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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

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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
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1 change: 1 addition & 0 deletions fix/expr_data/mpas_2024052700/obs_ctest
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@@ -0,0 +1 @@
../../.agent/expr_data/mpas_2024052700/obs_ctest
3 changes: 1 addition & 2 deletions rrfs-test/CMakeLists.txt
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@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!

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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.

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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
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19 changes: 10 additions & 9 deletions rrfs-test/scripts/link_mpasjedi_expr.sh
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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 @@ -48,11 +48,12 @@ 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
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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
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