Difficulty reading in 3D fieldset from NEMO

[mollyjames2]

Hi,
I am using the NEMO 3D tutorial to try and read in a NEMO dataset to run a 3D particle tracking simulation and I'm running into issues. to read the data i have the following code:
`dataset_folder = "/data/proteus1/scratch/moja/projects/SANH/Leak1H"
ufiles = sorted(glob(f"{dataset_folder}/SRIL34_1HL_*1h_grid_U.nc"))
vfiles = sorted(glob(f"{dataset_folder}/SRIL34_1HL_*1h_grid_V.nc "))
wfiles = sorted(glob(f"{dataset_folder}/SRIL34_1HL_*1h_grid_W.nc"))
mesh_mask = f"{dataset_folder}/coordinates.nc"

filenames = {
"U": {"lon": mesh_mask, "lat": mesh_mask, "depth": wfiles[0], "data": ufiles},
"V": {"lon": mesh_mask, "lat": mesh_mask, "depth": wfiles[0], "data": vfiles},
"W": {"lon": mesh_mask, "lat": mesh_mask, "depth": wfiles[0], "data": wfiles},
}

variables = {"U": "uoce", "V": "voce", "W": "woce"}

c_grid_dimensions = {
"lon": "glamf",
"lat": "gphif",
"depth": "depthw",
"time": "time_counter",
}
dimensions = {
"U": c_grid_dimensions,
"V": c_grid_dimensions,
"W": c_grid_dimensions,
}

fieldset = FieldSet.from_nemo(filenames, variables, dimensions)`

but I am getting the error:
OSError: FieldSet files not found for variable V: {'lon': ['/data/proteus1/scratch/moja/projects/SANH/Leak1H/coordinates.nc'], 'lat': ['/data/proteus1/scratch/moja/projects/SANH/Leak1H/coordinates.nc'], 'depth': ['/data/proteus1/scratch/moja/projects/SANH/Leak1H/SRIL34_1HL_20210501_20210531_1h_grid_W.nc'], 'data': []}

in my coordinates.nc the data is formatted as follows:
netcdf coordinates { dimensions: x = 324 ; y = 424 ; z = 1 ; time = 1 ; variables: float nav_lon(y, x) ; nav_lon:axis = "Longitude" ; nav_lon:short_name = "nav_lon" ; nav_lon:units = "degrees_east" ; nav_lon:long_name = "Longitude" ; float nav_lat(y, x) ; nav_lat:axis = "Latitude" ; nav_lat:short_name = "nav_lat" ; nav_lat:units = "degrees_east" ; nav_lat:long_name = "Latitude" ; float nav_lev(z) ; nav_lev:axis = "Model Level" ; nav_lev:short_name = "nav_lev" ; nav_lev:units = "unitless" ; nav_lev:long_name = "Model Level" ; float e1t(y, x) ; float e2t(y, x) ; float glamt(y, x) ; float gphit(y, x) ; float e1u(y, x) ; float e2u(y, x) ; float glamu(y, x) ; float gphiu(y, x) ; float e1v(y, x) ; float e2v(y, x) ; float glamv(y, x) ; float gphiv(y, x) ; float e1f(y, x) ; float e2f(y, x) ; float glamf(y, x) ; float gphif(y, x) ;

any help or advice on how to get this data read in would be greatly beneficial - thanks in advance

[erikvansebille]

Thanks for asking, @mollyjames2; but I think the error message says it all, in the last few words: [...] 'data': []}

Your list of data-files is empty for variable V. Are you sure that vfiles = sorted(glob(f"{dataset_folder}/SRIL34_1HL_*1h_grid_V.nc ")) does not give you an empty list? Do these files exist?

[mollyjames2]

thank you for your quik reply Erik - on closer inspection of the script it seems like the accidental space between .nc and " was the culprit! many thanks