Save model in netcdf format

analuzardi

Is there a way of saving the model (md) in netcdf format in Matlab? I'm not able to use the function export_netCDF in Matlab, only in Python. I tried using Matlab functions nccreate and ncwrite, but I had an error saying I could not save "type model" in the netcdf file. The reason I want to save the model in netcdf format is because I want to open the model in Python afterwards.

Thanks!!
-Ana

bdefleurian

Hei Ana
Export_netCDF should work in Matlab too and was writtenexactly for that translation purpose. Let me know what kind of error you are running into and I can try to fix that for you.
Basile

analuzardi

Hi Basile,

Thank you for your quick response! In Matlab I get the following message:

Undefined function 'export_netCDF' for input arguments of type 'model'.

I tried looking up this function for Matlab but I could only find examples of it being used in Python. I would appreciate any tip on how to import and use it in Matlab.

Thanks for your help!

bdefleurian

What kind of ISSM install are you using, do you have access to the source code to check if the export_netCDF is here?

analuzardi

I downloaded the pre-compiled binaries (followed steps from this link:https://issm.jpl.nasa.gov/download/binaries/), and I don't think I have access to the source code. Would it be inside of the ISSM-macOS-MATLAB folder? I'm sorry if this is a silly question. But I didn't find the function inside of my ISSM-macOS-MATLAB folder.

Thanks,
-Ana

bdefleurian

Yes it is very possible that the export netCDF was not introduced in the binaries that you have as it is a quite recent addition. I am not to confident about what is introduced in the binaries perhaps @justinquinn would know.
I guess you could get the matlab file from the source code (check here how to get it https://issm.jpl.nasa.gov/download/unix/) and have it somewhere where matlab would see it to export your model.

justinquinn

bdefleurian Okay, so the issue is that the export_netCDF is in your contrib/ directory. Is it okay if I move it to the src/ directory and rebuild the binaries?

justinquinn

Hi guys,
Let me look into this. It should be in there as I just generated new binaries. I will post back as soon as I have an answer for you.

bdefleurian

justinquinn Yep that is completely fine. I was not aware that this was not part of the binaires. While you are at it you can move the python version too. And perhaps some people would be interested in exportVTU (in paraview).

justinquinn

bdefleurian Okay, I've moved both to src/m.

@analuzardi I am generating new binaries which should be available later tonight.

analuzardi

justinquinn Great! Thanks so much both of you! Also I tried getting the "export_netCDF.m" file from someone else and that worked for me for what I needed so I'm able to use the function now. But it's still useful to generate new binaries so that other people won't have the same issue. Thanks!