Stderr output

<core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
21:41:11 (17490): wrapper (7.7.26015): starting
21:41:11 (17490): wrapper: running run_atlas (--nthreads 8)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '8']
THREADS=8
Checking for CVMFS
CVMFS is installed
OS:cat: /etc/redhat-release: No such file or directory

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is installed, version 2.4.2-dist
Testing the function of Singularity...
Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
Singularity Works...

copy /var/lib/boinc2/slots/1/shared/RTE.tar.gz
copy /var/lib/boinc2/slots/1/shared/ATLAS.root_0
copy /var/lib/boinc2/slots/1/shared/input.tar.gz
copy /var/lib/boinc2/slots/1/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=8;start atlas job with grep: pandaJobData.out: No such file or directory
cmd = singularity exec --pwd /var/lib/boinc2/slots/1 -B /cvmfs,/var /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.18604976._044129.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-10 06:01:37,848 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 06:01:37,848 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4441973519
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18604976
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-10 06:01:37,849 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 45630 s
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 9351
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 9351
2019-08-10 06:01:37,850 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 8
2019-08-10 06:01:37,851 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-10 06:01:37,851 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-10 06:01:37,851 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-10 06:01:37,851 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441973519 has completed
2019-08-10 06:01:37,851 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-10 06:01:37,856 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc2/slots/1/PanDA_Pilot-4441973519
2019-08-10 06:01:38,862 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [9351]
2019-08-10 06:01:38,862 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 9351
2019-08-10 06:01:38,862 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-10 06:01:39,866 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-10 06:01:39,866 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=9351
2019-08-10 06:01:39,973 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [9351] (in reverse order)
2019-08-10 06:01:40,062 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-10 06:01:40,063 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-10 06:01:40,063 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-10 06:01:40,063 | 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 06:01:40,570 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-10 06:01:50,618 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-10 06:01:50,618 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc2/slots/1
2019-08-10 06:01:50,644 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (275320406016 B)
2019-08-10 06:01:50,644 | 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 06:01:50,644 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-10 06:01:50,656 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-10 06:01:50,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-10 06:01:50,662 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(job, started 139915153667840)>, <ExcThread(copytool_in, started 139915035653888)>, <ExcThread(failed_post, started 139914515568384)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(payload, started 139915052439296)>, <ExcThread(queue_monitor, started 139914481997568)>, <ExcThread(validate, started 139915145275136)>, <ExcThread(data, started 139915069224704)>, <ExcThread(create_data_payload, started 139915027261184)>, <ExcThread(validate_post, started 139914523961088)>, <ExcThread(execute_payloads, started 139914498782976)>, <ExcThread(validate_pre, started 139915018868480)>, <ExcThread(copytool_out, started 139915060832000)>]
2019-08-10 06:01:50,675 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-10 06:01:50,691 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-10 06:01:50,840 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-10 06:01:50,840 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-10 06:01:50,874 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-10 06:01:51,064 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-10 06:01:51,064 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(copytool_in, started 139915035653888)>, <ExcThread(failed_post, started 139914515568384)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(payload, started 139915052439296)>, <ExcThread(queue_monitor, started 139914481997568)>, <ExcThread(validate, started 139915145275136)>, <ExcThread(data, started 139915069224704)>, <ExcThread(create_data_payload, started 139915027261184)>, <ExcThread(validate_post, started 139914523961088)>, <ExcThread(execute_payloads, started 139914498782976)>, <ExcThread(copytool_out, started 139915060832000)>]
2019-08-10 06:01:51,138 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-10 06:01:51,138 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-10 06:01:51,150 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-10 06:01:51,150 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-10 06:01:51,266 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-10 06:01:51,266 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(payload, started 139915052439296)>, <ExcThread(queue_monitor, started 139914481997568)>, <ExcThread(validate, started 139915145275136)>, <ExcThread(create_data_payload, started 139915027261184)>, <ExcThread(validate_post, started 139914523961088)>, <ExcThread(execute_payloads, started 139914498782976)>, <ExcThread(copytool_out, started 139915060832000)>]
2019-08-10 06:01:51,334 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-10 06:01:51,467 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-10 06:01:51,467 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(payload, started 139915052439296)>, <ExcThread(queue_monitor, started 139914481997568)>, <ExcThread(create_data_payload, started 139915027261184)>, <ExcThread(validate_post, started 139914523961088)>, <ExcThread(execute_payloads, started 139914498782976)>, <ExcThread(copytool_out, started 139915060832000)>]
2019-08-10 06:01:51,570 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-10 06:01:51,643 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-10 06:01:51,643 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-10 06:01:51,669 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-10 06:01:51,669 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(queue_monitor, started 139914481997568)>, <ExcThread(create_data_payload, started 139915027261184)>, <ExcThread(validate_post, started 139914523961088)>, <ExcThread(copytool_out, started 139915060832000)>]
2019-08-10 06:01:51,675 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-10 06:01:51,747 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-10 06:01:51,765 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-10 06:01:51,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-10 06:01:51,770 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>, <ExcThread(queue_monitor, started 139914481997568)>]
2019-08-10 06:01:52,058 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-10 06:01:52,058 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-10 06:01:52,072 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-10 06:01:52,072 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(queue_monitoring, started 139915044046592)>, <ExcThread(job_monitor, started 139914490390272)>]
2019-08-10 06:01:53,692 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-10 06:01:53,784 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-10 06:01:53,785 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139915369150208)>, <ExcThread(job_monitor, started 139914490390272)>]
2019-08-10 06:02:17,136 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-10 06:02:17,136 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-10 06:02:17,208 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-10 06:02:17,208 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-10 06:02:17,208 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-10 06:02:17 UTC [wrapper] ==== pilot stdout END ====
2019-08-10 06:02:17 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-10 06:02:17 UTC [wrapper] Pilot exit status: 0
2019-08-10 06:02:17 UTC [wrapper] STATUSCODE: 0
2019-08-10 06:02:17 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-rw-r--  1 320 320 11357 Jul 25 08:38 LICENSE
drwxrwxr-x 14 320 320  4096 Aug  9 21:42 pilot
-rwxrwxr-x  1 320 320 20463 Jul 25 08:38 pilot.py
-rw-r--r--  1 320 320     8 Aug  7 05:02 PILOTVERSION
-rw-rw-r--  1 320 320  2251 Jul 25 08:38 README.md
-rw-rw-r--  1 320 320   221 Jul 25 08:38 TODO.md

2019-08-10 06:02:17 UTC [wrapper] Test setup, not cleaning
2019-08-10 06:02:17 UTC [wrapper] ==== wrapper stdout END ====
2019-08-10 06:02:17 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8456.24s
KernelTime=722.49s
UserTime=45084.04s
CPUUsage=541%
MaxResidentMemory=1956768kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=458954
MinorPageFaults=15753733
Swaps=0
ForcedSwitches=3386430
WaitSwitches=6838011
Inputs=83292848
Outputs=540144
SocketReceived=0
SocketSent=0
Signals=0

nodename=wHewitt@d8
exitcode=0
******************************WorkDir***********************
total 381332
drwxrwxrwx  7 root root      4096 Aug 10 00:02 .
drwxrwxrwx 35 root root      4096 Aug  9 02:25 ..
-rw-------  1 root root   7408903 Aug  9 21:43 agis_ddmendpoints.json
-rw-------  1 root root   4507217 Aug  9 21:43 agis_schedconf.cvmfs.json
drwx------  2 root root      4096 Aug  9 21:41 .alrb
drwxr-xr-x  3 root root      4096 Aug  9 21:41 APPS
drwxr-xr-x  2 root root      4096 Aug  9 21:42 .arc
-rw-------  1 root root       543 Aug  9 21:41 .asetup
-rw-------  1 root root       829 Aug  9 21:45 .asetup.save
-rw-r--r--  1 root root         0 Aug  9 21:41 boinc_lockfile
-rw-r--r--  1 root root      8192 Aug 10 00:01 boinc_mmap_file
-rw-r--r--  1 root root       537 Aug  9 23:44 boinc_task_state.xml
-rw-------  1 root root       494 Aug 10 00:02 DKqKDmc7HGvnShfckohDCDFpABFKDmABFKDm4cyXDmABFKDm4gZSSn.diag
-rw-r--r--  1 root root 376055714 Aug  9 21:41 EVNT.17323813._000869.pool.root.1
-rw-------  1 root root     74989 Aug 10 00:01 heartbeat.json
-rw-r--r--  1 root root      8513 Aug  9 21:41 init_data.xml
-rw-r--r--  1 root root    262330 Aug  9 21:41 input.tar.gz
-rw-r--r--  1 root root       112 Aug  9 21:41 job.xml
-rw-------  1 root root    526142 Aug 10 00:02 log.18604976._044129.job.log.1
-rw-------  1 root root   1184007 Aug 10 00:01 log.18604976._044129.job.log.tgz.1
-rw-------  1 root root       391 Aug 10 00:02 output.list
-rw-------  1 4871 1028      2872 Aug  9 05:20 pandaJobData.out
drwxr-xr-x  3  320  320      4096 Aug  7 05:02 pilot2
-rw-r--r--  1 root root    253018 Aug  9 04:22 pilot2.tar.gz
-rw-------  1 root root     10755 Aug 10 00:02 pilotlog.txt
-rw-r--r--  1 root root      4468 Aug  9 05:20 queuedata.json
-rw-r--r--  1 root root       815 Aug  9 21:41 RTE.tar.gz
-rwxr-xr-x  1 root root      8648 Aug  9 21:41 run_atlas
-rwx------  1 4871 1028     15232 Aug  9 05:20 runpilot2-wrapper.sh
-rw-r--r--  1 root root       692 Aug 10 00:02 runtime_log
-rw-r--r--  1 root root      6844 Aug 10 00:02 runtime_log.err
drwxrwx--x  2 root root      4096 Aug 10 00:02 shared
-rw-r--r--  1 root root      8688 Aug  9 21:41 start_atlas.sh
-rw-r--r--  1 root root     18732 Aug 10 00:02 stderr.txt
-rw-r--r--  1 root root       107 Aug  9 21:41 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--  1 root root        27 Aug 10 00:01 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
00:02:18 (17490): run_atlas exited; CPU time 45084.372000
00:02:18 (17490): called boinc_finish(0)

</stderr_txt>
]]>

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