Open jpolton opened 3 years ago
@micdom found this module for ncap2
on ARCHER2
module load nco/4.9.6.
@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 @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
forsn_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.
@jpolton step 2 scripts and wiki updated.
@jpolton nothing to add
@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).
@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.
@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
@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
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.
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