Problem with InterpFromMeshToGrid in python

analuzardi

Hi all,

I am currently not able to use the function InterpFromMeshToGrid in python version of ISSM. Every time I try using that function to interpolate from the model mesh to a grid, the kernel dies (it uses a lot of memory). I am working in the EIS cloud and I have 64 GB of ram memory. I tried to interpolate to different grids, one of them has a 100km of resolution so it shouldn't use so much memory. I have no problem converting from grid to model mesh using InterpFromGridToMesh using the exact same dataset. I wonder if there is some issue with the function, and would appreciate a help to figure this out.

That's what I'm typing:
thick_grid = InterpFromMeshToGrid(md.mesh.elements, md.mesh.x, md.mesh.y, md.geometry.thickness, xgrid, ygrid,0)

xgrid's shape is 51 and ygrid's shape is 29.

Thanks,
-Ana

justinquinn

analuzardi Ana, working on this now. Can you send (to my business email again) the runme you're running, as well as any data/supplemental files, that is causing the InterpFromMeshToGrid error?

justinquinn

analuzardi Hi Ana, I can confirm the crash on CCR OnDemand, and on my local machine there is a crash with seg fault on the call to InterpFromMeshToGrid. That said, I'm not convinced it's an actual issue with ISSM. At the very least, we test the use of InterpFromGridToMesh in our nightly runs for the Examples/Tutorials. I will try to do the opposite recreate the crash doing the opposite using one of said examples. Further, I was trying to recreate your runme under MATLAB, but as noted before, I cannot load the model that you exported from EIS under Python. Would it be prohibitively expensive time-wise to recreate this model (igs_relax_setup1_transient1_part1_results) in MATLAB and export it from there? Actually, you could then test to see if InterpFromGridToMesh is working on the MATLAB side of things. If it is, your issue is likely a malformed model (which may or may not have to do with part of the Python API to ISSM that was used for model setup).

mathieumorlighem

Hello Ana

can I ask which version of ISSM you are using? I vaguely remember that we fixed a memory leak about a year ago. I quickly checked the code (which is now on Github) and it looked good as far as I can tell.
Mathieu

analuzardi

Hi Mathieu,

Thanks for the prompt response! The ISSM version that I'm using is 4.21, that's the one installed in EIS.

-Ana

justinquinn

analuzardi Hi Ana, If you run the same on CCR, do you encounter the same issue?

mathieumorlighem

ouch ... that's almost 2 years old. Sorry if this is complicated but I recommend updating to the latest version https://github.com/ISSMteam/ISSM
Mathieu

analuzardi

Hi Justin! I just tested on CCR and I had the same issue. I asked for 64GB of RAM memory in advanced options, which is the same as EIS provides. I checked and the ISSM version is the 4.24

justinquinn

analuzardi Hi Ana, thanks for checking and for letting us know. I'll look more into this. Do you have problems with any other modules that you're aware of?

analuzardi

Okay thank you Justin! 🙂 I don't have issues with any other functions for now.

analuzardi

Hi Justin! Actually, I'm having issues with another function. I'm trying to open in Matlab a model that I created in Python, which is saved in netcdf format. I tried using the function read_netCDF but had this error:

The ISSM version I have in my Matlab is 4.21.

I replaced the read_netCDF.m function in my ISSM installation with the one I found in Github, but then I got this other error message:

Not sure what's happening. Could you please check on that function as well?

Thank you so much!
-Ana

justinquinn

analuzardi Hi Ana,
And this is on EIS or CCR?

justinquinn

analuzardi Hi Ana, I totally missed a point here on my first reading (sorry, moving too fast): read_netCDF and like functions were developed by one of our Python users to only export models from MATLAB into Python. Unfortunately, the ability to go in the opposite direction is not available at this time. If you created the model on EIS, I might suggest recreating it on CCR (either on the terminal or via OnDemand)?

analuzardi

This is on my local Matlab installation in Matlab. I created the model on EIS, used export_netCDF to save the model in netcdf, then downloaded on my computer and am trying to open in my local Matlab.

analuzardi

Hi Justin, I just checked again and the InterpFromMeshToGrid function is working well in Matlab, but not in Python (the function InterpFromGridToMesh works well in both). I tested the same code in both Matlab and Python - the one in Python is not working as it uses a lot of memory and the kernel dies (I'm using 64GB). I'll email you both codes which uses dataset from the tutorials.

Thanks,
-Ana

justinquinn

For others experiencing the same, the bug has been identified and fix committed. Please update and recompile. We are also rebuilding our distributable packages.