Skip to content
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

Jump to bottom

Update ctests to include more obs types for more realistic testing #184

Merged
merged 47 commits into from
Oct 11, 2024
Merged

Update ctests to include more obs types for more realistic testing #184

Show file tree
Hide file tree
Changes from 42 commits
Commits
Show all changes
47 commits
Select commit Hold shift + click to select a range
76ad446
Link in new obs_ctest dir and use old testinput_expr for experiments
SamuelDegelia-NOAA Sep 27, 2024
ebaa642
Remove deprecated yaml files
SamuelDegelia-NOAA Sep 27, 2024
a273334
Move old testinput into testinput_expr
SamuelDegelia-NOAA Sep 27, 2024
fb9d75b
Restore link script to recent develop
SamuelDegelia-NOAA Sep 27, 2024
703d569
Add new testinput directory
SamuelDegelia-NOAA Sep 27, 2024
86ef13e
Add new basic_config for getkf and letkf
SamuelDegelia-NOAA Sep 27, 2024
8de5120
Restore to testoutput structure used in develop
SamuelDegelia-NOAA Sep 27, 2024
9789fc8
Add back in split getkf yamls
SamuelDegelia-NOAA Sep 27, 2024
8a57b3f
Updated validated yamls to include localization radii and obs distrib…
SamuelDegelia-NOAA Sep 30, 2024
ba02ff2
Remove GOMsaver so not outputting to data anymore
SamuelDegelia-NOAA Sep 30, 2024
3a84605
Add new basic_config yamls for split mode enkf
SamuelDegelia-NOAA Sep 30, 2024
2fc5677
Remove old merged yamls from testing
SamuelDegelia-NOAA Sep 30, 2024
095a07d
Added new version of gen_yaml.sh used specifically for ctests
SamuelDegelia-NOAA Sep 30, 2024
fbf2669
Do not track intermediate yaml files
SamuelDegelia-NOAA Sep 30, 2024
62db945
Ignore yamls created by gen_yaml_ctest.sh
SamuelDegelia-NOAA Sep 30, 2024
f4681ce
Update CMakelists for new letkf split ctest and add longer clock time
SamuelDegelia-NOAA Sep 30, 2024
0256213
Change 'mpasout' to 'restart'
SamuelDegelia-NOAA Sep 30, 2024
3377eef
Also change zero padding
SamuelDegelia-NOAA Sep 30, 2024
8b66105
Update basic_config
SamuelDegelia-NOAA Sep 30, 2024
277c47a
Add logic to gen_yaml_ctest for obs paths for enkf solver
SamuelDegelia-NOAA Sep 30, 2024
e71d95f
Removing letkf tests - way too slow
SamuelDegelia-NOAA Sep 30, 2024
41a988a
Add test reference section for envar yaml
SamuelDegelia-NOAA Sep 30, 2024
c21c3c7
Only running 6 ctests now so can edit run_rrfs_tests
SamuelDegelia-NOAA Sep 30, 2024
24a4829
Fix path to testoutput in basic_config yamls
SamuelDegelia-NOAA Sep 30, 2024
a8709a1
Automatically create yaml files for ctest during build
SamuelDegelia-NOAA Sep 30, 2024
a316a3a
Bug fix
SamuelDegelia-NOAA Sep 30, 2024
ae01ed9
Remove letkf from gitignore
SamuelDegelia-NOAA Sep 30, 2024
f8aaed2
Bug fix
SamuelDegelia-NOAA Sep 30, 2024
597ba22
Update test references
SamuelDegelia-NOAA Oct 1, 2024
e0fb3d6
Remove extra blank line
SamuelDegelia-NOAA Oct 1, 2024
f136beb
Remove vertical localization and reduce halo radius
SamuelDegelia-NOAA Oct 1, 2024
3064927
Update test reference
SamuelDegelia-NOAA Oct 1, 2024
da518d9
Bug fix
SamuelDegelia-NOAA Oct 1, 2024
b754d31
Update vertical localization for getkf
SamuelDegelia-NOAA Oct 1, 2024
0f1e17d
Update reference for using new vertical localization radius
SamuelDegelia-NOAA Oct 2, 2024
b828d49
Remove test comparison from older testinput_expr yamls
SamuelDegelia-NOAA Oct 2, 2024
694838d
Update setup_experiment
SamuelDegelia-NOAA Oct 2, 2024
d30b65c
Remove stale obs directory in rrfs-test
SamuelDegelia-NOAA Oct 2, 2024
6a28390
Merge branch 'develop' into feature/ctest_validated_yamls
guoqing-noaa Oct 4, 2024
252d224
Add atms obs to ctest
SamuelDegelia-NOAA Oct 4, 2024
edde1fc
Updated yamls in validated_yamls and testinput to be able to be parse…
SamuelDegelia-NOAA Oct 8, 2024
61539dd
Remove stale aliases from basic_config yaml files
SamuelDegelia-NOAA Oct 9, 2024
19bc1ea
Remove iteractionConfig anchor and copies of older fv3jedi yamls
SamuelDegelia-NOAA Oct 9, 2024
99f7896
Set level for 2d variables to last
SamuelDegelia-NOAA Oct 10, 2024
cdfa794
Add super yamls to repo and no longer create when building
SamuelDegelia-NOAA Oct 10, 2024
07084b6
Remove old comment
SamuelDegelia-NOAA Oct 10, 2024
c937745
Merge branch 'develop' into feature/ctest_validated_yamls
guoqing-noaa Oct 11, 2024
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
5 changes: 5 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -159,3 +159,8 @@ install*/
expr
fix/INIT_DONE
fix/.agent

# Ignore the yamls created by gen_yaml_ctest.sh
rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml
rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_observer.yaml
rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_solver.yaml
6 changes: 5 additions & 1 deletion build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -139,11 +139,15 @@ else
exit 1
fi

# Link in MPAS-JEDI test data
# Link in MPAS-JEDI test data and create ctest yaml files
if [[ $DYCORE == 'MPAS' || $DYCORE == 'FV3andMPAS' ]]; then
# Link in case data
echo "Linking in test data for MPAS-JEDI case"
$dir_root/rrfs-test/scripts/link_mpasjedi_expr.sh
echo "Creating yaml files for MPAS-JEDI ctests"
cd ${dir_root}/rrfs-test/validated_yamls
./gen_yaml_ctest.sh
cd ${BUILD_DIR}
fi

CMAKE_OPTS+=" -DMPIEXEC_MAX_NUMPROCS:STRING=120 -DBUILD_SUPER_EXE=$BUILD_SUPER_EXE"
Expand Down
1 change: 1 addition & 0 deletions fix/expr_data/mpas_2024052700/obs_ctest
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
../../.agent/expr_data/mpas_2024052700/obs_ctest
3 changes: 1 addition & 2 deletions rrfs-test/CMakeLists.txt
View file
Open in desktop
Copy link
Collaborator

Choose a reason for hiding this comment

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

@SamuelDegelia-NOAA line 54:
file(COPY ${src_yaml}/${case}.yaml DESTINATION ${casedir} )
and other copying lines.

These copying/linking only runs at the build time.

This is sometime inconvenient in the develop/debug process as we have to track down to find what files to copy/link and then manually do it for new changes (to avoid unnecessary long re-building process). It will be good if we have a common script which can be used by the build process and at the same time we can also run it outside of the build process to facilitate debugging/developing.

I have figured this out for my rrfs-test eror and manually copied/linked new files. So it is not a high priority at the moment but it is good to have this capability. Thanks!

Copy link
Contributor Author

Choose a reason for hiding this comment

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

For my ctest developments, I normally just run build.sh but add an exit command after the cmake command. But yeah adding a short shell script similar to rrfs-test/CMakeLists.txt could be a little easier. I'll do that at some point.

Copy link
Collaborator

Choose a reason for hiding this comment

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

That will be great! Thanks, @SamuelDegelia-NOAA!

Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,6 @@ add_to_dictionary(rrfs_fv3jedi_tests "rrfs_fv3jedi_letkf_2022052619" "fv3jedi_
# MPAS-JEDI tests
set(rrfs_mpasjedi_tests)
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_Ens3Dvar" "mpasjedi_variational.x")
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_letkf" "mpasjedi_enkf.x")
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_getkf" "mpasjedi_enkf.x")
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_getkf_observer" "mpasjedi_enkf.x")
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_getkf_solver" "mpasjedi_enkf.x")
add_to_dictionary(rrfs_mpasjedi_tests "rrfs_mpasjedi_2024052700_bumploc" "mpasjedi_error_covariance_toolbox.x")
Expand Down Expand Up @@ -76,6 +74,7 @@ if(FV3_DYCORE)
set(MPI_ARGS "${MPI_ARGS} --exclusive")
endif()
set(MPI_ARGS "${MPI_ARGS} --ntasks-per-node=4")
set(MPI_ARGS "${MPI_ARGS} --time=00:30:00")

get_all_keys(rrfs_mpasjedi_tests caselist)
foreach(case ${caselist})
Expand Down
Binary file removed rrfs-test/obs/msonet_singleob_airTemperature.nc4
View file
Open in desktop
Binary file not shown.
19 changes: 10 additions & 9 deletions rrfs-test/scripts/link_mpasjedi_expr.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,14 @@ cp -rp ${RDASApp}/fix/stream_list/* stream_list/
cp ${RDASApp}/sorc/mpas-jedi/test/testinput/obsop_name_map.yaml .
cp ${RDASApp}/sorc/mpas-jedi/test/testinput/namelists/keptvars.yaml .
cp ${RDASApp}/sorc/mpas-jedi/test/testinput/namelists/geovars.yaml .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_bumploc.yaml ./bumploc.yaml
cp ${RDASApp}/rrfs-test/testinput/namelist.atmosphere .
cp ${RDASApp}/rrfs-test/testinput/streams.atmosphere .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_letkf.yaml .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf.yaml .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_observer.yaml .
cp ${RDASApp}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_solver.yaml .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_bumploc.yaml ./bumploc.yaml
cp ${RDASApp}/rrfs-test/testinput_expr/namelist.atmosphere .
cp ${RDASApp}/rrfs-test/testinput_expr/streams.atmosphere .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_letkf.yaml .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf.yaml .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_observer.yaml .
cp ${RDASApp}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_solver.yaml .
if [[ "${exprname}" == "atl_2024052700" ]]; then
sed -i -e "s/conus12km_mpas.graph/atl12km.graph/" ./namelist.atmosphere
sed -i -e "s/conus12km-401km11levels/atl12km-401km11levels/" ./rrfs_mpasjedi_2024052700_Ens3Dvar.yaml
Expand All @@ -47,11 +47,12 @@ cp ${RDASApp}/rrfs-test/ush/mpasjedi_spread.py .

mkdir -p data
cd data
mkdir -p bumploc bkg obs ens
mkdir -p bumploc bkg obs obs_ctest ens
ln -snf ${RDASApp}/fix/bumploc/${BUMPLOC} bumploc/${BUMPLOC}
ln -snf ${RDASApp}/fix/expr_data/${exprname}/bkg/restart.2024-05-27_00.00.00.nc .
ln -snf ${RDASApp}/fix/expr_data/${exprname}/bkg/restart.2024-05-27_00.00.00.nc static.nc
ln -snf ${RDASApp}/fix/expr_data/${exprname}/obs/* obs/
ln -snf ${RDASApp}/fix/expr_data/${exprname}/obs_ctest/* obs_ctest/
ln -snf ${RDASApp}/fix/expr_data/${exprname}/ens/* ens/
ln -snf ${RDASApp}/fix/crtm/2.4.0 crtm

14 changes: 7 additions & 7 deletions rrfs-test/scripts/setup_experiment.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,12 +86,12 @@ elif [[ $DYCORE == "MPAS" ]]; then
mkdir -p graphinfo stream_list
ln -sf ${RDAS_DATA}/fix/graphinfo/* graphinfo/
cp -rp ${RDAS_DATA}/fix/stream_list/* stream_list/
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/bumploc.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/namelist.atmosphere .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_letkf.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput/streams.atmosphere .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/bumploc.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/namelist.atmosphere .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_letkf.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/rrfs-test/testinput_expr/streams.atmosphere .
cp ${YOUR_PATH_TO_RDASAPP}/sorc/mpas-jedi/test/testinput/obsop_name_map.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/sorc/mpas-jedi/test/testinput/namelists/keptvars.yaml .
cp ${YOUR_PATH_TO_RDASAPP}/sorc/mpas-jedi/test/testinput/namelists/geovars.yaml .
Expand Down Expand Up @@ -135,7 +135,7 @@ fi

# Copy rrts-test yamls and obs files.
#mkdir -p testinput
#cp -p $YOUR_PATH_TO_RDASAPP/rrfs-test/testinput/* testinput/.
#cp -p $YOUR_PATH_TO_RDASAPP/rrfs-test/testinput_expr/* testinput/.
#cp -p $YOUR_PATH_TO_RDASAPP/rrfs-test/obs/* Data/obs/.

# Copy GSI test data
Expand Down
111 changes: 0 additions & 111 deletions rrfs-test/scripts/setup_experiment.sh.new
View file
Open in desktop

This file was deleted.

Loading
Loading