Crash in libcdi library
Added by Richard Harvey 1 day ago
Hello,
I get an intermittent error when running cdo remap command, with a cryptic error message :
Interpolation Command: cdo -f nc4 -O -P 2 -m missval=-9999 -selgridcell,1/913 [ -copy -apply,-remap,/home/operation/scripts/nifi_forecast_processors/fps_canada/data/GEPS/2025052712/tmp/stations_unstruct_grid,/home/operation/scripts/nifi_forecast_processors/fps_canada/data/GEPS/2025052712/tmp/weights.nc [ CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P000_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P003_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P006_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P009_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P012_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P015_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P018_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P021_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P024_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P027_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P030_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P033_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P036_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P039_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P042_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P045_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P048_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P051_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P054_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P057_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P060_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P063_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P066_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P069_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P072_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P075_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P078_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P081_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P084_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P087_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P090_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P093_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P096_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P099_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P102_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P105_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P108_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P111_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P114_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P117_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P120_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P123_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P126_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P129_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P132_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P135_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P138_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P141_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P144_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P147_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P150_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P153_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P156_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P159_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P162_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P165_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P168_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P171_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P174_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P177_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P180_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P183_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P186_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P189_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P192_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P198_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P204_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P210_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P216_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P222_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P228_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P234_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P240_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P246_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P252_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P258_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P264_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P270_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P276_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P282_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P288_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P294_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P300_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P306_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P312_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P318_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P324_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P330_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P336_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P342_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P348_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P354_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P360_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P366_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P372_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P378_allmbrs.grib2 CMC_geps-raw_SPFH_TGL_2_latlon0p5x0p5_2025052712_P384_allmbrs.grib2 ] ] /home/operation/scripts/nifi_forecast_processors/fps_canada/data/GEPS/2025052712/tmp/tmpfile.nc
2025-05-27 17:21:28 - INFO - [bt] Execution path:
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libcdi.so.0(+0x63eb2) [0x7f31f735feb2]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libcdi.so.0(+0x6433c) [0x7f31f736033c]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libcdi.so.0(reshGetValue+0x9) [0x7f31f73608c9]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libcdi.so.0(vlistCheckVarID+0x10) [0x7f31f7398b20]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libcdi.so.0(vlistInqVarParam+0x22) [0x7f31f7399502]
2025-05-27 17:21:28 - INFO - [bt] cdo(+0x36a7de) [0x55b59ddc47de]
2025-05-27 17:21:28 - INFO - [bt] cdo(+0x1e8b48) [0x55b59dc42b48]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libc.so.6(+0x89134) [0x7f31f56a8134]
2025-05-27 17:21:28 - INFO - [bt] /lib/x86_64-linux-gnu/libc.so.6(+0x1097dc) [0x7f31f57287dc]
2025-05-27 17:21:28 - INFO - ERROR, reshGetElem, ../../../../libcdi/src/resource_handle.c, line 414, called from vlist_to_pointer
2025-05-27 17:21:28 - INFO - errorString: "Error while trying to resolve the ID "vlistID" in `vlist_to_pointer()`: list element not found. The failed ID is 224"
2025-05-27 17:21:28 - INFO - interpolate_data-> Error running cdo command: 'NoneType' object has no attribute 'read'
...
The error occurs intermittently, apparently randomly, with different input parameters, so the cause is hard to diagnose. Could this indicate that one or more input files are corrupt? Any other ideas?
Thanks in advance for any help.
Richard H.
Replies (1)
RE: Crash in libcdi library - Added by Richard Harvey about 13 hours ago
One more detail : output of cdo --version:
cdo --version
Climate Data Operators version 2.1.1 (https://mpimet.mpg.de/cdo)
System: x86_64-pc-linux-gnu
CXX Compiler: g++ -g -O2 -ffile-prefix-map=/build/cdo-zAriqP/cdo-2.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread
CXX version : g++ (Debian 12.2.0-10) 12.2.0
C Compiler: gcc -g -O2 -ffile-prefix-map=/build/cdo-zAriqP/cdo-2.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fPIC -fopenmp -pthread -pthread
C version : gcc (Debian 12.2.0-10) 12.2.0
F77 Compiler: f77 -g -O2 -ffile-prefix-map=/build/cdo-zAriqP/cdo-2.1.1=. -fstack-protector-strong
F77 version : GNU Fortran (Debian 12.2.0-10) 12.2.0
Features: 125GB 16threads c++17 OpenMP45 Fortran pthreads HDF5 NC4/HDF5/threadsafe OPeNDAP sz udunits2 proj magics curl fftw3 hirlam_extensions sse2
Libraries: yac/2.6.1 HDF5/1.10.8 proj/9.1.1 curl/7.88.1(h7.86.0) magics/4.13.0
CDI data types: SizeType=size_t
CDI file types: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5 nczarr
CDI library version : 2.1.1
ecCodes library version : 2.28.0
NetCDF library version : 4.9.0 of Aug 7 2022 23:41:41 $
HDF5 library version : library undefined
exse library version : 1.4.2
FILE library version : 1.9.1