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Error with "cdo mergetime inf1 inf2 Outf": (cdf_get_vara_float): NetCDF: HDF error

Added by 玲 张 over 3 years ago

Code:
inf1=tasmin_day_ACCESS-ESM1-5_ssp245_r1i1p1f1_gn_20150101-20641231.nc
inf2=tasmin_day_ACCESS-ESM1-5_ssp245_r1i1p1f1_gn_20650101-21001231.nc
Outf=mergData.nc
cdo mergetime inf1 inf2 Outf"

Error
cdf_get_vara_float : ncid = 65536 varid = 7
Error (cdf_get_vara_float) : NetCDF: HDF error
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5T.c line 1716 in H5Tclose(): not a datatype
major: Invalid arguments to routine
minor: Inappropriate type
Error (cdf_close) : NetCDF: HDF error

Sometimes as the following:
cdf_get_vara_float : ncid = 196608 varid = 7
Error (cdf_get_vara_float) : NetCDF: HDF error
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5T.c line 1716 in H5Tclose(): not a datatype
major: Invalid arguments to routine
minor: Inappropriate type
Error (cdf_close) : NetCDF: HDF error

OR:
cdf_get_vara_float : ncid = 131072 varid = 7
Error (cdf_get_vara_float) : NetCDF: HDF error
HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: H5T.c line 1716 in H5Tclose(): not a datatype
major: Invalid arguments to routine
minor: Inappropriate type
Error (cdf_close) : NetCDF: HDF error

Cdo version is as following:
Climate Data Operators version 1.8.0rc2 (http://mpimet.mpg.de/cdo)
Compiled: by root on login (x86_64-unknown-linux-gnu) Sep 19 2016 22:57:34
Compiler: icc -std=gnu99 -g -O2 -fopenmp
version: icc (ICC) 15.0.2 20150121
Features: DATA PTHREADS OpenMP4 HDF5 NC4/HDF5 OPeNDAP UDUNITS2 SSE2
Libraries: HDF5/1.8.17
Filetypes: srv ext ieg grb1 nc1 nc2 nc4 nc4c
CDI library version : 1.8.0rc2 of Sep 19 2016 22:49:03
CGRIBEX library version : 1.7.5 of Jun 3 2016 14:44:00
NetCDF library version : 4.4.1 of Sep 19 2016 21:56:30 $
HDF5 library version : 1.8.17
SERVICE library version : 1.4.0 of Sep 19 2016 22:48:47
EXTRA library version : 1.4.0 of Sep 19 2016 22:48:40
IEG library version : 1.4.0 of Sep 19 2016 22:48:44
FILE library version : 1.8.2 of Sep 19 2016 22:48:41

I have seen the same problem in https://code.mpimet.mpg.de/boards/1/topics/4230. I tried the solution "cdo -L mergetime inf1 inf2 Outf" and "cdo -b F64 mergetime inf1 inf2 Outf". I did not solve the problem. The same Error come out as "cdo mergtime inf1 inf2 Outf".

Each input file size is about 1.5G,so I can not upload the files.
You can download by the following link :
http://esgf.nci.org.au/thredds/fileServer/master/CMIP6/ScenarioMIP/CSIRO/ACCESS-ESM1-5/ssp245/r1i1p1f1/day/tasmin/gn/v20191115/tasmin_day_ACCESS-ESM1-5_ssp245_r1i1p1f1_gn_20150101-20641231.nc
http://esgf.nci.org.au/thredds/fileServer/master/CMIP6/ScenarioMIP/CSIRO/ACCESS-ESM1-5/ssp245/r1i1p1f1/day/tasmin/gn/v20191115/tasmin_day_ACCESS-ESM1-5_ssp245_r1i1p1f1_gn_20650101-21001231.nc

Thank you very much.


Replies (1)

RE: Error with "cdo mergetime inf1 inf2 Outf": (cdf_get_vara_float): NetCDF: HDF error - Added by Karin Meier-Fleischer over 3 years ago

Hi,

I would recommend to upgrade to the current CDO version. I used version 1.9.8 'cdo -O -mergetime file1.nc file2.nc outfile.nc' and it works fine for your files.

-Karin

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