Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
15:18:51 (323): wrapper (7.7.26015): starting
15:18:51 (323): 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=4446270490
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.18722465._010242.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 17:19:27,718 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 55360 s
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 17:19:27,719 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7099
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7099
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446270490 has completed
2019-08-16 17:19:27,720 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 17:19:27,728 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446270490
2019-08-16 17:19:28,733 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7099]
2019-08-16 17:19:28,733 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7099
2019-08-16 17:19:28,733 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 17:19:29,338 | INFO     | monitor             | pilot.control.monitor            | control                   | 14420 s have passed since pilot start
2019-08-16 17:19:29,739 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 17:19:29,739 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7099
2019-08-16 17:19:29,785 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7099] (in reverse order)
2019-08-16 17:19:29,827 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 17:19:29,828 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 17:19:29,828 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 17:19:29,828 | 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 17:19:30,338 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 17:19:40,378 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 17:19:40,379 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 17:19:40,415 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36242980864 B)
2019-08-16 17:19:40,415 | 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 17:19:40,415 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 17:19:40,428 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 17:19:40,433 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 17:19:40,556 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 17:19:40,556 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 17:19:40,692 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-16 17:19:40,692 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(job, started 139896553473792)>, <ExcThread(execute_payloads, started 139895959951104)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(create_data_payload, started 139896010307328)>, <ExcThread(copytool_out, started 139896536688384)>, <ExcThread(copytool_in, started 139896001914624)>, <ExcThread(data, started 139896545081088)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(validate_post, started 139895985129216)>, <ExcThread(validate_pre, started 139896494724864)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:40,706 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 17:19:40,707 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 17:19:40,775 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 17:19:40,797 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 17:19:40,797 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 17:19:40,797 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 17:19:40,800 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-16 17:19:40,801 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(create_data_payload, started 139896010307328)>, <ExcThread(copytool_out, started 139896536688384)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(validate_post, started 139895985129216)>, <ExcThread(validate_pre, started 139896494724864)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:41,208 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 17:19:41,213 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-16 17:19:41,213 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(copytool_out, started 139896536688384)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(validate_post, started 139895985129216)>, <ExcThread(validate_pre, started 139896494724864)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:41,428 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 17:19:41,515 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-16 17:19:41,516 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(validate_post, started 139895985129216)>, <ExcThread(validate_pre, started 139896494724864)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:41,549 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 17:19:41,616 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-16 17:19:41,617 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(validate_post, started 139895985129216)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:41,786 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 17:19:41,818 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-16 17:19:41,819 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(validate, started 139896519902976)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(failed_post, started 139895968343808)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:41,837 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 17:19:41,857 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 17:19:41,920 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 17:19:41,920 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(queue_monitor, started 139895406327552)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:42,154 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 17:19:42,210 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 17:19:42,210 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 17:19:42,222 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 17:19:42,222 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(queue_monitoring, started 139896503117568)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:45,156 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 17:19:45,242 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 17:19:45,242 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139896769746688)>, <ExcThread(job_monitor, started 139895976736512)>]
2019-08-16 17:19:50,649 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-16 17:19:50,650 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 17:19:50,679 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 17:19:50,679 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 17:19:50,679 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 17:19:50 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 17:19:50 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 17:19:50 UTC [wrapper] Pilot exit status: 0
2019-08-16 17:19:50 UTC [wrapper] STATUSCODE: 0
2019-08-16 17:19:50 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 16 15:19 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

2019-08-16 17:19:50 UTC [wrapper] Test setup, not cleaning
2019-08-16 17:19:50 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 17:19:50 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 17:19:50 UTC [wrapper] wrapper wrapperexiting ec=0, duration=14456
2019-08-16 17:19:50 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=14456.92s
KernelTime=399.53s
UserTime=55149.04s
CPUUsage=384%
MaxResidentMemory=1945280kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=435632
MinorPageFaults=18113191
Swaps=0
ForcedSwitches=6376929
WaitSwitches=9231323
Inputs=105378952
Outputs=886520
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 235732
drwxrwx--x. 6 grid grid      4096 Aug 16 19:19 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7413078 Aug 16 15:19 agis_ddmendpoints.json
-rw-------. 1 grid grid   4400295 Aug 16 15:19 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 16 15:18 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 16 15:18 APPS
-rw-------. 1 grid grid       538 Aug 16 15:18 .asetup
-rw-------. 1 grid grid       826 Aug 16 15:19 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 16 15:18 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 19:19 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 16 19:15 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 227268918 Aug 16 15:18 EVNT.18605785._000196.pool.root.1
-rw-------. 1 grid grid     76478 Aug 16 19:19 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 16 15:18 init_data.xml
-rw-rw-r--. 1 grid grid    261610 Aug 16 15:18 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 16 15:18 job.xml
-rw-------. 1 grid grid       518 Aug 16 19:19 jptNDmteMIvnShfckohDCDFpABFKDmABFKDmLLMbDmABFKDmQOIg2m.diag
-rw-------. 1 grid grid    706761 Aug 16 19:19 log.18722465._010242.job.log.1
-rw-------. 1 grid grid    841351 Aug 16 19:19 log.18722465._010242.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 19:19 output.list
-rw-------. 1 grid grid      2955 Aug 15 06:35 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 15 06:27 pilot2.tar.gz
-rw-------. 1 grid grid     11018 Aug 16 19:19 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 15 06:35 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 16 15:18 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 16 15:18 run_atlas
-rwx------. 1 grid grid     12641 Aug 15 06:35 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 19:19 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 19:19 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 19:19 shared
-rw-rw-r--. 1 grid grid      8688 Aug 16 15:18 start_atlas.sh
-rw-rw-r--. 1 grid grid     18689 Aug 16 19:19 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 16 15:18 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 16 19:19 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
19:19:51 (323): run_atlas exited; CPU time 55149.428640
19:19:51 (323): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN