Bring feature/gdas-validation up to date with develop

.github/workflows/unittests.yaml

@@ -15,15 +15,6 @@ jobs:
         pip install netCDF4
         pip install xarray
 
-    - name: Install other dependencies
-      run: |
-        wget https://ftp.emc.ncep.noaa.gov/static_files/public/GDASApp/r2d2-bb361c2.tar.gz
-        wget https://ftp.emc.ncep.noaa.gov/static_files/public/GDASApp/solo-877b414.tar.gz
-        tar -xvf r2d2-bb361c2.tar.gz
-        tar -xvf solo-877b414.tar.gz
-        cd solo && pip install . && cd ..
-        cd r2d2 && pip install . && cd ..
-
     - name: Checkout wxflow
       uses: actions/checkout@v3
       with:

.gitignore

@@ -146,33 +146,40 @@ build*/
 install*/
 
 # Ignore the following bundle repositories
-ecbuild/
-atlas/
-crtm/
-eckit/
-fckit/
-femps/
-fms/
-fv3/
-fv3-jedi/
-fv3-jedi-data/
-fv3-jedi-lm/
-gsibec/
-gsw/
-icepack/
-/ioda/
-ioda-data/
-iodaconv/
-jedicmake/
-land-imsproc/
-land-jediincr/
-mom6/
-oops/
-saber/
-saber-data/
-/soca/
-test-data-release/
-ufo/
-ufo-data/
-vader/
+/ecbuild
+/atlas
+/crtm
+/eckit
+/fckit
+/femps
+/fms
+/fv3
+/fv3-jedi
+/fv3-jedi-data
+/fv3-jedi-lm
+/gsibec
+/gsw
+/icepack
+/ioda
+/ioda-data
+/iodaconv
+/jedicmake
+/land-imsproc
+/land-jediincr
+/mom6
+/oops
+/saber
+/saber-data
+/soca
+/test-data-release
+/ufo
+/ufo-data
+/vader
 /gdas-utils
+/sorc/fv3-jedi-data
+/sorc/ufo-data
+/sorc/ioda-data
+/sorc/test-data-release
+/sorc/gdas
+/sorc/gdas-utils
+

.gitmodules

@@ -0,0 +1,78 @@
+[submodule "sorc/jedicmake"]
+  path = sorc/jedicmake
+  url = https://github.com/jcsda/jedi-cmake.git
+[submodule "sorc/gsibec"]
+  path = sorc/gsibec
+  url = https://github.com/GEOS-ESM/GSIbec.git
+  branch = develop
+[submodule "sorc/gsw"]
+  path = sorc/gsw
+  url = https://github.com/jcsda-internal/GSW-Fortran.git
+  branch = develop
+[submodule "sorc/oops"]
+  path = sorc/oops
+  url = https://github.com/jcsda/oops.git
+  branch = develop
+[submodule "sorc/vader"]
+  path = sorc/vader
+  url = https://github.com/jcsda/vader.git
+  branch = develop
+[submodule "sorc/saber"]
+  path = sorc/saber
+  url = https://github.com/jcsda/saber.git
+  branch = develop
+[submodule "sorc/ioda"]
+  path = sorc/ioda
+  url = https://github.com/jcsda/ioda.git
+  branch = develop
+[submodule "sorc/ufo"]
+  path = sorc/ufo
+  url = https://github.com/jcsda/ufo.git
+  branch = develop
+[submodule "sorc/fv3"]
+  path = sorc/fv3
+  url = https://github.com/jcsda/GFDL_atmos_cubed_sphere.git
+  branch = release-stable
+[submodule "sorc/femps"]
+  path = sorc/femps
+  url = https://github.com/jcsda/femps.git
+  branch = develop
+[submodule "sorc/fv3-jedi-lm"]
+  path = sorc/fv3-jedi-lm
+  url = https://github.com/jcsda/fv3-jedi-linearmodel.git
+  branch = develop
+[submodule "sorc/fv3-jedi"]
+  path = sorc/fv3-jedi
+  url = https://github.com/jcsda/fv3-jedi.git
+  branch = develop
+[submodule "sorc/icepack"]
+  path = sorc/icepack
+  url = https://github.com/JCSDA-internal/Icepack.git
+  branch = feature/ecbuild-new
+[submodule "sorc/mom6"]
+  path = sorc/mom6
+  url = https://github.com/jcsda-internal/MOM6.git
+  branch = main-ecbuild
+[submodule "sorc/soca"]
+  path = sorc/soca
+  url = https://github.com/jcsda-internal/soca.git
+  branch = develop
+[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-PSL/land-IMS_proc.git
+  branch = develop
+[submodule "sorc/land-jediincr"]
+  path = sorc/land-jediincr
+  url = https://github.com/NOAA-PSL/land-apply_jedi_incr.git
+  branch = develop
+[submodule "sorc/crtm"]
+  path = sorc/crtm
+  url = https://github.com/jcsda/crtm.git
+[submodule "sorc/fms"]
+	path = sorc/fms
+	url = https://github.com/jcsda/fms.git
+  branch = release-stable

CMakeLists.txt

@@ -1,5 +1,5 @@
 # ------------------------------------------------------------------------- #
-# Application for all the components needed for the GDAS system             #
+# Application for the GDAS system             #
 # ------------------------------------------------------------------------- #
 
 # Check for minimim cmake requirement
@@ -36,135 +36,8 @@ 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)
 
-# Initialize bundle
-# -----------------
-ecbuild_bundle_initialize()
-
-# Build bundle source code.
-if(BUILD_GDASBUNDLE)
-
-# jedi-cmake
-  ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda/jedi-cmake.git" TAG 1.4.0 RECURSIVE )
-  include( jedicmake/cmake/Functions/git_functions.cmake )
-
-# ECMWF libraries
-  option("BUNDLE_SKIP_ECKIT" "Don't build eckit" "ON" ) # Skip eckit build unless user passes -DBUNDLE_SKIP_ECKIT=OFF
-  option("BUNDLE_SKIP_FCKIT" "Don't build fckit" "ON") # Skip fckit build unless user passes -DBUNDLE_SKIP_FCKIT=OFF
-  option("BUNDLE_SKIP_ATLAS" "Don't build atlas" "ON") # Skip atlas build unless user passes -DBUNDLE_SKIP_ATLAS=OFF
-
-# turn off optional OOPS toy models
-  option( ENABLE_LORENZ95_MODEL "Build LORENZ95 toy model" OFF )
-  option( ENABLE_QG_MODEL "Build QG toy model" OFF )
-
-  ecbuild_bundle( PROJECT eckit GIT "https://github.com/ecmwf/eckit.git" TAG 1.16.0 )
-  ecbuild_bundle( PROJECT fckit GIT "https://github.com/ecmwf/fckit.git" TAG 0.9.2 )
-  ecbuild_bundle( PROJECT atlas GIT "https://github.com/ecmwf/atlas.git" TAG 0.35.0 )
-
-# External (required) observation operators
-  option("BUNDLE_SKIP_CRTM" "Don't build CRTM" "OFF") # Don't build crtm unless user passes -DBUNDLE_SKIP_CRTM=OFF
-  ecbuild_bundle( PROJECT crtm GIT "https://github.com/JCSDA/crtm.git"   TAG v2.4.1-jedi.1 )
-
-# Build GSI-B
-  option(BUILD_GSIBEC "Build GSI-B" OFF)
-  if(BUILD_GSIBEC)
-    ecbuild_bundle( PROJECT gsibec GIT "https://github.com/GEOS-ESM/GSIbec.git" TAG 1.1.2 )
-  endif()
-
-# Gibbs seawater
-  ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git" BRANCH develop )
-
-# Core JEDI repositories
-  ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  BRANCH develop)
-  ecbuild_bundle( PROJECT vader GIT "https://github.com/jcsda/vader.git" BRANCH develop )
-  ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda/saber.git" BRANCH develop )
-  option(ENABLE_IODA_DATA "Obtain ioda test data from ioda-data repository (vs tarball)" ON)
-  ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda/ioda.git" BRANCH develop  )
-  option(ENABLE_UFO_DATA "Obtain ufo test data from ufo-data repository (vs tarball)" ON)
-  ecbuild_bundle( PROJECT ufo   GIT "https://github.com/jcsda/ufo.git" BRANCH develop )
-
-# FMS and FV3 dynamical core
-  ecbuild_bundle( PROJECT fms GIT "https://github.com/jcsda/FMS.git" BRANCH release-stable )
-  ecbuild_bundle( PROJECT fv3 GIT "https://github.com/jcsda/GFDL_atmos_cubed_sphere.git" BRANCH release-stable )
-
-# fv3-jedi and associated repositories
-  ecbuild_bundle( PROJECT femps       GIT "https://github.com/jcsda/femps.git"                BRANCH develop )
-  ecbuild_bundle( PROJECT fv3-jedi-lm GIT "https://github.com/jcsda/fv3-jedi-linearmodel.git" BRANCH develop )
-  option(ENABLE_FV3_JEDI_DATA "Obtain fv3-jedi test data from fv3-jedi-data repository (vs tarball)" ON)
-  ecbuild_bundle( PROJECT fv3-jedi    GIT "https://github.com/jcsda/fv3-jedi.git"             BRANCH develop )
-
-# SOCA associated repositories
-# TODO: Move the Icepack fork to EMC github
-  set(BUILD_ICEPACK "ON" CACHE STRING "Build the icepack library")
-  if ( BUILD_ICEPACK )
-    ecbuild_bundle( PROJECT icepack GIT "https://github.com/JCSDA-internal/Icepack.git" BRANCH feature/ecbuild-new )
-  endif()
-  ecbuild_bundle( PROJECT mom6 GIT "https://github.com/jcsda-internal/MOM6.git" BRANCH main-ecbuild RECURSIVE )
-  ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH develop )
-
-  # Build JEDI/DA or other peripherals
-  ecbuild_bundle( PROJECT gdas-utils SOURCE "./utils" )
-
-# Build IODA converters
-  option(BUILD_IODA_CONVERTERS "Build IODA Converters" ON)
-  if(BUILD_IODA_CONVERTERS)
-    ecbuild_bundle( PROJECT iodaconv GIT "https://github.com/JCSDA-internal/ioda-converters.git" BRANCH develop )
-  endif()
-
-# Land associated repositories
-  ecbuild_bundle( PROJECT land-imsproc  GIT "https://github.com/NOAA-PSL/land-IMS_proc.git"  TAG 6373819 )
-  ecbuild_bundle( PROJECT land-jediincr GIT "https://github.com/NOAA-PSL/land-apply_jedi_incr.git"  TAG 2923344)
-
-# ioda, ufo, fv3-jedi, and saber test data
-#---------------------------------
-if(CLONE_JCSDADATA)
-
-  # If IODA branch is being built set GIT_BRANCH_FUNC to IODA's current branch.
-  # If a tagged version of IODA is being built set GIT_TAG_FUNC to ioda's current tag. In this case,
-  # IODA test files will be download from UCAR DASH and ioda-data repo will not be cloned.
-  # When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
-  # in a local directory, ioda-data repo will not be cloned
-
-    find_branch_name(REPO_DIR_NAME ioda)
-  # When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
-  # in a local directory, ioda-data repo will not be cloned
-    if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
-      ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop )
-
-      # If IODA's current branch is available in ioda-data repo, that branch will be checked out
-      branch_checkout (REPO_DIR_NAME ioda-data
-                      BRANCH ${GIT_BRANCH_FUNC} )
-    endif()
-
-  # same procedure for ufo-data
-    find_branch_name(REPO_DIR_NAME ufo)
-    if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
-      ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop )
-
-      # If UFO's current branch is available in ioda-data repo, that branch will be checked out
-      branch_checkout (REPO_DIR_NAME ufo-data
-                      BRANCH ${GIT_BRANCH_FUNC} )
-    endif()
-
-  # same procedure for fv3-jedi-data
-    find_branch_name(REPO_DIR_NAME fv3-jedi)
-    if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
-      ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH develop )
-
-      # If fv3-jedi's current branch is available in ioda-data repo, that branch will be checked out
-      branch_checkout (REPO_DIR_NAME fv3-jedi-data
-                      BRANCH ${GIT_BRANCH_FUNC} )
-    endif()
-
-  endif(CLONE_JCSDADATA)
-
-endif(BUILD_GDASBUNDLE)
-
 # Install utility scripts.
 add_subdirectory(ush)
 
 # Include testing.
 add_subdirectory(test)
-
-# Finalize bundle
-# ---------------
-ecbuild_bundle_finalize()

build.sh

@@ -70,7 +70,7 @@ while getopts "p:t:c:hvdfa" opt; do
 done
 
 case ${BUILD_TARGET} in
-  hera | orion)
+  hera | orion | hercules)
     echo "Building GDASApp on $BUILD_TARGET"
     source $dir_root/ush/module-setup.sh
     module use $dir_root/modulefiles
@@ -103,6 +103,7 @@ CMAKE_OPTS+=" -DWORKFLOW_TESTS=${WORKFLOW_BUILD}"
 
 # JCSDA changed test data things, need to make a dummy CRTM directory
 if [[ $BUILD_TARGET == 'hera' ]]; then
+  if [ -d "$dir_root/test-data-release/" ]; then rm -rf $dir_root/test-data-release/; fi
   mkdir -p $dir_root/test-data-release/
   ln -sf $GDASAPP_TESTDATA/crtm $dir_root/test-data-release/crtm
 fi
@@ -112,7 +113,7 @@ echo "Configuring ..."
 set -x
 cmake \
   ${CMAKE_OPTS:-} \
-  $dir_root
+  $dir_root/sorc
 set +x
 
 # Build

ci/driver.sh

@@ -64,7 +64,7 @@ for pr in $open_pr_list; do
   cd $GDAS_CI_ROOT/PR/$pr
 
   # clone copy of repo
-  git clone $repo_url
+  git clone --recursive $repo_url
   cd GDASApp
 
   # checkout pull request

ci/gw_driver.sh

@@ -65,17 +65,14 @@ for pr in $open_pr_list; do
   cd $GDAS_CI_ROOT/workflow/PR/$pr
 
   # clone global workflow develop branch
-  git clone $workflow_url
-
-  # run checkout script for all other components
-  cd $GDAS_CI_ROOT/workflow/PR/$pr/global-workflow/sorc
-  ./checkout.sh -u
+  git clone --recursive $workflow_url
 
   # checkout pull request
-  cd gdas.cd
+  cd $GDAS_CI_ROOT/workflow/PR/$pr/global-workflow/sorc/gdas.cd
   git checkout develop
   git pull
   gh pr checkout $pr
+  git submodule update --init --recursive
 
   # get commit hash
   commit=$(git log --pretty=format:'%h' -n 1)

ci/run_gw_ci.sh

@@ -42,7 +42,7 @@ export WORKFLOW_BUILD="ON"
 cd $repodir/sorc
 module purge
 rm -rf log.build
-./build_all.sh &>> log.build
+./build_all.sh -u &>> log.build
 build_status=$?
 if [ $build_status -eq 0 ]; then
   echo "Build:                                 *SUCCESS*" >> $outfile