:12 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 23:58 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 23:58 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 23:58 shared
-rw-rw-r--. 1 grid grid      8688 Aug 10 21:41 start_atlas.sh
-rw-rw-r--. 1 grid grid     18680 Aug 10 23:58 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 10 21:41 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 10 23:58 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
23:58:52 (10281): run_atlas exited; CPU time 30400.718567
23:58:52 (10281): called boinc_finish(0)

</stderr_txt>
]]>

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