Jobsub ID 79838.140@justin-prod-sched02.dune.hep.ac.uk
Jobsub ID | 79838.140@justin-prod-sched02.dune.hep.ac.uk |
Workflow ID | 3513 |
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 05:32:32 |
Site | US_FNAL-T1 |
Entry | CMSHTPC_T1_US_FNAL_condce_opp1_whole |
Last heartbeat | 2024-09-27 10:07:37 |
From worker node | Hostname | dunegli-35088-0-cmswn2324.fnal.gov |
cpuinfo | Intel(R) Xeon(R) CPU E5-2670 v3 @ 2.30GHz |
OS release | Scientific Linux release 7.9 (Nitrogen) |
Processors | 1 |
RSS bytes | 4193255424 (3999 MiB) |
Wall seconds limit | 171000 (47 hours) |
Inner Apptainer? | True |
Job state | jobscript_error |
Allocator name | justin-allocator-pro.dune.hep.ac.uk |
Started | 2024-09-27 09:04:18 |
Input files | hd-protodune:np04hd_raw_run027358_0002_dataflow2_datawriter_0_20240621T230418.hdf5
|
Jobscript | Exit code | 139 |
Real time | 0m (0s) |
CPU time | 0m (0s = 0%) |
Outputting started | |
Output files | |
Finished | 2024-09-27 10:07:37 |
Saved logs | justin-logs:79838.140-justin-prod-sched02.dune.hep.ac.uk.logs.tgz |
List job events Wrapper job log |
Jobscript log (last 10,000 characters)
: Can'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 10:03:34 2024
, filename = 'root://dcdndoor.sdcc.bnl.gov:1094//pnfs/sdcc.bnl.gov/data/dune/RSE/hd-protodune/3d/49/np04hd_raw_run027358_0002_dataflow2_datawriter_0_20240621T230418.hdf5', file descriptor = 24, errno = 116, error message = 'Stale file handle', buf = 0xd9b1270, 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 4.6592e-05 81.4153 217.464 57.4764 64.0319 10
-----------------------------------------------------------------------------------------------------------------------------------
source:HDF5RawInput3(read) 2.3944e-05 0.000116682 0.000593903 5.425e-05 0.000164916 10
produce:tpcrawdecoder:PDHDTPCReader 22.6496 61.7213 182.727 30.3481 58.3372 9
produce:triggerrawdecoder:PDHDTriggerReader3 0.0513245 0.143485 0.589291 0.0521421 0.180436 9
produce:timingrawdecoder:PDHDTimingRawDecoder 0.0253877 0.0563434 0.201362 0.025756 0.0594174 9
produce:pdhddaphne:DAPHNEReaderPDHD 4.56045 6.5103 12.0105 5.20661 2.64218 9
produce:fembfilter:PDHDFEMBFilter 0.000116947 0.000413581 0.000945029 0.000357873 0.000309186 9
produce:wclsdatahdfilter:WireCellToolkit 15.8256 16.2277 16.6113 16.222 0.249456 9
[art]:TriggerResults:TriggerResultInserter 2.2662e-05 9.23743e-05 0.000497411 3.9872e-05 0.000144563 9
end_path:out1:RootOutput 3.192e-06 1.02913e-05 2.5533e-05 8.633e-06 6.14579e-06 9
end_path:out1:RootOutput(write) 5.63027 5.80039 6.24441 5.6926 0.205826 9
===================================================================================================================================
====================================================================================================
MemoryTracker summary (base-10 MB units used)
Peak virtual memory usage (VmPeak) : 3213.08 MB
Peak resident set size usage (VmHWM): 1710.79 MB
Details saved in: 'mem.db'
====================================================================================================
%MSG-s ArtException: PostEndJob 27-Sep-2024 10:03:36 UTC 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: 27358 subRun: 1 event: 318
Unable to open the dataset "/TriggerRecord00318.0000/RawData/Detector_Readout_0x00000193_WIBEth": (Low-level I/O) Read failed
---- StdException END
Exception going through path produce
---- ScheduleExecutionFailure END
---- EventProcessorFailure END
%MSG
../justin-jobscript: line 145: 1313 Segmentation fault (core dumped) LD_PRELOAD=$XROOTD_LIB/libXrdPosixPreload.so lar -c ${FCL1} -n ${nevents} ${extra_line} ${pfn}
Error in reco1