ds.rio.write_crs('epsg:4326', inplace=True) gives an error

[shuai-zhou]

I did some tests on my Windows machine, everything works fine. But when I was working on a Linux-based HPC, the following line:

ds.rio.write_crs('epsg:4326', inplace=True)

gives an error:

ERROR 1: PROJ: proj_create_from_database: conda_env_name/share/proj/proj.db lacks DATABASE.LAYOUT.VERSION.MAJOR / DATABASE.LAYOUT.VERSION.MINOR metadata. It comes from another PROJ installation.

This error did not stop the script, but when clipping a dataset using clipped = ds.rio.clip(geodf.geometry.apply(mapping), geodf.crs), another error occurs:

CRS not found. Please set the CRS with 'rio.write_crs()'. Data variable: precipitation

Probably because the first error (Error 1: PROJ: proj_create_from_database...) did not write a CRS? How can I fix the first error? Thanks.

[snowman2]

For the first error, it seems GDAL is having issues finding the PROJ database that is expected. I would check the PROJ_LIB environment variable.

[shuai-zhou]

I changed the 'PROJ_LIB' to '~/storage/home/my_account/work/envs/spatial/share/proj/proj.db', is this what you mean about full path? the error ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db persists

[snowman2]

Can you change it to: /storage/home/my_account/work/envs/spatial/share/proj ?

[shuai-zhou]

I remembered you mentioned somewhere that do not try pip install in a conda environment. So I checked my pip list, and there was another rioxarray, I uninstalled it using pip uninstall rioxarray.

Then without specifying the two environment variables, ds.rio.write_crs('epsg:4326', inplace=True) still gave the same error, but I was able to run clipped = ds.rio.clip(geodf.geometry.apply(mapping), geodf.crs) successfully. Maybe ERROR 1: PROJ: proj_create_from_database: conda_env_name/share/proj/proj.db lacks DATABASE.LAYOUT.VERSION.MAJOR / DATABASE.LAYOUT.VERSION.MINOR metadata. It comes from another PROJ installation. is not a fatal error in this situation?

[snowman2]

Sounds like the database worked, even if it wasn't the version PROJ expected. It could be a fatal error depending on how PROJ is used and if there are breaking changes between database. But, it sounds like you got lucky in this scenario.

[shuai-zhou]

Yeah, thanks for your time and patience. I also asked for help from the HPC support team, if there are some other system-specific settings that could solve this issue, I will post their solution here.