Port file prep to ARCHER2

[jpolton]

Some pre processing happens on livljobs8 because of nco command availability.
It would be easy to rapidly cycle through the build process if everything was on ARCHER2.

Action:

• Migrate wiki notes on preparing bathymetry and other things(?) to work on ARCHER2

[jpolton]

@micdom found this module for ncap2 on ARCHER2

    module load nco/4.9.6.

[micdom]

@jpolton @mpayopayo
The section Prepare PyNEMO files in 3. Make tidal boundary conditions. is very confusing.

It is not clear what are the files required in the namelist*.bdy for sn_src_hgr, sn_src_zgr, sn_src_msk.

I don't have access to the /projectsa/accord folder (and probably I shouldn't to run this script. Thinking about porting to ARCHER2, this doesn't really work).

[jpolton]

@jpolton @mpayopayo
The section Prepare PyNEMO files in 3. Make tidal boundary conditions. is very confusing.

It is not clear what are the files required in the namelist*.bdy for sn_src_hgr, sn_src_zgr, sn_src_msk.

I don't have access to the /projectsa/accord folder (and probably I shouldn't to run this script. Thinking about porting to ARCHER2, this doesn't really work).

I agree - it is not clear. This is partly why I wrote these as I forget instantly... I am revisiting the Step 2. (domain thingy) at the moment. And looking at doing it on ARCHER2. I will move onto Step 3 next. If @micdom @mpayopayo have edits to the wiki or SCRIPTS it would be good to get them in before I make divergent changes.

[micdom]

@jpolton step 2 scripts and wiki updated.

[mpayopayo]

@jpolton nothing to add

[micdom]

@jpolton @mpayopayo I'm back to this:
what are the files you're listing in namelist*.bdy for sn_src_hgr, sn_src_zgr, sn_src_msk?
I don't have access to the /projectsa/accord folder (and probably I shouldn't to run a different configuration).

[mpayopayo]

@micdom my understanding is that those files contain the domain from which the tides are picked up to be generated into our domain, maybe @jpolton can confim? I'm opening a different issue on this particular thing.

[micdom]

@jpolton @mpayopayo re-posting here for files that are needed for porting to archer2 (which I have not tried to do yet):

• /projectsa/accord/SANH_jenjar/CMEMS_SANH/CMEMS_subdomain_coordinates.nc and it has to be that file, if I link another file with the same name it doesn't work.

• /projectsa/accord/SANH_jenjar/CMEMS_SANH/, this is specified in ./NCML/CMEMS_2005.ncml (which is sn_src_dir = ./NCML/CMEMS_2005.ncml in namelist_FES14.bdy)

• in the namelist_FES14.bdy I've changed sn_src_hgr and sn_src_msk (see below) and it seems to work fine. The sn_src_zgr is from accord and I've copied it locally.

sn_src_hgr = '/projectsa/NEMO/nibrun/ARCHER_DATA/INPUTS/AMM15/coordinates.nc'   !  parent /grid/
   sn_src_zgr = 'inputs_src_zgr.ncml'   !  parent
   sn_dst_hgr = '../DOMAIN/domain_cfg.nc'  ! child
   sn_dst_zgr = 'inputs_dst.ncml' ! rename output variables
   sn_src_msk = '/projectsa/NEMO/nibrun/ARCHER_DATA/INPUTS/AMM15/amm15_mask.nc'      ! parent
   sn_bathy   = '../DOMAIN/bathy_meter.nc'        ! child

[micdom]

@jpolton @mpayopayo
hello, I've run the tidal boundary generation on ARCHER2 with PyNEMO.
It works, but to have it working I've transferred CMEMS data from our local projectsa to ARCHER2, I suspect that the data is not actually needed to generate the tidal boundaries (and there is a mismatch in the year). I guess the script is supposed to generate the full boundaries and not only the tidal boundaries, so to be fixed in the future.
I made a start in writing the instructions here