Extend GDASApp to run atmospheric JEDI variational DA with GSI EnKF (NOAA-EMC#1973)

# Description

This PR contains changes needed to run JEDI atmospheric variational DA
with a GSI-based EnKF ensemble. This configuration is currently being
used in the near realtime global parallel running on WCOSS2.

---------

Co-authored-by: CoryMartin-NOAA <cory.r.martin@noaa.gov>

Author: 2 people

.github/pull_request_template.md

@@ -23,3 +23,4 @@ Refs NOAA-EMC/repo#5678
 - [ ] C48mx500_3DVarAOWCDA <!-- JEDI low-res marine 3DVar cycled DA  !-->
 - [ ] C48mx500_hybAOWCDA <!-- JEDI marine hybrid envar cycled DA !-->
 - [ ] C96C48_hybatmDA <!-- GSI atm cycled DA !-->
+- [ ] C96C48_ufsgsi_hybatmDA <!-- JEDI atm Var with GSI EnKF cycled DA !-->

.gitmodules

@@ -41,11 +41,6 @@
   path = sorc/soca
   url = https://github.com/NOAA-EMC/soca.git
   branch = dev/emc
-  ignore = dirty
-[submodule "sorc/iodaconv"]
-  path = sorc/iodaconv
-  url = https://github.com/JCSDA-internal/ioda-converters.git
-  branch = develop
 [submodule "sorc/land-imsproc"]
   path = sorc/land-imsproc
   url = https://github.com/NOAA-EMC/land-SCF_proc.git

build.sh

@@ -25,6 +25,7 @@ usage() {
   echo "  -f  force a clean build             DEFAULT: NO"
   echo "  -d  include JCSDA ctest data        DEFAULT: NO"
   echo "  -a  build everything in bundle      DEFAULT: NO"
+  echo "  -i  clone and build ioda-converters DEFAULT: NO"
   echo "  -h  display this message and quit"
   echo
   exit 1
@@ -38,12 +39,14 @@ CMAKE_INSTALL_LIBDIR="lib"
 CMAKE_OPTS=""
 BUILD_TARGET="${MACHINE_ID:-'localhost'}"
 BUILD_VERBOSE="NO"
+BUILD_TESTING="OFF"
 CLONE_JCSDADATA="NO"
 CLEAN_BUILD="NO"
 COMPILER="${COMPILER:-intel}"
 WORKFLOW_BUILD=${WORKFLOW_BUILD:-"OFF"}
+BUILD_IODA_CONVERTERS=${BUILD_IODA_CONVERTERS:-"NO"}
 
-while getopts "w:t:c:hvdfa" opt; do
+while getopts "w:t:c:hvdfai" opt; do
   case $opt in
     w)
       HOMEgfs=$OPTARG
@@ -63,6 +66,9 @@ while getopts "w:t:c:hvdfa" opt; do
     f)
       CLEAN_BUILD=YES
       ;;
+    i)
+      BUILD_IODA_CONVERTERS=YES
+      ;;
     h|\?|:)
       usage
       ;;
@@ -75,7 +81,7 @@ case ${BUILD_TARGET} in
     source $dir_root/ush/module-setup.sh
     module use $dir_root/modulefiles
     module load GDAS/$BUILD_TARGET.$COMPILER
-    CMAKE_OPTS+=" -DMPIEXEC_EXECUTABLE=$MPIEXEC_EXEC -DMPIEXEC_NUMPROC_FLAG=$MPIEXEC_NPROC -DBUILD_GSIBEC=ON"
+    CMAKE_OPTS+=" -DMPIEXEC_EXECUTABLE=$MPIEXEC_EXEC -DMPIEXEC_NUMPROC_FLAG=$MPIEXEC_NPROC -DBUILD_GSIBEC=ON -DBUILD_IODA_CONVERTERS=$BUILD_IODA_CONVERTERS"
     module list
     ;;
   $(hostname))
@@ -86,7 +92,7 @@ case ${BUILD_TARGET} in
     ;;
 esac
 
-CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA -DMACHINE=$BUILD_TARGET"
+CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA -DMACHINE=$BUILD_TARGET -DBUILD_TESTING=$BUILD_TESTING"
 
 # TODO: Remove LD_LIBRARY_PATH line as soon as permanent solution is available
 if [[ $BUILD_TARGET == 'wcoss2' ]]; then
@@ -116,6 +122,11 @@ else
   git clone https://github.com/jcsda/soca "$dir_root/sorc/soca" --recurse-submodules
 fi
 
+if [[ $BUILD_IODA_CONVERTERS == 'YES' ]]; then
+  # Clone and build ioda-converters
+  git clone https://github.com/jcsda-internal/ioda-converters "$dir_root/sorc/iodaconv"
+fi
+
 # Set INSTALL_PREFIX as CMake option
 CMAKE_OPTS+=" -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX}"
 

bundle/CMakeLists.txt

@@ -36,6 +36,7 @@ option(BUILD_GDASBUNDLE "Build GDAS Bundle" ON)
 option(CLONE_JCSDADATA "Clone JCSDA test data repositories" OFF)
 option(WORKFLOW_TESTS "Include global-workflow dependent tests" OFF)
 option(BUILD_REGRID_STATES "Build regrid states land DA utility" ON)
+option(BUILD_IODA_CONVERTERS "Build IODA Converters" OFF)
 
 # Depend path for non-ecbuild packages
 set(DEPEND_LIB_ROOT ${CMAKE_CURRENT_BINARY_DIR}/Depends)
@@ -113,7 +114,6 @@ if(BUILD_GDASBUNDLE)
   ecbuild_bundle( PROJECT da-utils SOURCE "../sorc/da-utils" )
 
 # Build IODA converters
-  option(BUILD_IODA_CONVERTERS "Build IODA Converters" ON)
   if(BUILD_IODA_CONVERTERS)
     ecbuild_bundle( PROJECT iodaconv SOURCE "../sorc/iodaconv" )
   endif()

modulefiles/GDAS/gaeac6.intel.lua

@@ -70,6 +70,7 @@ load("py-xarray/2024.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 load("py-click/8.1.7")
+load("py-wheel/0.41.2")
 
 --unload("cray-libsci")
 

modulefiles/GDAS/hera.intel.lua

@@ -69,6 +69,7 @@ load("py-xarray/2024.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 load("py-click/8.1.7")
+load("py-wheel/0.41.2")
 
 setenv("CC","mpiicc")
 setenv("CXX","mpiicpc")

modulefiles/GDAS/hercules.intel.lua

@@ -75,6 +75,7 @@ load("py-xarray/2024.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 load("py-click/8.1.7")
+load("py-wheel/0.41.2")
 
 setenv("CC","mpiicc")
 setenv("CXX","mpiicpc")

modulefiles/GDAS/orion.intel.lua

@@ -74,6 +74,7 @@ load("py-xarray/2024.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 load("py-click/8.1.7")
+load("py-wheel/0.41.2")
 
 setenv("CC","mpiicc")
 setenv("CXX","mpiicpc")

modulefiles/GDAS/ursa.intel.lua

@@ -71,6 +71,7 @@ load("py-xarray/2024.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 load("py-click/8.1.7")
+load("py-wheel/0.41.2")
 
 setenv("CC","mpiicx")
 setenv("CXX","mpiicpx")

parm/aero/aero_bias_files.yaml.j2

@@ -1,4 +1,4 @@
 bias_files:
-  viirs_npp_aod: aero_varbc_params.tar
-  viirs_n20_aod: aero_varbc_params.tar
-  viirs_n21_aod: aero_varbc_params.tar
+  retrieval_aod_viirs_npp: aero_varbc_params.tar
+  retrieval_aod_viirs_n20: aero_varbc_params.tar
+  retrieval_aod_viirs_n21: aero_varbc_params.tar