Segmentation fault (core dumped) with many functions
Added by S BR over 5 years ago
Dear Users,
Recently I am experiencing Segmentation fault (core dumped) with many functions in CDO. Following is an example.
cdo sellonlatbox,60,150,10,55 pr_Amon_MPI-ESM-P_data.nc pr_Amon_MPI-ESM-P_data_area.nc
Segmentation fault (core dumped)
The same command used to work fine but now it doesn't work.
I tried with '-L' and also with '-selvar,varname' but still it doesn't work. Any idea?
The following is my CDO details.
cdo -V
Climate Data Operators version 1.9.5 (http://mpimet.mpg.de/cdo)
System: x86_64-redhat-linux-gnu
CXX Compiler: g++ -std=c++0x -fpermissive -I/usr/include/json-c -I/usr/include/cdTime -fopenmp
CXX version : g++ (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
C Compiler: gcc -I/usr/include/json-c -I/usr/include/cdTime -fopenmp
C version : gcc (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
F77 Compiler: gfortran -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules
F77 version : GNU Fortran (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
Features: 31GB 8threads C++11 Fortran DATA PTHREADS OpenMP45 NC4/HDF5/threadsafe OPeNDAP UDUNITS2 PROJ.4 CURL FFTW3 CMOR SSE2
Libraries: proj/4.9 CMOR/3.3.2 curl/7.19.7
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.5
CGRIBEX library version : 1.9.1
GRIB_API library version : 2.4.1
NetCDF library version : 4.4.1.1 of Sep 25 2017 16:11:15 $
HDF5 library version : 1.10.1 threadsafe
EXSE library version : 1.4.0
FILE library version : 1.8.3
Replies (6)
RE: Segmentation fault (core dumped) with many functions - Added by Ralf Mueller over 5 years ago
hi S BR!
please upload some sample data if possible
cheers
ralf
RE: Segmentation fault (core dumped) with many functions - Added by S BR over 5 years ago
Hi Ralf,
Please find herewith attached the file. The size of my original file is 3.3 GB. I have taken a small part of it, which is 69 MB, but still CDO doesn't work.
Thanks.
SBR
RE: Segmentation fault (core dumped) with many functions - Added by Ralf Mueller over 5 years ago
thx - btw: gzip is pretty effective on nc files
RE: Segmentation fault (core dumped) with many functions - Added by S BR over 5 years ago
Hi Ralf,
Do you ask me to send the zipped NetCDF file.
Thanks
S BR
RE: Segmentation fault (core dumped) with many functions - Added by Ralf Mueller over 5 years ago
not at all, sry.
cheers
ralf
RE: Segmentation fault (core dumped) with many functions - Added by Uwe Schulzweida over 5 years ago
Thanks for the data! I can't reproduce the error on our systems but I found a CDO internal memory problem with your data. Parsing the attribute pr:associated_files causes the memory problem. This problem will be solved in the next CDO release. A prerelease for testing is available in the download area.
Cheers,
Uwe