Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:55:16 (26528): wrapper (7.7.26015): starting
14:55:16 (26528): 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=4443210193
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._024513.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 30781 s
2019-08-13 15:13:36,605 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 724
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 724
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443210193 has completed
2019-08-13 15:13:36,606 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 15:13:36,613 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443210193
2019-08-13 15:13:37,619 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [724]
2019-08-13 15:13:37,619 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 724
2019-08-13 15:13:37,619 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 15:13:38,624 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 15:13:38,624 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=724
2019-08-13 15:13:38,672 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [724] (in reverse order)
2019-08-13 15:13:38,713 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 15:13:38,713 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 15:13:38,713 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 15:13:38,713 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 15:13:39,222 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 15:13:49,269 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 15:13:49,269 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 15:13:49,308 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35181821952 B)
2019-08-13 15:13:49,308 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 15:13:49,309 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 15:13:49,345 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 15:13:49,350 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 15:13:49,524 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-13 15:13:49,525 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(job, started 140187458082560)>, <ExcThread(execute_payloads, started 140186449078016)>, <ExcThread(validate_post, started 140187019486976)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(payload, started 140187424511744)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(data, started 140187441297152)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(failed_post, started 140186457470720)>, <ExcThread(validate_pre, started 140187036272384)>, <ExcThread(monitor, started 140187044665088)>, <ExcThread(copytool_out, started 140187416119040)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:49,535 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 15:13:49,630 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 15:13:49,631 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 15:13:49,757 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 15:13:49,780 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 15:13:49,780 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 15:13:49,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-13 15:13:49,790 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(job, started 140187458082560)>, <ExcThread(execute_payloads, started 140186449078016)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(failed_post, started 140186457470720)>, <ExcThread(validate_pre, started 140187036272384)>, <ExcThread(copytool_out, started 140187416119040)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:49,852 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 15:13:49,907 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 15:13:49,907 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 15:13:49,907 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-13 15:13:49,907 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(execute_payloads, started 140186449078016)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(failed_post, started 140186457470720)>, <ExcThread(copytool_out, started 140187416119040)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:49,977 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 15:13:50,008 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 15:13:50,009 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(failed_post, started 140186457470720)>, <ExcThread(copytool_out, started 140187416119040)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:50,290 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 15:13:50,311 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-13 15:13:50,311 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(copytool_out, started 140187416119040)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:50,350 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 15:13:50,412 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-13 15:13:50,412 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(validate, started 140187449689856)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:50,611 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 15:13:50,613 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-13 15:13:50,614 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(copytool_in, started 140187053057792)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:50,616 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 15:13:50,715 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 15:13:50,715 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(create_data_payload, started 140187432904448)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:50,721 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 15:13:50,816 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 15:13:50,816 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(queue_monitor, started 140187011094272)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:51,025 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 15:13:51,025 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 15:13:51,118 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 15:13:51,118 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(queue_monitoring, started 140187407726336)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:52,347 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 15:13:52,427 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 15:13:52,427 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140187674355456)>, <ExcThread(job_monitor, started 140187027879680)>]
2019-08-13 15:13:54,743 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 15:13:54,744 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 15:13:54,844 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 15:13:54,844 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 15:13:54,845 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 15:13:55 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 15:13:55 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 15:13:55 UTC [wrapper] Pilot exit status: 0
2019-08-13 15:13:55 UTC [wrapper] STATUSCODE: 0
2019-08-13 15:13:55 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 13 14:55 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

2019-08-13 15:13:55 UTC [wrapper] Test setup, not cleaning
2019-08-13 15:13:55 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 15:13:55 UTC [wrapper] ==== wrapper stderr END ====
2019-08-13 15:13:55 UTC [wrapper] wrapper wrapperexiting ec=0, duration=8315
2019-08-13 15:13:55 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8314.28s
KernelTime=259.15s
UserTime=30671.65s
CPUUsage=372%
MaxResidentMemory=1945324kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=315394
MinorPageFaults=14128813
Swaps=0
ForcedSwitches=3588145
WaitSwitches=6162843
Inputs=76508904
Outputs=609272
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 214416
drwxrwx--x. 6 grid grid      4096 Aug 13 17:13 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409065 Aug 13 14:55 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517361 Aug 13 14:55 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 14:55 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 14:55 APPS
-rw-------. 1 grid grid       538 Aug 13 14:55 .asetup
-rw-------. 1 grid grid       826 Aug 13 14:56 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 14:55 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 17:13 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 13 17:08 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 205534232 Aug 13 14:55 EVNT.18605775._000485.pool.root.1
-rw-------. 1 grid grid     84371 Aug 13 17:13 heartbeat.json
-rw-rw-r--. 1 grid grid      5863 Aug 13 14:55 init_data.xml
-rw-rw-r--. 1 grid grid    261624 Aug 13 14:55 input.tar.gz
-rw-------. 1 grid grid       516 Aug 13 17:13 iVFODmV8aHvnShfckohDCDFpABFKDmABFKDm9Z7ZDmABFKDmmysFDo.diag
-rw-rw-r--. 1 grid grid       112 Aug 13 14:55 job.xml
-rw-------. 1 grid grid    499295 Aug 13 17:13 log.18722398._024513.job.log.1
-rw-------. 1 grid grid    833672 Aug 13 17:13 log.18722398._024513.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 13 17:13 output.list
-rw-------. 1 grid grid      2957 Aug 13 03:50 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 03:26 pilot2.tar.gz
-rw-------. 1 grid grid     12610 Aug 13 17:13 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 03:50 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 14:55 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 14:55 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 03:50 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 17:13 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 17:13 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 17:13 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 14:55 start_atlas.sh
-rw-rw-r--. 1 grid grid     19683 Aug 13 17:13 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 14:55 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 13 17:13 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
17:13:55 (26528): run_atlas exited; CPU time 30672.144890
17:13:55 (26528): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN