Preprocessing
All .gr3 and .prop inputs can be visualized/generated using xmgredit5. For other inputs, you can find some useful pre-proc tools in the src/Utility directory. In general, all of our FORTRAN scripts have a header that explains its purpose, how to use it (inputs/outputs) and sample compilation command.
Grid conversion¶
2dm2gr3_m2m.pl and grd2sms.pl : These 2 perl scripts are used to convert between .2dm (SMS) and .gr3.
Interpolation¶
interpolate_unstructured.f90: This efficient script can be used to interpolate depths from .gr3 onto another
.gr3 quickly. It uses a bucket search algorithm along either x or y direction.
To interpolate from raster files (.asc), use interpolate_depth_structured2.f90.
\(LSC^2\) scripts¶
gen_vqs.f90 and plot_VQS.m: The FORTRAN script can be used as a start for creating a \(LSC^2\) grid and you need to use the matlab script to plot out transects to see if the vertical grid makes sense. You may lump multiple transects into 1 transect.bp. If you want to use this type of vgrid, make sure you go through the FORTRAN script carefully and understand the details.
Nudging scripts¶
gen_nudge.f90, gen_nudge2.f90: the two scripts generate either a simple elliptic nudging zone or a zone with fixed distance from boundary as *_nudge.gr3.
gen_nudge_from_hycom.f90: This
script generates the actual nudge data for tracers *_nu.nc from HYCOM (you may modify this
for other gridded data sources from other structured-grid models).
Hotstart¶
Gen_Hotstart/change_hotstart4.f90: This simple script shows you the internal structure of hotstart.nc and how to manipulate it.
Gen_Hotstart/gen_*_from_hycom.f90: These scripts show you how to create hotstart.nc and *.th.nc from gridded outputs
like HYCOM. It essentially consists of 3D interpolations.
Sflux_nc¶
The matlab scripts inside Sflux_nc dir show you the structure of sflux*.nc as well as how to generate your own files.
METIS for offline domain decomposition¶
You'll only need to do this if you invoked offline partitioning in compilation (e.g. with NO_PARMETIS turned ON in cmake)
to bypass ParMETIS.
If so, you'll need to prepare an input called partion.prop (which is essentially the MPI process # for each element).
Step 1: build METIS v5.1.0 by (src/metis-5.1.0) following README inside. You only need gpmetis.
Step 2: run a pre-processor for METIS: src/Utility/Grid_Scripts/metis_prep.f90, which only requires hgrid.gr3
(with B.C. parts) and vgrid.in, to get graphinfo;
Step 3: run METIS: ./gpmetis graphinfo <nproc> -ufactor=1.01 -seed=15
where <nproc> is # of
compute cores excluding scribes. The output is graphinfo.part.<nproc>, and then use awk to get partion.prop:
awk '{print NR,$0}' graphinfo.part.<nproc> > partition.prop
(replace <nproc> with actual # of cores).
(For VIMS users, there is a simple perl wrapper in /sciclone/home10/yinglong/bin/partition_offline.pl)