Skip to content

[rrfs-mpas-jedi] Replace JEDI obs offline domain check with a JEDI Polygon Check pre-filter. #1293

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
SamuelTrahanNOAA wants to merge 12 commits into
base: rrfs-mpas-jedi
Choose a base branch
from
Draft

[rrfs-mpas-jedi] Replace JEDI obs offline domain check with a JEDI Polygon Check pre-filter. #1293

Show file tree
Hide file tree
Changes from 8 commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
6f120c1
a script that copies a domain boundary to yaml
SamuelTrahanNOAA Jan 29, 2026
ee1e546
add polygon filter to jedivar.yaml
SamuelTrahanNOAA Jan 29, 2026
4a84e9b
remove offline filter
SamuelTrahanNOAA Jan 29, 2026
04b8376
copy polygon to jedivar.yaml (and enable some debugging)
SamuelTrahanNOAA Jan 29, 2026
07ebfa0
fix syntax errors in jedivar.yaml
SamuelTrahanNOAA Feb 2, 2026
eac7d17
fix syntax error in polygon
SamuelTrahanNOAA Feb 2, 2026
3bc9699
Polygon Check filter from UFS PR
SamuelTrahanNOAA Feb 2, 2026
e5e16ce
copy workaround files for polygon check
SamuelTrahanNOAA Feb 2, 2026
45fa8f0
make linter happier
SamuelTrahanNOAA Feb 2, 2026
51f7884
yamllint exceptions for *POLY
SamuelTrahanNOAA Feb 2, 2026
3f6456a
note which files and lines should be removed
SamuelTrahanNOAA Feb 2, 2026
a983a4e
Changes from review of ufo code
SamuelTrahanNOAA Feb 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
135 changes: 133 additions & 2 deletions parm/jedivar.yaml
View file
Open in desktop

Large diffs are not rendered by default.

17 changes: 3 additions & 14 deletions scripts/exrrfs_ioda_bufr.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -121,26 +121,15 @@ ln -sf abibufr "rap.t${cyc}z.gsrcsr.tm00.bufr_d"
cp "rap.t${cyc}z.abi_g16.tm00.nc" "ioda_abi_g16.nc"
cp "rap.t${cyc}z.abi_g18.tm00.nc" "ioda_abi_g18.nc"

# run offline IODA tools
${cpreq} "${USHrrfs}"/offline_domain_check.py .
${cpreq} "${USHrrfs}"/offline_domain_check_satrad.py .
${cpreq} "${USHrrfs}"/offline_ioda_tweak.py .
${cpreq} "${USHrrfs}"/offline_vad_thinning.py .

for ioda_file in ioda*nc; do
grid_file="${FIXrrfs}/${MESH_NAME}/${MESH_NAME}.static.nc"
#if [[ "${ioda_file}" == *abi* || "${ioda_file}" == *atms* || "${ioda_file}" == *cris* ]]; then
if [[ "${ioda_file}" == *abi* ]]; then
echo " ${ioda_file} ioda file detected: running offline_domain_check_satrad.py"
./offline_domain_check_satrad.py -o "${ioda_file}" -g "${grid_file}" -s 0.005
base_name=$(basename "$ioda_file" .nc)
mv "${base_name}_dc.nc" "${base_name}.nc"
elif [[ "${ioda_file}" == *atms* || "${ioda_file}" == *cris* ]]; then
echo " ${ioda_file} ioda file detected: temporarily skipping offline domain check"
if [[ "${ioda_file}" == *abi* || "${ioda_file}" == *atms* || "${ioda_file}" == *cris* ]]; then
echo " ${ioda_file} ioda tweak is skipped for abi, atms, and cris"
else
./offline_domain_check.py -o "${ioda_file}" -g "${grid_file}" -s 0.005
base_name=$(basename "$ioda_file" .nc)
mv "${base_name}_dc.nc" "${base_name}.nc"
echo " ${ioda_file} running ioda tweak"
./offline_ioda_tweak.py -o "${ioda_file}"
base_name=$(basename "$ioda_file" .nc)
mv "${base_name}_llp.nc" "${base_name}.nc"
Expand Down
10 changes: 8 additions & 2 deletions scripts/exrrfs_jedivar.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -136,10 +136,16 @@
;;
esac

if ( grep -E '\*POLY' jedivar.yaml > /dev/null ) ; then
cp jedivar.yaml no_polygon_jedivar.yaml
${USHrrfs}/yamlify_domain_edge.py -g "invariant.nc" -i '' > polygon.yaml
cat polygon.yaml no_polygon_jedivar.yaml > jedivar.yaml
fi
Copy link
Contributor

@guoqing-noaa guoqing-noaa Feb 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@SamuelTrahanNOAA Thanks for getting this ready for retro testing.
I understand that this is still a draft PR. But a heads up that the polygon generation will only need to run once for each domain in its lifetime. So we will NOT include lines 139-143 in exrrfs_jedivar.sh, but instead run it manually once and then put the results somewhere (either as a fix file or as a exp setting option).

Copy link
Contributor Author

@SamuelTrahanNOAA SamuelTrahanNOAA Feb 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Perhaps we can do this?

  1. Add a variable $BOUNDARY_POLYGON_YAML
  2. If that variable is set to a valid path, use that file,
  3. Otherwise, automatically generate it.

A side-effect of the automatic generation fallback is to give you the polygon boundary file you need to put in parm/

Copy link
Contributor

@guoqing-noaa guoqing-noaa Feb 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I will test your branch and then talk further with you on this. Thanks!


if [[ ${start_type} == "warm" ]] || [[ ${start_type} == "cold" && ${COLDSTART_CYCS_DO_DA^^} == "TRUE" ]]; then
# run mpasjedi_variational.x
#export OOPS_TRACE=1
#export OOPS_DEBUG=1
export OOPS_TRACE=1
export OOPS_DEBUG=1
export OMP_NUM_THREADS=1

source prep_step
Expand Down
Loading
Loading