Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
16:52:31 (8053): wrapper (7.7.26015): starting
16:52:31 (8053): 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 PandaID=4447424214
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.18605019._043513.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 22472 s
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-14 16:37:57,347 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 14748
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 14748
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4447424214 has completed
2019-08-14 16:37:57,348 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-14 16:37:57,363 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4447424214
2019-08-14 16:37:58,364 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [14748]
2019-08-14 16:37:58,364 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 14748
2019-08-14 16:37:58,364 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-14 16:37:59,369 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-14 16:37:59,370 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=14748
2019-08-14 16:37:59,466 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [14748] (in reverse order)
2019-08-14 16:37:59,634 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-14 16:37:59,634 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-14 16:37:59,634 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-14 16:37:59,634 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-14 16:38:00,158 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-14 16:38:09,514 | INFO     | monitor             | pilot.control.monitor            | control                   | 6312 s have passed since pilot start
2019-08-14 16:38:10,192 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-14 16:38:10,192 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-14 16:38:10,231 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34871443456 B)
2019-08-14 16:38:10,232 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-14 16:38:10,232 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-14 16:38:10,520 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-14 16:38:10,538 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-14 16:38:10,539 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(job, started 140443606374144)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(data, started 140443597981440)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(validate_pre, started 140443207591680)>, <ExcThread(copytool_in, started 140443182413568)>, <ExcThread(failed_post, started 140442603611904)>, <ExcThread(validate_post, started 140443174020864)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>, <ExcThread(create_data_payload, started 140443572803328)>, <ExcThread(payload, started 140443581196032)>]
2019-08-14 16:38:10,618 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-14 16:38:10,618 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-14 16:38:10,625 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-14 16:38:10,730 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-14 16:38:10,730 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-14 16:38:10,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-14 16:38:10,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(data, started 140443597981440)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(validate_pre, started 140443207591680)>, <ExcThread(copytool_in, started 140443182413568)>, <ExcThread(validate_post, started 140443174020864)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>, <ExcThread(create_data_payload, started 140443572803328)>]
2019-08-14 16:38:10,826 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-14 16:38:10,942 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-14 16:38:10,942 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(data, started 140443597981440)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(validate_pre, started 140443207591680)>, <ExcThread(copytool_in, started 140443182413568)>, <ExcThread(validate_post, started 140443174020864)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:10,977 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-14 16:38:11,144 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-14 16:38:11,144 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(data, started 140443597981440)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(copytool_in, started 140443182413568)>, <ExcThread(validate_post, started 140443174020864)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:11,181 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-14 16:38:11,182 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-14 16:38:11,220 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-14 16:38:11,245 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-14 16:38:11,245 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(copytool_in, started 140443182413568)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:11,484 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-14 16:38:11,551 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-14 16:38:11,551 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(validate, started 140443589588736)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(execute_payloads, started 140442595219200)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:11,686 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-14 16:38:11,692 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-14 16:38:11,692 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-14 16:38:11,693 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-14 16:38:11,753 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-14 16:38:11,753 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(queue_monitor, started 140442612004608)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:11,822 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-14 16:38:11,822 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-14 16:38:11,855 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-14 16:38:11,855 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(copytool_out, started 140443564410624)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:12,693 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-14 16:38:12,763 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-14 16:38:12,763 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(queue_monitoring, started 140443199198976)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:14,688 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-14 16:38:14,781 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-14 16:38:14,782 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140443822638848)>, <ExcThread(job_monitor, started 140443165628160)>]
2019-08-14 16:38:29,824 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-14 16:38:29,824 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-14 16:38:29,910 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-14 16:38:29,910 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-14 16:38:29,911 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-14 16:38:30 UTC [wrapper] ==== pilot stdout END ====
2019-08-14 16:38:30 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-14 16:38:30 UTC [wrapper] Pilot exit status: 0
2019-08-14 16:38:30 UTC [wrapper] STATUSCODE: 0
2019-08-14 16:38:30 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 14 16:52 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

2019-08-14 16:38:30 UTC [wrapper] Test setup, not cleaning
2019-08-14 16:38:30 UTC [wrapper] ==== wrapper stdout END ====
2019-08-14 16:38:30 UTC [wrapper] ==== wrapper stderr END ====
2019-08-14 16:38:30 UTC [wrapper] wrapper wrapperexiting ec=0, duration=6355
2019-08-14 16:38:30 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6354.43s
KernelTime=210.18s
UserTime=22393.77s
CPUUsage=355%
MaxResidentMemory=1944544kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=276024
MinorPageFaults=12860119
Swaps=0
ForcedSwitches=2585344
WaitSwitches=5119307
Inputs=67236344
Outputs=514160
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 384684
drwxrwx--x. 6 grid grid      4096 Aug 14 18:38 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 14 18:38 5mbMDmsgqHvnShfckohDCDFpABFKDmABFKDmWbXaDmABFKDmgCZ5Qm.diag
-rw-------. 1 grid grid   7409110 Aug 14 16:52 agis_ddmendpoints.json
-rw-------. 1 grid grid   4447860 Aug 14 16:52 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 14 16:52 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 14 16:52 APPS
-rw-------. 1 grid grid       538 Aug 14 16:52 .asetup
-rw-------. 1 grid grid       826 Aug 14 16:53 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 14 16:52 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 14 18:38 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 14 18:31 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 380077673 Aug 14 16:52 EVNT.17323843._000828.pool.root.1
-rw-------. 1 grid grid     65610 Aug 14 18:37 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 14 16:52 init_data.xml
-rw-rw-r--. 1 grid grid    261623 Aug 14 16:52 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 14 16:52 job.xml
-rw-------. 1 grid grid    414970 Aug 14 18:38 log.18605019._043513.job.log.1
-rw-------. 1 grid grid    816066 Aug 14 18:37 log.18605019._043513.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 14 18:38 output.list
-rw-------. 1 grid grid      2887 Aug 13 20:27 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 20:26 pilot2.tar.gz
-rw-------. 1 grid grid     12187 Aug 14 18:38 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 20:26 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 14 16:52 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 14 16:52 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 20:27 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 14 18:38 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 14 18:38 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 14 18:38 shared
-rw-rw-r--. 1 grid grid      8688 Aug 14 16:52 start_atlas.sh
-rw-rw-r--. 1 grid grid     19415 Aug 14 18:38 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 14 16:52 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 14 18:38 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
18:38:31 (8053): run_atlas exited; CPU time 22394.268719
18:38:31 (8053): called boinc_finish(0)

</stderr_txt>
]]>

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