Stderr output

<core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
10:23:35 (30181): wrapper (7.7.26015): starting
10:23:35 (30181): 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/7/shared/RTE.tar.gz
copy /var/lib/boinc2/slots/7/shared/ATLAS.root_0
copy /var/lib/boinc2/slots/7/shared/input.tar.gz
copy /var/lib/boinc2/slots/7/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/7 -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.18722261._011535.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722261
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 20:26:36,585 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 91208 s
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 10088
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 10088
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 8
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 20:26:36,586 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 20:26:36,587 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442251312 has completed
2019-08-09 20:26:36,587 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 20:26:36,592 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc2/slots/7/PanDA_Pilot-4442251312
2019-08-09 20:26:37,596 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [10088]
2019-08-09 20:26:37,596 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 10088
2019-08-09 20:26:37,596 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 20:26:38,602 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 20:26:38,602 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=10088
2019-08-09 20:26:38,773 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [10088] (in reverse order)
2019-08-09 20:26:38,929 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 20:26:38,929 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 20:26:38,930 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 20:26:38,930 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-09 20:26:39,440 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 20:26:49,490 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 20:26:49,490 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc2/slots/7
2019-08-09 20:26:49,551 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (251145486336 B)
2019-08-09 20:26:49,551 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-09 20:26:49,551 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 20:26:49,575 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 20:26:49,583 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 20:26:49,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-09 20:26:49,701 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(job, started 140591766963968)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(payload, started 140591660791552)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(create_data_payload, started 140591635613440)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(data, started 140591750178560)>, <ExcThread(failed_post, started 140590914201344)>, <ExcThread(validate, started 140591758571264)>, <ExcThread(queue_monitoring, started 140591627220736)>, <ExcThread(validate_post, started 140591610435328)>, <ExcThread(monitor, started 140591644006144)>]
2019-08-09 20:26:49,726 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 20:26:50,066 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 20:26:50,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-09 20:26:50,104 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(job, started 140591766963968)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(payload, started 140591660791552)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(create_data_payload, started 140591635613440)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(data, started 140591750178560)>, <ExcThread(failed_post, started 140590914201344)>, <ExcThread(validate, started 140591758571264)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:50,126 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 20:26:50,126 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 20:26:50,135 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 20:26:50,135 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 20:26:50,280 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 20:26:50,280 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 20:26:50,305 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-09 20:26:50,305 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(create_data_payload, started 140591635613440)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(failed_post, started 140590914201344)>, <ExcThread(validate, started 140591758571264)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:50,308 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 20:26:50,406 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-09 20:26:50,406 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(create_data_payload, started 140591635613440)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(failed_post, started 140590914201344)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:50,606 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 20:26:50,607 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 20:26:50,607 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(failed_post, started 140590914201344)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:50,689 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 20:26:50,810 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 20:26:50,904 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 20:26:50,909 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-09 20:26:50,910 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(validate_pre, started 140591652398848)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:50,990 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 20:26:51,010 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 20:26:51,011 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(queue_monitor, started 140590889023232)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:51,089 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 20:26:51,089 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 20:26:51,111 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-09 20:26:51,112 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(copytool_out, started 140591741785856)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:51,689 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 20:26:51,716 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 20:26:51,716 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(job_monitor, started 140590905808640)>, <ExcThread(queue_monitoring, started 140591627220736)>]
2019-08-09 20:26:53,906 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 20:26:53,935 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 20:26:53,935 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140591982446336)>, <ExcThread(job_monitor, started 140590905808640)>]
2019-08-09 20:27:35,406 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-09 20:27:35,406 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 20:27:35,459 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 20:27:35,459 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 20:27:35,459 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 20:27:35 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 20:27:35 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 20:27:35 UTC [wrapper] Pilot exit status: 0
2019-08-09 20:27:35 UTC [wrapper] STATUSCODE: 0
2019-08-09 20:27:35 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 10:25 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

2019-08-09 20:27:35 UTC [wrapper] Test setup, not cleaning
2019-08-09 20:27:35 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 20:27:35 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=14631.13s
KernelTime=1363.48s
UserTime=90128.62s
CPUUsage=625%
MaxResidentMemory=1982864kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=663053
MinorPageFaults=22293586
Swaps=0
ForcedSwitches=7075346
WaitSwitches=10278495
Inputs=137718576
Outputs=898288
SocketReceived=0
SocketSent=0
Signals=0

nodename=wHewitt@d8
exitcode=0
******************************WorkDir***********************
total 276200
drwxrwx--x  7 root root      4096 Aug  9 14:27 .
drwxrwxrwx 35 root root      4096 Aug  9 02:25 ..
-rw-------  1 root root   7408903 Aug  9 10:25 agis_ddmendpoints.json
-rw-------  1 root root   4507132 Aug  9 10:25 agis_schedconf.cvmfs.json
drwx------  2 root root      4096 Aug  9 10:23 .alrb
drwxr-xr-x  3 root root      4096 Aug  9 10:23 APPS
drwxr-xr-x  2 root root      4096 Aug  9 10:25 .arc
-rw-------  1 root root       543 Aug  9 10:24 .asetup
-rw-------  1 root root       829 Aug  9 10:28 .asetup.save
-rw-r--r--  1 root root         0 Aug  9 10:23 boinc_lockfile
-rw-r--r--  1 root root      8192 Aug  9 14:27 boinc_mmap_file
-rw-r--r--  1 root root       538 Aug  9 14:04 boinc_task_state.xml
-rw-r--r--  1 root root 268117372 Aug  9 10:23 EVNT.18605752._000225.pool.root.1
-rw-------  1 root root     87906 Aug  9 14:26 heartbeat.json
-rw-------  1 root root       498 Aug  9 14:27 IE3LDm3jLGvnShfckohDCDFpABFKDmABFKDmEm4XDmABFKDm6NfaEn.diag
-rw-r--r--  1 root root      8513 Aug  9 10:23 init_data.xml
-rw-r--r--  1 root root    262342 Aug  9 10:23 input.tar.gz
-rw-r--r--  1 root root       112 Aug  9 10:23 job.xml
-rw-------  1 root root    780703 Aug  9 14:27 log.18722261._011535.job.log.1
-rw-------  1 root root   1203247 Aug  9 14:26 log.18722261._011535.job.log.tgz.1
-rw-------  1 root root       391 Aug  9 14:27 output.list
-rw-------  1 4871 1028      2921 Aug  9 09:12 pandaJobData.out
drwxr-xr-x  3  320  320      4096 Aug  7 05:02 pilot2
-rw-r--r--  1 root root    253018 Aug  9 08:26 pilot2.tar.gz
-rw-------  1 root root     11665 Aug  9 14:27 pilotlog.txt
-rw-r--r--  1 root root      4468 Aug  9 09:10 queuedata.json
-rw-r--r--  1 root root       815 Aug  9 10:23 RTE.tar.gz
-rwxr-xr-x  1 root root      8648 Aug  9 10:23 run_atlas
-rwx------  1 4871 1028     15232 Aug  9 09:12 runpilot2-wrapper.sh
-rw-r--r--  1 root root       692 Aug  9 14:27 runtime_log
-rw-r--r--  1 root root      6844 Aug  9 14:27 runtime_log.err
drwxrwx--x  2 root root      4096 Aug  9 14:27 shared
-rw-r--r--  1 root root      8688 Aug  9 10:23 start_atlas.sh
-rw-r--r--  1 root root     19068 Aug  9 14:27 stderr.txt
-rw-r--r--  1 root root       107 Aug  9 10:23 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--  1 root root        28 Aug  9 14:27 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
14:27:36 (30181): run_atlas exited; CPU time 90128.860000
14:27:36 (30181): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN