Stderr output

<core_client_version>7.16.1</core_client_version>
<![CDATA[
<stderr_txt>
08:10:25 (1961349): wrapper (7.7.26015): starting
08:10:25 (1961349): wrapper: running run_atlas (--nthreads 4)
2019-09-30 08:10:25,201: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-30 08:10:25,201: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-30 08:10:25,202: THREADS=4

2019-09-30 08:10:25,202: Checking for CVMFS
2019-09-30 08:10:25,869: CVMFS is installed
2019-09-30 08:10:25,869: Checking Singularity...
2019-09-30 08:10:25,892: Singularity is installed, version singularity version 3.4.0-1.2.el7
2019-09-30 08:10:25,892: Testing the function of Singularity...
2019-09-30 08:10:25,892: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-30 08:10:25,965: Singularity Works...
2019-09-30 08:10:25,965: copy /home/dcameron/boinc/slots/0/shared/ATLAS.root_0
2019-09-30 08:10:26,553: copy /home/dcameron/boinc/slots/0/shared/input.tar.gz
2019-09-30 08:10:26,553: copy /home/dcameron/boinc/slots/0/shared/RTE.tar.gz
2019-09-30 08:10:26,553: copy /home/dcameron/boinc/slots/0/shared/start_atlas.sh
2019-09-30 08:10:26,554: export ATHENA_PROC_NUMBER=4;
2019-09-30 08:10:26,566: start atlas job with PandaID=4494479989
2019-09-30 08:10:26,566: 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
2019-09-30 13:07:34,325: running cmd return value is 0
2019-09-30 13:07:34,325: Moving ./HITS.19056259._006706.pool.root.1 to shared/HITS.pool.root.1
2019-09-30 13:07:34,326: HITS result file:
2019-09-30 13:07:34,330: -rw-------. 1 dcameron zp 245924494 Sep 30 13:04 shared/HITS.pool.root.1
2019-09-30 13:07:34,331: *****************The last 100 lines of the pilot log******************
2019-09-30 13:07:34,333: 2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4494479989 has completed
2019-09-30 11:06:58,534 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-30 11:06:58,538 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/dcameron/boinc/slots/0/PanDA_Pilot-4494479989
2019-09-30 11:06:59,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [1968132]
2019-09-30 11:06:59,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 1968132
2019-09-30 11:06:59,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-30 11:07:00,541 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-30 11:07:00,541 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=1968132
2019-09-30 11:07:00,611 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [1968132] (in reverse order)
2019-09-30 11:07:00,647 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-30 11:07:00,647 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-30 11:07:00,648 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-30 11:07:00,648 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-30 11:07:00,650 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 11:07:00,650 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-30 11:07:00,651 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 11:07:00,651 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-30 11:07:00,651 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-30 11:07:00,713 | 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
2019-09-30 11:07:00,713 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-30 11:07:01,216 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/dcameron/boinc/slots/0
2019-09-30 11:07:01,232 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (69886541824 B)
2019-09-30 11:07:01,232 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-30 11:07:01,233 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-30 11:07:01,279 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-30 11:07:01,478 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-30 11:07:01,511 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-09-30 11:07:01,511 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(job, started 140597627856640)>, <ExcThread(copytool_in, started 140597079824128)>, <ExcThread(queue_monitor, started 140597046253312)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(payload, started 140597585893120)>, <ExcThread(monitor, started 140597088216832)>, <ExcThread(copytool_out, started 140597594285824)>, <ExcThread(queue_monitoring, started 140597096609536)>, <ExcThread(validate_pre, started 140597071431424)>, <ExcThread(data, started 140597611071232)>, <ExcThread(validate, started 140597619463936)>, <ExcThread(execute_payloads, started 140596551345920)>, <ExcThread(create_data_payload, started 140597602678528)>, <ExcThread(validate_post, started 140597054646016)>]
2019-09-30 11:07:01,672 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-30 11:07:01,797 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-30 11:07:01,797 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-30 11:07:01,913 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-30 11:07:01,913 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(job, started 140597627856640)>, <ExcThread(copytool_in, started 140597079824128)>, <ExcThread(queue_monitor, started 140597046253312)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(payload, started 140597585893120)>, <ExcThread(copytool_out, started 140597594285824)>, <ExcThread(queue_monitoring, started 140597096609536)>, <ExcThread(validate_pre, started 140597071431424)>, <ExcThread(validate, started 140597619463936)>, <ExcThread(execute_payloads, started 140596551345920)>, <ExcThread(create_data_payload, started 140597602678528)>, <ExcThread(validate_post, started 140597054646016)>]
2019-09-30 11:07:01,951 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-30 11:07:01,998 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-30 11:07:02,117 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-30 11:07:02,117 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-30 11:07:02,158 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-30 11:07:02,214 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-09-30 11:07:02,214 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(queue_monitor, started 140597046253312)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(payload, started 140597585893120)>, <ExcThread(copytool_out, started 140597594285824)>, <ExcThread(queue_monitoring, started 140597096609536)>, <ExcThread(validate_pre, started 140597071431424)>, <ExcThread(create_data_payload, started 140597602678528)>, <ExcThread(validate_post, started 140597054646016)>]
2019-09-30 11:07:02,245 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-30 11:07:02,245 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-30 11:07:02,279 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-30 11:07:02,315 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-09-30 11:07:02,315 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(queue_monitor, started 140597046253312)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(queue_monitoring, started 140597096609536)>, <ExcThread(validate_pre, started 140597071431424)>, <ExcThread(create_data_payload, started 140597602678528)>, <ExcThread(validate_post, started 140597054646016)>]
2019-09-30 11:07:02,502 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-30 11:07:02,503 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-30 11:07:02,507 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-30 11:07:02,507 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-30 11:07:02,516 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-09-30 11:07:02,516 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(queue_monitoring, started 140597096609536)>, <ExcThread(create_data_payload, started 140597602678528)>]
2019-09-30 11:07:02,615 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-30 11:07:02,617 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-30 11:07:02,617 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(job_monitor, started 140597063038720)>, <ExcThread(queue_monitoring, started 140597096609536)>]
2019-09-30 11:07:03,504 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-30 11:07:06,505 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-30 11:07:06,538 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-30 11:07:06,539 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140597844129536)>, <ExcThread(job_monitor, started 140597063038720)>]
2019-09-30 11:07:33,994 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-09-30 11:07:33,994 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-30 11:07:34,090 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-30 11:07:34,090 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-30 11:07:34,090 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-30 11:07:34 UTC [wrapper] ==== pilot stdout END ====
2019-09-30 11:07:34 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-30 11:07:34 UTC [wrapper] Pilot exit status: 0
2019-09-30 11:07:34 UTC [wrapper] STATUSCODE: 0
2019-09-30 11:07:34 UTC [wrapper] apfmon messages muted
---- find pandaIDs.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 30 08:10 pandaIDs.out
drwx------. 14 dcameron zp   216 Sep 30 08:10 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

2019-09-30 11:07:34 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 dcameron zp 11 Sep 30 08:10 /home/dcameron/boinc/slots/0/pilot2/pandaIDs.out
2019-09-30 11:07:34 UTC [wrapper] pandaIDs.out content:
4494479989

2019-09-30 11:07:34 UTC [wrapper] Test setup, not cleaning
2019-09-30 11:07:34 UTC [wrapper] ==== wrapper stdout END ====
2019-09-30 11:07:34 UTC [wrapper] ==== wrapper stderr END ====
2019-09-30 11:07:34 UTC [wrapper] wrapper wrapperexiting ec=0, duration=17828
2019-09-30 11:07:34 UTC [wrapper] apfmon messages muted
2019-09-30 13:07:34,335: ***************diag file************
2019-09-30 13:07:34,336: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=17827.60s
KernelTime=542.33s
UserTime=69439.95s
CPUUsage=392%
MaxResidentMemory=1945400kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=590690
MinorPageFaults=21802328
Swaps=0
ForcedSwitches=1911137
WaitSwitches=12273299
Inputs=134795968
Outputs=1037528
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@pcoslo5.cern.ch
exitcode=0
2019-09-30 13:07:34,339: ******************************WorkDir***********************
2019-09-30 13:07:34,339: total 282560
drwxrwx--x. 7 dcameron zp      4096 Sep 30 13:07 .
drwxrwx--x. 4 dcameron zp        24 Sep 26 17:13 ..
-rw-------. 1 dcameron zp   7579780 Sep 30 08:10 agis_ddmendpoints.json
-rw-------. 1 dcameron zp   3948687 Sep 30 08:10 agis_schedconf.cvmfs.json
drwx------. 2 dcameron zp         6 Sep 30 08:10 .alrb
drwxr-xr-x. 3 dcameron zp        17 Sep 30 08:10 APPS
-rw-------. 1 dcameron zp       548 Sep 30 08:10 .asetup
-rw-------. 1 dcameron zp       826 Sep 30 08:11 .asetup.save
drwx------. 2 dcameron zp         6 Sep 30 08:10 .asetup-sysbin_1965347
-rw-r--r--. 1 dcameron zp         0 Sep 30 08:10 boinc_lockfile
-rw-r--r--. 1 dcameron zp      8192 Sep 30 13:07 boinc_mmap_file
-rw-r--r--. 1 dcameron zp       537 Sep 30 12:59 boinc_task_state.xml
-rw-------. 1 dcameron zp       517 Sep 30 13:07 DzXMDmIqlYvnShfckohDCDFpABFKDmABFKDmGXTSDmABFKDmUUNDjm.diag
-rw-r--r--. 1 dcameron zp 275241058 Sep 30 08:10 EVNT.18605762._000122.pool.root.1
-rw-------. 1 dcameron zp     81655 Sep 30 13:06 heartbeat.json
-rw-r--r--. 1 dcameron zp      6290 Sep 30 08:10 init_data.xml
-rw-r--r--. 1 dcameron zp    267503 Sep 30 08:10 input.tar.gz
-rw-r--r--. 1 dcameron zp       112 Sep 30 08:10 job.xml
-rw-------. 1 dcameron zp    960299 Sep 30 13:07 log.19056259._006706.job.log.1
-rw-------. 1 dcameron zp    826900 Sep 30 13:06 log.19056259._006706.job.log.tgz.1
-rw-------. 1 dcameron zp       463 Sep 30 13:07 output.list
-rw-------. 1 dcameron zp      2842 Sep 29 12:42 pandaJobData.out
drwx------. 3 dcameron zp       229 Sep 30 08:10 pilot2
-rw-r--r--. 1 dcameron zp    259319 Sep 29 12:37 pilot2.tar.gz
-rw-------. 1 dcameron zp     10883 Sep 30 13:07 pilotlog.txt
-rw-r--r--. 1 dcameron zp      4480 Sep 29 12:42 queuedata.json
-rw-r--r--. 1 dcameron zp       815 Sep 30 08:10 RTE.tar.gz
-rwxr-xr-x. 1 dcameron zp      7941 Sep 30 08:10 run_atlas
-rwx------. 1 dcameron zp     12762 Sep 29 12:42 runpilot2-wrapper.sh
-rw-r--r--. 1 dcameron zp       692 Sep 30 13:07 runtime_log
-rw-r--r--. 1 dcameron zp      8044 Sep 30 13:07 runtime_log.err
-rw-------. 1 dcameron zp       240 Sep 30 08:10 setup.sh.local
drwxrwx--x. 2 dcameron zp       131 Sep 30 13:07 shared
-rw-r--r--. 1 dcameron zp      8688 Sep 30 08:10 start_atlas.sh
-rw-r--r--. 1 dcameron zp     17560 Sep 30 13:07 stderr.txt
-rw-r--r--. 1 dcameron zp       107 Sep 30 08:10 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 dcameron zp        28 Sep 30 13:07 wrapper_checkpoint.txt

2019-09-30 13:07:34,339: running start_atlas return value is 0
2019-09-30 13:07:34,339: Parent exit 0
2019-09-30 13:07:34,340: child process exit 0
13:07:34 (1961349): run_atlas exited; CPU time 69440.257933
13:07:34 (1961349): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN