Error (cdf_put_vara_double): NetCDF: HDF error

Hi there,

I am new to CDO. I just installed cdo by following step.

  1. tar xf cdo-$VERSION.tar and cd cd cdo-$VERSION
  2. ./configure -prefix=/home/cdo and make
  3. make install

And then I want to rearrange data from longitude 0 to 360 degrees to -180 to 180 degrees. So I use the sellonlatbox option

cdo -sellonlatbox,-180,180,-90,90 test.nc test_output.nc

However, I got error informaiton like this

cdf_put_vara_double: name=c2h6fire  type=NC_FLOAT  minval=0.000000  maxval=0.000000

Error (cdf_put_vara_double): NetCDF: HDF error
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: H5T.c line 1754 in H5Tclose(): not a datatype
    major: Invalid arguments to routine
    minor: Inappropriate type

Error (cdf_close): NetCDF: HDF error

I wonder how to fix this kind of error. Also, I got the output data with the modified longitude even though there is error informaiton. I wonder if this kind of error would corrupt the output data.

Cheers,
Lixu

Replies (4)

RE: Error (cdf_put_vara_double): NetCDF: HDF error - Added by Ralf Mueller over 5 years ago

hi!

In order to compile CDO with netcdf support you need to use the --with-netcdf options accordingly. please check the documentation of the options with

./configure --help

Especially for unix/linux systems there are installation methods without compiling it manually like Anaconda, or system-packages for debian/ubuntu, SuSE, fedora and archlinux.

cheers
ralf

RE: Error (cdf_put_vara_double): NetCDF: HDF error - Added by Lixu Jin over 5 years ago

Hi Ralf,

Thanks for answering. I just used use the --with-netcdf. Still, there is an error.

home/lixujin> cdo -sellonlatbox,-180,180,-90,90 GFAS_201810.nc output.nc

Error (cdf_enddef): NetCDF: HDF error
Segmentation fault

Do you have any advice on it?

Cheers,
Lixu

RE: Error (cdf_put_vara_double): NetCDF: HDF error - Added by Lixu Jin over 5 years ago

Also, my cdo -v information is listed below

Climate Data Operators version 1.9.7.1 (http://mpimet.mpg.de/cdo)
System: x86_64-pc-linux-gnu
CXX Compiler: /glade/u/apps/ch/opt/ncarcompilers/0.5.0/gnu/8.3.0/g++ -fPIC -fopenmp
CXX version : unknown
C Compiler: gcc -fPIC -fopenmp
C version : gcc (GCC) 8.3.0
F77 Compiler: gfortran -fPIC
F77 version : GNU Fortran (GCC) 8.3.0
Features: 125GB 72threads C++14 Fortran DATA PTHREADS OpenMP45 HDF5 NC4/HDF5 OPeNDAP SZ PROJ.4 SSE2
Libraries: HDF5/1.10.5 proj/5.2
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
     CDI library version : 1.9.7.1
 cgribex library version : 1.9.3
 ecCodes library version : 2.12.5
  NetCDF library version : 4.6.3 of Jul  5 2019 11:25:22 $
    hdf5 library version : 1.10.5
    exse library version : 1.4.1
    FILE library version : 1.8.3

RE: Error (cdf_put_vara_double): NetCDF: HDF error - Added by Lixu Jin over 5 years ago

I make it work. The segmentation is due to limited storage in the remote server.

Thanks,
Lixu

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