CDO

Hi Alex,

cdo mergetime *.nc outfile

cdo cat *.cat outfile

Do you solve this problem?
I just have the same problem, i use 'cdo mergetime *.nc outfile' and 'cdo cat *.nc outfile', and they are all going wrong with the message like bellow:

Assertion failed: pxp->bf_offset <= offset && offset < pxp->bf_offset + (off_t) pxp->bf_extent, file posixio.c, line 325

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.

thank you very much!!!

Jinghua

This error message came directly from the netCDF library.
In most cases the resulting file size will be larger than 2GB.
To solve this problem you have to change the output file type to netCDF2 (nc2):

 cdo -f nc2 mergetime *.nc outfile

Thank you very much!!!

Hi, I'm encountering the same error, as my output file is greater than 2GB
I tried the followings:
cdo -f nc2 mergetime *.nc outfile
cdo -f nc2 mergetime *.nc outfile.nc2
cdo -f nc2 mergetime *.nc2 outfile.nc2
cdo mergetime *.nc2 outfile.nc
cdo mergetime *.nc2 outfile.nc2

All to no avail. Same error(Assertion failed: pxp->bf_offset <= offset && offset < pxp->bf_offset + (off_t) pxp->bf_extent, file posixio.c, line 325)
Mr Uwe, what can i do to resolve this?
Mr Chen Jinghua, did you solve the issue?

the reason is the file is too large(>2GB).
you may try with "cdo -f nc2" or "cdo -f nc4"

any progress? i have the same problem when trying to merge more than 2 gb files. couldnt solve it.

Hi,

May be your file system is 32-bit? Anyway, can you please post the output of "cdo -V"

Cheers,
J.

SOLVED .....

the files couldnt be merged under windows because been more than 2gb.

I run virtual machine and tried to merge them under Ubuntu 10 lts and it worked like charm.

Thank you. try doing it under linux.

Have you tried cygwin? in the minimal configuration, it gives you a unix-like prompt with all the great command line tools.

Hi
You can easily do this by Netcdf Extractor. It's a windows tool that in this tool, the user can extract data from many netcdf files without any knowledge about programming.
https://agrimetsoft.com/Netcdf-Extractor.aspx

It worked for me doing it this way
cdo -f nc .nc outfile.nc

hi,

I do the same ( cdo -f nc mergetime era5_*.nc era5_hrs.nc) but it seems to be that my timesteps reach the limit of CDO when I merge files in one. The text appears as:
" cdo mergetime (Warning): Some data values (min=-10233 max=33136) are outside the valid range (-32768 - 32767) of the used output precision! Use the CDO option -b 32 or -b 64 to increase the output precision. "
So, I want to ask, How to do as the machine suggests? Is it cdo -b 64 -f nc mergetime era5_*.nc era5_hrs.nc? or cdo -f nc -b 64 mergetime era5_*.nc era5_hrs.nc?
Thanks so much!

Hi Puri,

the warning says that the values are outside the value range and tells you what you can do.

cdo -f nc -b F32 mergetime era5_*.nc era5_hrs.nc

should work.

-Karin

yes, it works!!!!!

I have separate daily nc files of three parameters (temp,WD and WS). Would like to merge parameter wise example temp_2022

I have separate daily nc files of three parameters (temp,WD and WS) of ERA5. Would like to merge parameter wise per year, example temp_2022.

Is their any specific command in CDO.

hi!

You can use mergetime or merge. in case you have each variable in separate files, you can also use cat on these files, only.

Something like

cdo -merge temp_* all_temp.nc

cdo -mergetime temp_* all_temp.nc

cdo -timesort -cat [ temp_* ] all_temp.nc

give it a try

cheers
ralf

Hi
Thanks for reply.
I have used cdo mergetime. More than 24 hours no output.
Will try other two commands suggested by you.
Suvarna

Hi
I have used commands but hard luck.

cdo -timesort -cat [ _130*.nc ] all_130.nc

Error msg:Operator not found

cdo -merge _130*.nc all_130.nc
Error msg:Open failed on >_130*<
No such file or directory

Could you please help further?
my file names are as bellow , want to merge all _130 file for year 2019.
temp: 'E5ml00_1H_2019-05-01_130.nc'
WD: 'E5ml00_1H_2019-08-31_131.nc'
WD: 'E5ml00_1H_2019-12-31_132.nc'

Thanks
Suvarna

1. The operator name is timsort not timesort.
2. you need to specify the file names (there are no 130*.nc files - do you mean E5ml00_1H*_130.nc ?

Try:

cdo -timsort -cat [ E5ml00_1H_*_130.nc ] all_130.nc

Thanks a lot.
its started processing.

It get stopped with msg "cdo(1) cat: 3%Killed"

How many files do you try to merge? Maybe it is a memory issue or you have to use a job for it.

I have files are ranging from 340 to 365.