Jobsub ID 264685.25@justin-prod-sched01.dune.hep.ac.uk
| Jobsub ID | 264685.25@justin-prod-sched01.dune.hep.ac.uk |
| Workflow ID | 3510 |
| Stage ID | 1 |
| User name | calcuttj@fnal.gov |
| HTCondor Group | group_dune.prod_mcsim |
| Requested | Processors | 1 |
| RSS bytes | 4193255424 (3999 MiB) |
| Wall seconds limit | 18000 (5 hours) |
| Submitted time | 2024-09-27 05:56:21 |
| Site | US_Wisconsin |
| Entry | HCCHTPC_US_Wisconsin_osg01_rhel7 |
| Last heartbeat | 2024-09-27 08:05:36 |
| From worker node | Hostname | herringa2001 |
| cpuinfo | AMD EPYC 7763 64-Core Processor |
| OS release | Scientific Linux release 7.9 (Nitrogen) |
| Processors | 1 |
| RSS bytes | 4193255424 (3999 MiB) |
| Wall seconds limit | 82800 (23 hours) |
| Inner Apptainer? | True |
| Job state | jobscript_error |
| Allocator name | justin-allocator-pro.dune.hep.ac.uk |
| Started | 2024-09-27 07:25:27 |
| Input files | hd-protodune:np04hd_raw_run027325_0093_dataflow3_datawriter_0_20240620T115618.hdf5
|
| Jobscript | Exit code | 139 |
| Real time | 0m (0s) |
| CPU time | 0m (0s = 0%) |
| Outputting started | |
| Output files | |
| Finished | 2024-09-27 08:05:36 |
| Saved logs | justin-logs:264685.25-justin-prod-sched01.dune.hep.ac.uk.logs.tgz |
| List job events Wrapper job log |
Jobscript log (last 10,000 characters)
an't open object
#002: /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 1877 in H5VL__dataset_open(): dataset open failed
major: Virtual Object Layer
minor: Can't open object
#003: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset
major: Dataset
minor: Can't open object
#004: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Dint.c line 1475 in H5D__open_name(): can't get object type
major: Dataset
minor: Can't get value
#005: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Oint.c line 1651 in H5O_obj_type(): unable to load object header
major: Object header
minor: Unable to protect metadata
#006: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Oint.c line 1051 in H5O_protect(): unable to load object header
major: Object header
minor: Unable to protect metadata
#007: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5AC.c line 1426 in H5AC_protect(): H5C_protect() failed
major: Object cache
minor: Unable to protect metadata
#008: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5C.c line 2370 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#009: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5C.c line 7209 in H5C__load_entry(): Can't read image*
major: Object cache
minor: Read failed
#010: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Fio.c line 148 in H5F_block_read(): read through page buffer failed
major: Low-level I/O
minor: Read failed
#011: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5PB.c line 721 in H5PB_read(): read through metadata accumulator failed
major: Page Buffering
minor: Read failed
#012: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5Faccum.c line 202 in H5F__accum_read(): driver read request failed
major: Low-level I/O
minor: Read failed
#013: /scratch/workspace/build-single/BUILDTYPE/prof/QUAL/e26/label1/swarm/label2/SLF7/build/hdf5/v1_12_2a/source/hdf5-1.12.2/src/H5FDint.c line 189 in H5FD_read(): driver read request failed
major: Virtual File Layer
minor: Read failed
#014: /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 755 in H5FD__sec2_read(): file read failed: time = Fri Sep 27 03:04:38 2024
, filename = 'root://dcdndoor.sdcc.bnl.gov:1094//pnfs/sdcc.bnl.gov/data/dune/RSE/hd-protodune/e6/af/np04hd_raw_run027325_0093_dataflow3_datawriter_0_20240620T115618.hdf5', file descriptor = 24, errno = 116, error message = 'Stale file handle', buf = 0x10c67960, total read size = 512, bytes this sub-read = 512, bytes actually read = 18446744073709551615, offset = 0
major: Low-level I/O
minor: Read failed
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 = 95, error message = 'Operation not supported'
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 5.1577e-05 83.1055 178.309 81.1028 56.7165 5
-----------------------------------------------------------------------------------------------------------------------------------
source:HDF5RawInput3(read) 4.261e-05 9.05018e-05 0.000235672 5.1577e-05 7.38015e-05 5
produce:tpcrawdecoder:PDHDTPCReader 45.7444 76.4518 149.939 55.0619 42.6271 4
produce:triggerrawdecoder:PDHDTriggerReader3 0.0877525 0.0892816 0.0914302 0.0889718 0.00136628 4
produce:timingrawdecoder:PDHDTimingRawDecoder 0.0440198 0.0445492 0.0459145 0.0441313 0.000790727 4
produce:pdhddaphne:DAPHNEReaderPDHD 4.92551 6.96068 8.83279 7.0422 1.59935 4
produce:fembfilter:PDHDFEMBFilter 0.000126007 0.000397374 0.000833736 0.000314876 0.000265776 4
produce:wclsdatahdfilter:WireCellToolkit 13.3157 14.9124 16.7738 14.7801 1.58807 4
[art]:TriggerResults:TriggerResultInserter 3.2191e-05 5.54417e-05 0.00011697 3.6303e-05 3.55642e-05 4
end_path:out1:RootOutput 7.874e-06 1.73653e-05 3.7841e-05 1.1873e-05 1.22214e-05 4
end_path:out1:RootOutput(write) 4.54886 5.42113 6.43463 5.3505 0.866995 4
===================================================================================================================================
====================================================================================================
MemoryTracker summary (base-10 MB units used)
Peak virtual memory usage (VmPeak) : 3181.11 MB
Peak resident set size usage (VmHWM): 1715.47 MB
Details saved in: 'mem.db'
====================================================================================================
%MSG-s ArtException: PostEndJob 27-Sep-2024 03:04:39 CDT ModuleEndJob
---- EventProcessorFailure BEGIN
EventProcessor: an exception occurred during current event processing
---- ScheduleExecutionFailure BEGIN
Path: ProcessingStopped.
---- StdException BEGIN
An exception was thrown while processing module PDHDTPCReader/tpcrawdecoder run: 27325 subRun: 1 event: 13051
Unable to open the dataset "/TriggerRecord13051.0000/RawData/Detector_Readout_0x00000071_WIBEth": (Low-level I/O) Read failed
---- StdException END
Exception going through path produce
---- ScheduleExecutionFailure END
---- EventProcessorFailure END
%MSG
../justin-jobscript: line 145: 1314 Segmentation fault (core dumped) LD_PRELOAD=$XROOTD_LIB/libXrdPosixPreload.so lar -c ${FCL1} -n ${nevents} ${extra_line} ${pfn}
Error in reco1 