Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
12:04:30 (1231530): wrapper (7.7.26015): starting
12:04:30 (1231530): wrapper: running run_atlas (--nthreads 4)
2019-09-26 12:04:30,125: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-26 12:04:30,125: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-26 12:04:30,125: THREADS=4

2019-09-26 12:04:30,126: Checking for CVMFS
2019-09-26 12:04:30,843: CVMFS is installed
2019-09-26 12:04:30,843: Checking Singularity...
2019-09-26 12:04:30,858: Singularity is installed, version singularity version 3.4.0-1.2.el7
2019-09-26 12:04:30,858: Testing the function of Singularity...
2019-09-26 12:04:30,859: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-26 12:04:30,936: Singularity Works...
2019-09-26 12:04:30,937: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-09-26 12:04:33,835: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-09-26 12:04:33,836: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-09-26 12:04:33,836: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-09-26 12:04:33,836: export ATHENA_PROC_NUMBER=4;
2019-09-26 12:04:33,849: start atlas job with PandaID=4002876565
2019-09-26 12:04:33,850: cmd = singularity exec --pwd /home/dcameron/boinc/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
2019-09-26 12:18:29,494: running cmd return value is 0
2019-09-26 12:18:29,495: Moving ./HITS.000649-2008926-20067._078090.pool.root.1 to shared/HITS.pool.root.1
2019-09-26 12:18:29,495: HITS result file:
2019-09-26 12:18:29,500: -rw-------. 1 dcameron zp 9166719 Sep 26 12:15 shared/HITS.pool.root.1
2019-09-26 12:18:29,500: *****************The last 100 lines of the pilot log******************
2019-09-26 12:18:29,503: 2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 1238377
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4002876565 has completed
2019-09-26 10:17:33,269 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-26 10:17:33,273 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4002876565
2019-09-26 10:17:34,277 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [1238377]
2019-09-26 10:17:34,277 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 1238377
2019-09-26 10:17:34,277 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-26 10:17:35,281 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-26 10:17:35,281 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=1238377
2019-09-26 10:17:35,365 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [1238377] (in reverse order)
2019-09-26 10:17:35,404 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-26 10:17:35,404 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-26 10:17:35,404 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-26 10:17:35,404 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-26 10:17:35,407 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:17:35,407 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-26 10:17:35,407 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:17:35,407 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-26 10:17:35,408 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-26 10:17:35,480 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | 
LSB Version:	:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch
Distributor ID:	ScientificCERNSLC
Description:	Scientific Linux CERN SLC release 6.10 (Carbon)
Release:	6.10
Codename:	Carbon
2019-09-26 10:17:35,480 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-26 10:17:35,983 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-09-26 10:17:36,001 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (70049071104 B)
2019-09-26 10:17:36,001 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-26 10:17:36,001 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-26 10:17:36,025 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-26 10:17:36,119 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-26 10:17:36,119 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-26 10:17:36,131 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-26 10:17:36,131 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-26 10:17:36,148 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-26 10:17:36,244 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-26 10:17:36,245 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(job, started 140678068008704)>, <ExcThread(copytool_out, started 140678042830592)>, <ExcThread(copytool_in, started 140677778216704)>, <ExcThread(validate_post, started 140677216200448)>, <ExcThread(queue_monitor, started 140677207807744)>, <ExcThread(validate, started 140678059616000)>, <ExcThread(execute_payloads, started 140677191022336)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>, <ExcThread(monitor, started 140677803394816)>]
2019-09-26 10:17:36,593 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-26 10:17:36,626 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-26 10:17:36,656 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-26 10:17:36,847 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-09-26 10:17:36,847 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(job, started 140678068008704)>, <ExcThread(copytool_out, started 140678042830592)>, <ExcThread(copytool_in, started 140677778216704)>, <ExcThread(queue_monitor, started 140677207807744)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>, <ExcThread(monitor, started 140677803394816)>]
2019-09-26 10:17:36,850 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-26 10:17:36,860 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-26 10:17:36,860 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-26 10:17:36,948 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-09-26 10:17:36,948 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(copytool_out, started 140678042830592)>, <ExcThread(copytool_in, started 140677778216704)>, <ExcThread(queue_monitor, started 140677207807744)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>]
2019-09-26 10:17:37,026 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-26 10:17:37,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-09-26 10:17:37,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(copytool_in, started 140677778216704)>, <ExcThread(queue_monitor, started 140677207807744)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>]
2019-09-26 10:17:37,223 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-26 10:17:37,223 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-26 10:17:37,250 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-26 10:17:37,251 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(copytool_in, started 140677778216704)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>]
2019-09-26 10:17:37,295 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-26 10:17:37,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-26 10:17:37,351 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(failed_post, started 140677199415040)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(validate_pre, started 140677786609408)>, <ExcThread(queue_monitoring, started 140677811787520)>]
2019-09-26 10:17:37,373 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-26 10:17:37,410 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-26 10:17:37,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-26 10:17:37,452 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(job_monitor, started 140677224593152)>, <ExcThread(queue_monitoring, started 140677811787520)>]
2019-09-26 10:17:38,793 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-26 10:17:41,794 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-26 10:17:41,879 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-26 10:17:41,879 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140678287767296)>, <ExcThread(job_monitor, started 140677224593152)>]
2019-09-26 10:18:29,187 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-09-26 10:18:29,187 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-26 10:18:29,260 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-26 10:18:29,260 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-26 10:18:29,261 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-26 10:18:29 UTC [wrapper] ==== pilot stdout END ====
2019-09-26 10:18:29 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-26 10:18:29 UTC [wrapper] Pilot exit status: 0
2019-09-26 10:18:29 UTC [wrapper] STATUSCODE: 0
2019-09-26 10:18:29 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 56
-rw-------.  1 dcameron zp 11357 Jul 25 16:38 LICENSE
-rw-------.  1 dcameron zp    20 Sep  9 13:04 MANIFEST.IN
-rw-------.  1 dcameron zp    11 Sep 26 12:04 pandaIDs.out
drwx------. 14 dcameron zp   216 Sep 26 12:04 pilot
-rwx------.  1 dcameron zp 20136 Sep  9 13:04 pilot.py
-rw-------.  1 dcameron zp     9 Sep  9 13:04 PILOTVERSION
-rw-------.  1 dcameron zp  2251 Jul 25 16:38 README.md
-rw-------.  1 dcameron zp   760 Aug 22 11:01 setup.py
-rw-------.  1 dcameron zp   221 Jul 25 16:38 TODO.md
-rw-------. 1 dcameron zp 11 Sep 26 12:04 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
4002876565

2019-09-26 10:18:29 UTC [wrapper] Test setup, not cleaning
2019-09-26 10:18:29 UTC [wrapper] ==== wrapper stdout END ====
2019-09-26 10:18:29 UTC [wrapper] ==== wrapper stderr END ====
2019-09-26 10:18:29 UTC [wrapper] wrapper wrapperexiting ec=0, duration=836
2019-09-26 10:18:29 UTC [wrapper] apfmon messages muted
2019-09-26 12:18:29,506: ***************diag file************
2019-09-26 12:18:29,506: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=835.48s
KernelTime=50.51s
UserTime=1707.89s
CPUUsage=210%
MaxResidentMemory=1944916kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=179162
MinorPageFaults=9210011
Swaps=0
ForcedSwitches=56770
WaitSwitches=3308487
Inputs=41657584
Outputs=84376
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-09-26 12:18:29,510: ******************************WorkDir***********************
2019-09-26 12:18:29,510: total 369608
drwxrwx--x. 7 dcameron zp      4096 Sep 26 12:18 .
drwxrwx--x. 3 dcameron zp        15 Sep 16 13:48 ..
-rw-------. 1 dcameron zp   7579510 Sep 26 12:04 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   4044801 Sep 26 12:04 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Sep 26 12:04 .alrb
drwxr-xr-x. 3 dcameron zp        17 Sep 26 12:04 APPS
-rw-------. 1 dcameron zp       548 Sep 26 12:04 .asetup
-rw-------. 1 dcameron zp       826 Sep 26 12:05 .asetup.save
drwx------. 2 dcameron zp         6 Sep 26 12:05 .asetup-sysbin_1235592
-rw-r--r--. 1 dcameron zp         0 Sep 26 12:04 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Sep 26 12:18 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       534 Sep 26 12:13 boinc_task_state.xml
-rw-r--r--. 1 dcameron zp 365251149 Sep 26 12:04 EVNT.14296418._001447.pool.root.1
-rw-------. 1 dcameron zp     14670 Sep 26 12:17 heartbeat.json
-rw-r--r--. 1 dcameron zp      6290 Sep 26 12:04 init_data.xml
-rw-r--r--. 1 dcameron zp    266070 Sep 26 12:04 input.tar.gz
-rw-------. 1 dcameron zp       506 Sep 26 12:18 JbNNDmqfsRvnShfckohDCDFpABFKDmABFKDmQ6FKDm5BFKDmcEyqRo.diag
-rw-r--r--. 1 dcameron zp       112 Sep 26 12:04 job.xml
-rw-------. 1 dcameron zp    713666 Sep 26 12:17 log.000649-2008926-20067._078090.job.log.tgz.1
-rw-------. 1 dcameron zp    178493 Sep 26 12:18 log.14568781._078090.job.log.1
-rw-------. 1 dcameron zp       499 Sep 26 12:18 output.list
-rw-------. 1 dcameron zp      2958 Sep 10 12:35 pandaJobData.out
drwx------. 3 dcameron zp       229 Sep 26 12:04 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 10 12:31 pilot2.tar.gz
-rw-------. 1 dcameron zp     11195 Sep 26 12:18 pilotlog.txt
-rw-------. 1 dcameron zp      5077 Sep 26 12:04 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Sep 26 12:04 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      7941 Sep 26 12:04 run_atlas
-rwx------. 1 dcameron zp     12641 Sep 10 12:35 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       618 Sep 26 12:18 runtime_log
-rw-r--r--. 1 dcameron zp      8100 Sep 26 12:18 runtime_log.err
-rw-------. 1 dcameron zp       240 Sep 26 12:04 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Sep 26 12:18 shared
-rw-r--r--. 1 dcameron zp      8494 Sep 26 12:04 start_atlas.sh
-rw-r--r--. 1 dcameron zp     17893 Sep 26 12:18 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Sep 26 12:04 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        25 Sep 26 12:18 wrapper_checkpoint.txt

2019-09-26 12:18:29,510: running start_atlas return value is 0
2019-09-26 12:18:29,510: Parent exit 0
2019-09-26 12:18:29,511: child process exit 0
12:18:30 (1231530): run_atlas exited; CPU time 1708.220959
12:18:30 (1231530): called boinc_finish(0)

</stderr_txt>
]]>

©2025 CERN