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Jobsub ID 98340.163@justin-prod-sched02.dune.hep.ac.uk

Jobsub ID98340.163@justin-prod-sched02.dune.hep.ac.uk
Workflow ID4114
Stage ID1
User namegvittist@fnal.gov
HTCondor Groupgroup_dune
RequestedProcessors1
RSS bytes4194304000 (4000 MiB)
Wall seconds limit18000 (5 hours)
Submitted time2024-11-16 02:41:43
SiteUK_QMUL
EntryDUNE_UK_London_QMUL_arcce02
Last heartbeat2024-11-16 07:06:48
From worker nodeHostnamecn081.htc.esc.qmul
cpuinfoIntel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz
OS releaseScientific Linux release 7.9 (Nitrogen)
Processors1
RSS bytes4194304000 (4000 MiB)
Wall seconds limit171000 (47 hours)
Inner Apptainer?True
Job stateoutputting_failed
Allocator namejustin-allocator-pro.dune.hep.ac.uk
Started2024-11-16 02:42:55
Input fileshd-protodune:np04hd_raw_run029197_1025_dataflow3_datawriter_0_20240917T014145.hdf5
JobscriptExit code0
Real time4h (15815s)
CPU time15m (953s = 6%)
Outputting started2024-11-16 07:06:30
Output files
Finished2024-11-16 07:06:48
List job events     Wrapper job log

Jobscript log (last 10,000 characters)

Input PFN = root://eospublic.cern.ch:1094//eos/experiment/neutplatform/protodune/dune/hd-protodune/97/ee/np04hd_raw_run029197_1025_dataflow3_datawriter_0_20240917T014145.hdf5
Setting up larsoft UPS area... /cvmfs/larsoft.opensciencegrid.org
Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/
/cvmfs/larsoft.opensciencegrid.org/products/xrootd/v5_5_5a/Linux64bit+3.10-2.17-e26-p3915-prof/lib/libXrdPosixPreload.so
../justin-jobscript: line 64:  1136 Segmentation fault      (core dumped) lar -c $FCL_FILE $events_option -o $outFile "$pfn" > ${fname}_reco_${now}.log 2>&1
=== Start last 100 lines of lar log file ===
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
RawFrameSource: got 10240 raw::RawDigit objects
	input nticks=5859 keeping as is
Retagger: tagging trace set: raw with 10240 traces, 0 summary
wclsFrameSaver: saving raw::RawDigits tagged "raw"
wclsFrameSaver: found empty channel masks for "bad"
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
WARNING: Could not find offline channel for 9 0 32
RawFrameSource: got 10240 raw::RawDigit objects
	input nticks=5859 keeping as is
Retagger: tagging trace set: raw with 10240 traces, 0 summary
wclsFrameSaver: saving raw::RawDigits tagged "raw"
wclsFrameSaver: found empty channel masks for "bad"
16-Nov-2024 07:05:03 GMT  Closed output file "np04hd_raw_run029197_1025_dataflow3_datawriter_0_20240917T014145_reco_2024-10-27T_024258Z.root"
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0:
  #000: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5I.c line 456 in H5Idec_ref(): can't decrement ID ref count
    major: Object atom
    minor: Unable to decrement reference count
  #001: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Iint.c line 1018 in H5I_dec_app_ref(): can't decrement ID ref count
    major: Object atom
    minor: Unable to decrement reference count
  #002: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Fint.c line 251 in H5F__close_cb(): unable to close file
    major: File accessibility
    minor: Unable to close file
  #003: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5VLcallback.c line 3983 in H5VL_file_close(): file close failed
    major: Virtual Object Layer
    minor: Unable to close file
  #004: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5VLcallback.c line 3952 in H5VL__file_close(): file close failed
    major: Virtual Object Layer
    minor: Unable to close file
  #005: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5VLnative_file.c line 838 in H5VL__native_file_close(): can't close file
    major: File accessibility
    minor: Unable to decrement reference count
  #006: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Fint.c line 2349 in H5F__close(): can't close file
    major: File accessibility
    minor: Unable to close file
  #007: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Fint.c line 2522 in H5F_try_close(): problems closing file
    major: File accessibility
    minor: Unable to close file
  #008: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Fint.c line 1605 in H5F__dest(): unable to close file
    major: File accessibility
    minor: Unable to close file
  #009: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5FD.c line 830 in H5FD_close(): close failed
    major: Virtual File Layer
    minor: Unable to close file
  #010: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5FDsec2.c line 456 in H5FD__sec2_close(): unable to close file, errno = 110, error message = 'Connection timed out'
    major: Low-level I/O
    minor: Unable to close file
HighFive::~Object: reference counter decrease failure

===================================================================================================================================
TimeTracker printout (sec)                           Min           Avg           Max         Median          RMS         nEvts   
===================================================================================================================================
Full event                                         39.1258       244.93        944.824       173.376       249.306        31     
-----------------------------------------------------------------------------------------------------------------------------------
source:HDF5RawInput3(read)                       2.5452e-05    5.01417e-05   0.000176179   4.5366e-05    2.63355e-05      31     
produce:tpcrawdecoder:PDHDTPCReader                9.40127       10.2791       11.185        10.2625      0.325902        31     
produce:triggerrawdecoder:PDHDTriggerReader3      0.441285      0.465688      0.710625      0.459697      0.0452161       31     
produce:timingrawdecoder:PDHDTimingRawDecoder     0.0164399     0.0167617     0.0219792     0.0165648    0.00095752       31     
produce:pdhddaphne:DAPHNEReaderPDHD                12.2868       72.2019       260.907       31.5884       67.4727        31     
produce:fembfilter:PDHDFEMBFilter                0.000126303   0.000222532   0.000970226   0.000155595   0.000165259      31     
produce:wclsdatahdfilter:WireCellToolkit           11.3949       11.9764       14.6957       11.7821      0.615014        31     
[art]:TriggerResults:TriggerResultInserter       1.6029e-05    2.28863e-05   6.9974e-05     2.182e-05    9.18466e-06      31     
end_path:out1:RootOutput                          2.452e-06    4.44613e-06   1.8545e-05     3.906e-06    2.84855e-06      31     
end_path:out1:RootOutput(write)                    3.86357       149.989       751.439       36.9174       218.731        31     
===================================================================================================================================

====================================================================================================
MemoryTracker summary (base-10 MB units used)

  Peak virtual memory usage (VmPeak)  : 3250.46 MB
  Peak resident set size usage (VmHWM): 1814.9 MB
  Details saved in: 'mem.db'
====================================================================================================
=== End last 100 lines of lar log file ===
lar exit code 0
justIN time: 2024-11-17 07:53:40 UTC       justIN version: 01.01.09