Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
18:57:51 (8786): wrapper (7.7.26015): starting
18:57:51 (8786): wrapper: running run_atlas (--nthreads 4)
2019-08-21 18:57:51,201: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-21 18:57:51,201: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-21 18:57:51,202: THREADS=4

2019-08-21 18:57:51,204: Checking for CVMFS
2019-08-21 18:57:53,112: CVMFS is installed
2019-08-21 18:57:53,115: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-21 18:57:53,116: This is not SLC6, need to run with Singularity....
2019-08-21 18:57:53,116: Checking Singularity...
2019-08-21 18:57:53,118: Singularity is not installed, using version from CVMFS
2019-08-21 18:57:53,119: Testing the function of Singularity...
2019-08-21 18:57:53,119: 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
2019-08-21 18:57:53,404: Singularity Works...
2019-08-21 18:57:53,404: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-21 18:57:53,899: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-21 18:57:53,900: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-21 18:57:53,900: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-21 18:57:53,901: export ATHENA_PROC_NUMBER=4;
2019-08-21 18:57:53,921: start atlas job with PandaID=4454073462
2019-08-21 18:57:53,921: 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
2019-08-21 20:36:30,166: running cmd return value is 0
2019-08-21 20:36:30,169: Moving ./HITS.18722355._015285.pool.root.1 to shared/HITS.pool.root.1
2019-08-21 20:36:30,170: *****************The last 100 lines of the pilot log******************
2019-08-21 20:36:30,177: 2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722355
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 20997 s
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-21 18:35:31,330 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 15590
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 15590
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4454073462 has completed
2019-08-21 18:35:31,331 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-21 18:35:31,339 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4454073462
2019-08-21 18:35:32,345 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [15590]
2019-08-21 18:35:32,345 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 15590
2019-08-21 18:35:32,345 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-21 18:35:33,348 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-21 18:35:33,349 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=15590
2019-08-21 18:35:33,407 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [15590] (in reverse order)
2019-08-21 18:35:33,458 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-21 18:35:33,459 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-21 18:35:33,459 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-21 18:35:33,459 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-21 18:35:33,972 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-21 18:35:43,973 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-21 18:35:43,973 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-21 18:35:44,019 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36378247168 B)
2019-08-21 18:35:44,019 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-21 18:35:44,020 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-21 18:35:44,084 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-21 18:35:44,099 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-21 18:35:44,120 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-21 18:35:44,121 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(job, started 139676910528256)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(payload, started 139676799186688)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(create_data_payload, started 139676815972096)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(copytool_in, started 139676262315776)>, <ExcThread(validate, started 139676832757504)>, <ExcThread(copytool_out, started 139676790793984)>, <ExcThread(failed_post, started 139676245530368)>, <ExcThread(monitor, started 139676295886592)>, <ExcThread(job_monitor, started 139676782401280)>, <ExcThread(data, started 139676824364800)>]
2019-08-21 18:35:44,133 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-21 18:35:44,133 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-21 18:35:44,233 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-21 18:35:44,388 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-21 18:35:44,389 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-21 18:35:44,523 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-21 18:35:44,523 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(job, started 139676910528256)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(create_data_payload, started 139676815972096)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(copytool_in, started 139676262315776)>, <ExcThread(validate, started 139676832757504)>, <ExcThread(copytool_out, started 139676790793984)>, <ExcThread(monitor, started 139676295886592)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:44,597 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-21 18:35:44,712 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-21 18:35:44,825 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-21 18:35:44,825 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(job, started 139676910528256)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(copytool_in, started 139676262315776)>, <ExcThread(validate, started 139676832757504)>, <ExcThread(copytool_out, started 139676790793984)>, <ExcThread(monitor, started 139676295886592)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:44,868 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-21 18:35:44,923 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-21 18:35:44,924 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-21 18:35:44,926 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-21 18:35:44,926 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(copytool_in, started 139676262315776)>, <ExcThread(validate, started 139676832757504)>, <ExcThread(copytool_out, started 139676790793984)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:44,988 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-21 18:35:45,027 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-21 18:35:45,027 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(copytool_in, started 139676262315776)>, <ExcThread(copytool_out, started 139676790793984)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:45,081 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-21 18:35:45,100 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-21 18:35:45,128 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-21 18:35:45,128 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(validate_pre, started 139676287493888)>, <ExcThread(validate_post, started 139676253923072)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:45,147 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-21 18:35:45,222 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-21 18:35:45,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-21 18:35:45,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(queue_monitor, started 139676270708480)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:45,645 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-21 18:35:45,645 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-21 18:35:45,733 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-21 18:35:45,733 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(queue_monitoring, started 139676279101184)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:35:47,599 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-21 18:35:47,647 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-21 18:35:47,647 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139677126801152)>, <ExcThread(job_monitor, started 139676782401280)>]
2019-08-21 18:36:29,667 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-21 18:36:29,667 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-21 18:36:29,737 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-21 18:36:29,737 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-21 18:36:29,737 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-21 18:36:29 UTC [wrapper] ==== pilot stdout END ====
2019-08-21 18:36:29 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-21 18:36:29 UTC [wrapper] Pilot exit status: 0
2019-08-21 18:36:29 UTC [wrapper] STATUSCODE: 0
2019-08-21 18:36:29 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 21 18:58 pilot
-rwx------.  1 grid grid 20628 Aug 19 14:00 pilot.py
-rw-------.  1 grid grid     9 Aug 19 14:00 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-21 18:36:30 UTC [wrapper] Test setup, not cleaning
2019-08-21 18:36:30 UTC [wrapper] ==== wrapper stdout END ====
2019-08-21 18:36:30 UTC [wrapper] ==== wrapper stderr END ====
2019-08-21 18:36:30 UTC [wrapper] wrapper wrapperexiting ec=0, duration=5916
2019-08-21 18:36:30 UTC [wrapper] apfmon messages muted
2019-08-21 20:36:30,181: ***************diag file************
2019-08-21 20:36:30,181: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5915.90s
KernelTime=200.27s
UserTime=20896.88s
CPUUsage=356%
MaxResidentMemory=1944804kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=268898
MinorPageFaults=12706529
Swaps=0
ForcedSwitches=2433810
WaitSwitches=5162014
Inputs=65509008
Outputs=522152
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-21 20:36:30,191: ******************************WorkDir***********************
2019-08-21 20:36:30,192: total 208076
drwxrwx--x. 6 grid grid      4096 Aug 21 20:36 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7469803 Aug 21 18:58 agis_ddmendpoints.json
-rw-------. 1 grid grid   4330639 Aug 21 18:58 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 21 18:57 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 21 18:57 APPS
-rw-------. 1 grid grid       538 Aug 21 18:57 .asetup
-rw-------. 1 grid grid       826 Aug 21 18:59 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 21 18:57 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 21 20:36 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 21 20:29 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 199304400 Aug 21 18:57 EVNT.18605773._000304.pool.root.1
-rw-------. 1 grid grid     63499 Aug 21 20:35 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 21 18:57 init_data.xml
-rw-rw-r--. 1 grid grid    263694 Aug 21 18:57 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 21 18:57 job.xml
-rw-------. 1 grid grid    390508 Aug 21 20:36 log.18722355._015285.job.log.1
-rw-------. 1 grid grid    816054 Aug 21 20:35 log.18722355._015285.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 21 20:36 output.list
-rw-------. 1 grid grid       516 Aug 21 20:36 p3PLDmt8RKvnShfckohDCDFpABFKDmABFKDmJaANDmABFKDmcszjFn.diag
-rw-------. 1 grid grid      2957 Aug 21 00:50 pandaJobData.out
drwx------. 3 grid grid       174 Aug 19 14:00 pilot2
-rw-r--r--. 1 grid grid    255033 Aug 21 00:25 pilot2.tar.gz
-rw-------. 1 grid grid     11351 Aug 21 20:36 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 21 00:49 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 21 18:57 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 21 18:57 run_atlas
-rwx------. 1 grid grid     12641 Aug 21 00:50 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 21 20:36 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 21 20:36 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 21 20:36 shared
-rw-rw-r--. 1 grid grid      8688 Aug 21 18:57 start_atlas.sh
-rw-rw-r--. 1 grid grid     19633 Aug 21 20:36 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 21 18:57 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 21 20:36 wrapper_checkpoint.txt

2019-08-21 20:36:30,192: running start_atlas return value is 0
2019-08-21 20:36:30,192: Parent exit 0
2019-08-21 20:36:30,194: child process exit 0
20:36:30 (8786): run_atlas exited; CPU time 20897.271542
20:36:30 (8786): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN