pschism executable location

[TPCollings]

Hi again,

I've install schism using conda install -c gbrey pschism.

I'm trying to validate the mesh produced using the MESH.ipynb in the tutorial, however the function cannot find the schism executable file.

I've tried to set the path environment variable using the 'epath' kwarg, but I can't find the the correct folder to point it to. Do I need to run the build_schism.sh script after installing pschism?

Example of the error below.

Cheers.

Tom

**Without setting 'epath'

m.validate(rpath='./test/val/')

INFO:pyposeidon.mesh:start mesh validation

INFO:pyposeidon.mesh:writing mesh to file ./test/val/hgrid.gr3 WARNING:pyposeidon.mesh:Schism executable path (epath) not given -> using default

DEBUG:pyposeidon.mesh:b'' INFO:pyposeidon.mesh:mesh fails.. exiting

[brey]

Try checking the file ./test/val/outputs/fatal.error for a hint. Let me know.

[TPCollings]

My ./test/val/outputs/ is empty.

[brey]

There is no need to run anything after installing from conda. All epath is not needed (it is there to link a locally compiled version of SCHISM).

Can you post the output of

conda list | grep schism

I assume that you've installed schism in the same env as pyposeidon. Another way to have a fully functional env is using the binder/environment.yml with the addition in the yml file of

- numpy<1.23.0

So, after adding the above, execute

conda env create -f binder/environment.yml

[TPCollings]

(pypos_main1) tom@uTELEMAC-VM:~$ conda list | grep schism pschism 5.9.0 mpi_openmpi_hd7ccc92_0 gbrey

I will try creating a new environment from using the binder yml and see if that solves the problem.

Cheers

[brey]

First you can try the following:

Check if there is a

ls $CONDA_PREFIX/bin/schism

if not then create it with

ln -s $CONDA_PREFIX/bin/pschism_TVD-VL $CONDA_PREFIX/bin/schism

Some of the original builds didn't have this included and I see you have the zero build.

Then try again your validation.

[TPCollings]

Ah that solves it. Thanks very much.