Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
06:26:30 (13549): wrapper (7.7.26015): starting
06:26:30 (13549): wrapper: running run_atlas (--nthreads 1)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '1']
THREADS=1
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.4.1708 (Core) 

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is installed, version 2.6.1-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 /root/slots/4/shared/ATLAS.root_0
copy /root/slots/4/shared/input.tar.gz
copy /root/slots/4/shared/RTE.tar.gz
copy /root/slots/4/shared/start_atlas.sh
start atlas job with PandaID=4443290924
cmd = singularity exec --pwd /root/slots/4 -B /cvmfs,/root /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._024922.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 03:19:55,778 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 82220 s
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 20667
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 20667
2019-08-16 03:19:55,779 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-16 03:19:55,780 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 03:19:55,780 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 03:19:55,780 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 03:19:55,780 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443290924 has completed
2019-08-16 03:19:55,780 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 03:19:55,784 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /root/slots/4/PanDA_Pilot-4443290924
2019-08-16 03:19:56,787 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [20667]
2019-08-16 03:19:56,788 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 20667
2019-08-16 03:19:56,788 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 03:19:57,788 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 03:19:57,789 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=20667
2019-08-16 03:19:57,863 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [20667] (in reverse order)
2019-08-16 03:19:57,945 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 03:19:57,945 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 03:19:57,945 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 03:19:57,945 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-16 03:19:58,468 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 03:20:08,520 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 03:20:08,520 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /root/slots/4
2019-08-16 03:20:08,583 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (15289286656 B)
2019-08-16 03:20:08,584 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-16 03:20:08,584 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 03:20:08,612 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 03:20:08,656 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 03:20:08,770 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 03:20:08,771 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 03:20:08,771 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 03:20:08,829 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-16 03:20:08,830 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(job, started 139778630268672)>, <ExcThread(validate_post, started 139778234251008)>, <ExcThread(execute_payloads, started 139778200680192)>, <ExcThread(failed_post, started 139778225858304)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(copytool_in, started 139778192287488)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>, <ExcThread(copytool_out, started 139778605090560)>, <ExcThread(create_data_payload, started 139778217465600)>, <ExcThread(data, started 139778613483264)>]
2019-08-16 03:20:09,087 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 03:20:09,134 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 03:20:09,134 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(job, started 139778630268672)>, <ExcThread(execute_payloads, started 139778200680192)>, <ExcThread(failed_post, started 139778225858304)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(copytool_in, started 139778192287488)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>, <ExcThread(copytool_out, started 139778605090560)>, <ExcThread(create_data_payload, started 139778217465600)>, <ExcThread(data, started 139778613483264)>]
2019-08-16 03:20:09,391 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 03:20:09,434 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 03:20:09,434 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 03:20:09,455 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-16 03:20:09,455 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(execute_payloads, started 139778200680192)>, <ExcThread(failed_post, started 139778225858304)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>, <ExcThread(copytool_out, started 139778605090560)>, <ExcThread(create_data_payload, started 139778217465600)>, <ExcThread(data, started 139778613483264)>]
2019-08-16 03:20:09,477 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 03:20:09,478 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 03:20:09,528 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 03:20:09,581 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-16 03:20:09,582 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(execute_payloads, started 139778200680192)>, <ExcThread(failed_post, started 139778225858304)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>, <ExcThread(copytool_out, started 139778605090560)>]
2019-08-16 03:20:09,582 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 03:20:09,657 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 03:20:09,682 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 03:20:09,683 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(execute_payloads, started 139778200680192)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>]
2019-08-16 03:20:09,728 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 03:20:09,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 03:20:09,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(validate_pre, started 139778588305152)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>]
2019-08-16 03:20:09,809 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 03:20:09,895 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 03:20:09,895 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(queue_monitor, started 139777554769664)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>]
2019-08-16 03:20:10,337 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 03:20:10,338 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 03:20:10,422 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 03:20:10,423 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(job_monitor, started 139777563162368)>, <ExcThread(queue_monitoring, started 139778209072896)>]
2019-08-16 03:20:11,635 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 03:20:14,671 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 03:20:14,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 03:20:14,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139778846541568)>, <ExcThread(job_monitor, started 139777563162368)>]
2019-08-16 03:20:46,370 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 03:20:46,370 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 03:20:46,415 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 03:20:46,416 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 03:20:46,416 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 03:20:46 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 03:20:46 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 03:20:46 UTC [wrapper] Pilot exit status: 0
2019-08-16 03:20:46 UTC [wrapper] STATUSCODE: 0
2019-08-16 03:20:46 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
insgesamt 44
-rw-rw-r--.  1 320 320 11357 25. Jul 16:38 LICENSE
drwxrwxr-x. 14 320 320   234 15. Aug 06:51 pilot
-rwxrwxr-x.  1 320 320 20463 25. Jul 16:38 pilot.py
-rw-r--r--.  1 320 320     8  7. Aug 13:02 PILOTVERSION
-rw-rw-r--.  1 320 320  2251 25. Jul 16:38 README.md
-rw-rw-r--.  1 320 320   221 25. Jul 16:38 TODO.md

2019-08-16 03:20:46 UTC [wrapper] Test setup, not cleaning
2019-08-16 03:20:46 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 03:20:46 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 03:20:46 UTC [wrapper] wrapper wrapperexiting ec=0, duration=82432
2019-08-16 03:20:46 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=82432.01s
KernelTime=3395.12s
UserTime=82003.52s
CPUUsage=103%
MaxResidentMemory=1943656kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=1382871
MinorPageFaults=41873589
Swaps=0
ForcedSwitches=2718005
WaitSwitches=42348705
Inputs=330387488
Outputs=372848
SocketReceived=0
SocketSent=0
Signals=0

nodename=maeax@HPi7COS7
exitcode=0
******************************WorkDir***********************
insgesamt 218360
drwxrwx--x. 6 root root      4096 16. Aug 05:20 .
drwxrwx--x. 7 root root        69 15. Aug 06:27 ..
-rw-------. 1 root root   7409162 15. Aug 06:28 agis_ddmendpoints.json
-rw-------. 1 root root   4448398 15. Aug 06:28 agis_schedconf.cvmfs.json
drwx------. 2 root root         6 15. Aug 06:26 .alrb
drwxr-xr-x. 3 root root        17 15. Aug 06:26 APPS
-rw-------. 1 root root       533 15. Aug 06:27 .asetup
-rw-------. 1 root root       826 15. Aug 06:30 .asetup.save
-rw-r--r--. 1 root root         0 15. Aug 06:26 boinc_lockfile
-rw-r--r--. 1 root root      8192 16. Aug 05:20 boinc_mmap_file
-rw-r--r--. 1 root root       537 16. Aug 05:17 boinc_task_state.xml
-rw-------. 1 root root        59 15. Aug 06:27 .directory
-rw-r--r--. 1 root root 206760239 15. Aug 06:26 EVNT.18605775._000493.pool.root.1
-rw-------. 1 root root     71245 16. Aug 05:19 heartbeat.json
-rw-r--r--. 1 root root      5868 15. Aug 06:26 init_data.xml
-rw-r--r--. 1 root root    261622 15. Aug 06:26 input.tar.gz
-rw-r--r--. 1 root root       112 15. Aug 06:26 job.xml
-rw-------. 1 root root   3551201 16. Aug 05:20 log.18722398._024922.job.log.1
-rw-------. 1 root root    419100 16. Aug 05:19 log.18722398._024922.job.log.tgz.1
-rw-------. 1 root root       503 16. Aug 05:20 nAQNDmy2fHvnShfckohDCDFpABFKDmABFKDmjdFaDmABFKDmfVc7Hn.diag
-rw-------. 1 root root       391 16. Aug 05:20 output.list
-rw-------. 1 4871 1028      2957 13. Aug 09:05 pandaJobData.out
drwxr-xr-x. 3  320  320       192 15. Aug 06:51 pilot2
-rw-r--r--. 1 root root    253018 13. Aug 08:21 pilot2.tar.gz
-rw-------. 1 root root     11033 16. Aug 05:20 pilotlog.txt
-rw-r--r--. 1 root root      4468 13. Aug 09:05 queuedata.json
-rw-r--r--. 1 root root       815 15. Aug 06:26 RTE.tar.gz
-rwxr-xr-x. 1 root root      8779 15. Aug 06:26 run_atlas
-rwx------. 1 4871 1028     12641 13. Aug 09:05 runpilot2-wrapper.sh
-rw-r--r--. 1 root root       692 16. Aug 05:20 runtime_log
-rw-r--r--. 1 root root      6667 16. Aug 05:20 runtime_log.err
drwxrwx--x. 2 root root       131 16. Aug 05:20 shared
-rw-r--r--. 1 root root      8659 15. Aug 06:26 start_atlas.sh
-rw-r--r--. 1 root root     18459 16. Aug 05:20 stderr.txt
-rw-r--r--. 1 root root       107 15. Aug 06:26 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 root root        28 16. Aug 05:20 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
05:20:47 (13549): run_atlas exited; CPU time 82004.187294
05:20:47 (13549): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN