Merge branch 'develop' into feature/b2i

needed for the PR

.gitignore

@@ -183,4 +183,5 @@ install*/
 /sorc/gdas
 /sorc/gdas-utils
 !/bundle/CMakeLists.txt
+!/bundle/fv3-interface.cmake
 /bundle/*

.gitmodules

@@ -49,10 +49,6 @@
   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
@@ -73,10 +69,10 @@
   path = sorc/crtm
   url = https://github.com/jcsda/crtm.git
   branch = release/crtm_jedi_v2.4.1
-[submodule "sorc/fms"]
-  path = sorc/fms
-  url = https://github.com/jcsda/fms.git
-  branch = release-stable
+[submodule "sorc/jcb"]
+  path = sorc/jcb
+  url = https://github.com/noaa-emc/jcb.git
+  branch = develop
 [submodule "parm/jcb-gdas"]
   path = parm/jcb-gdas
   url = https://github.com/noaa-emc/jcb-gdas
@@ -85,3 +81,11 @@
   path = parm/jcb-algorithms
   url = https://github.com/noaa-emc/jcb-algorithms
   branch = develop
+[submodule "sorc/da-utils"]
+  path = sorc/da-utils
+  url = https://github.com/noaa-emc/da-utils.git
+  branch = develop
+[submodule "sorc/bufr-query"]
+  path = sorc/bufr-query
+  url = https://github.com/noaa-emc/bufr-query.git
+  branch = develop

README.md

@@ -3,6 +3,25 @@ Global Data Assimilation System Application
 
 The one app to rule them all
 
+## Notes to developers
+
+1 - As a developer, you will have to build the GDASApp againt the `dev/gdasapp` branch of the `global-workflow`
+
+```bash
+git clone --recursive --jobs 8 --branch dev/gdasapp https://github.com/NOAA-EMC/global-workflow.git
+```
+
+2 - For the most part (boundaries of that terminology is stil TBD), changes to the `global-workflow` related to the `GDASApp` developement will be issued in the `dev/gdasapp` branch.
+
+3 - If your feature development involves changes to the global-workflow and the GDASApp, you will have to issue a PR in each repository. The GDASApp PR will have to have the same name in order for the GDASApp CI to build and run the correct branches.
+
+4 - If your work is contained within the `global-workflow` only, you will have to submit a dummy PR in the `GDASApp` with the same branch name.
+To submit a dummy PR, just create a branch with an empty commit:
+```
+git commit --allow-empty -m "Dummy commit to trigger PR"
+```
+
+
 [![Orion](https://github.com/NOAA-EMC/GDASApp/actions/workflows/orion.yaml/badge.svg)](https://github.com/NOAA-EMC/GDASApp/actions/workflows/orion.yaml)
 [![Hera](https://github.com/NOAA-EMC/GDASApp/actions/workflows/hera.yaml/badge.svg)](https://github.com/NOAA-EMC/GDASApp/actions/workflows/hera.yaml)
 

build.sh

@@ -87,7 +87,7 @@ case ${BUILD_TARGET} in
     ;;
 esac
 
-CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA"
+CMAKE_OPTS+=" -DCLONE_JCSDADATA=$CLONE_JCSDADATA -DMACHINE=$BUILD_TARGET"
 
 BUILD_DIR=${BUILD_DIR:-$dir_root/build}
 if [[ $CLEAN_BUILD == 'YES' ]]; then
@@ -126,7 +126,7 @@ set -x
 if [[ $BUILD_JCSDA == 'YES' ]]; then
   make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE
 else
-  builddirs="gdas iodaconv land-imsproc land-jediincr gdas-utils"
+  builddirs="gdas iodaconv land-imsproc land-jediincr gdas-utils bufr-query"
   for b in $builddirs; do
     cd $b
     make -j ${BUILD_JOBS:-6} VERBOSE=$BUILD_VERBOSE

bundle/CMakeLists.txt

@@ -36,6 +36,19 @@ 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)
 
+# Depend path for non-ecbuild packages
+set(DEPEND_LIB_ROOT ${CMAKE_CURRENT_BINARY_DIR}/Depends)
+list(APPEND CMAKE_PREFIX_PATH ${DEPEND_LIB_ROOT})
+
+# Library path for non-ecbuild packages
+link_directories(${CMAKE_CURRENT_BINARY_DIR}/lib)
+
+include( GNUInstallDirs )
+if(APPLE)
+  list( APPEND CMAKE_INSTALL_RPATH $ENV{llvm_openmp_ROOT}/lib )
+endif()
+list( APPEND CMAKE_INSTALL_RPATH ${CMAKE_CURRENT_BINARY_DIR}/fv3 )
+
 # Initialize bundle
 # -----------------
 ecbuild_bundle_initialize()
@@ -75,6 +88,9 @@ if(BUILD_GDASBUNDLE)
 # Gibbs seawater
   ecbuild_bundle( PROJECT gsw SOURCE "../sorc/gsw" )
 
+# EMC BUFR-query library
+  ecbuild_bundle( PROJECT bufr-query SOURCE "../sorc/bufr-query" )
+
 # Core JEDI repositories
   ecbuild_bundle( PROJECT oops SOURCE "../sorc/oops" )
   ecbuild_bundle( PROJECT vader SOURCE "../sorc/vader" )
@@ -84,8 +100,8 @@ if(BUILD_GDASBUNDLE)
   option(ENABLE_UFO_DATA "Obtain ufo test data from ufo-data repository (vs tarball)" ON)
   ecbuild_bundle( PROJECT ufo SOURCE "../sorc/ufo" )
 
-# FMS and FV3 dynamical core
-  ecbuild_bundle( PROJECT fms SOURCE "../sorc/fms" )
+# FV3 dynamical core
+  include(fv3-interface.cmake)
   ecbuild_bundle( PROJECT fv3 SOURCE "../sorc/fv3" )
 
 # fv3-jedi and associated repositories
@@ -100,11 +116,11 @@ if(BUILD_GDASBUNDLE)
   if ( BUILD_ICEPACK )
     ecbuild_bundle( PROJECT icepack SOURCE "../sorc/icepack" )
   endif()
-  ecbuild_bundle( PROJECT mom6 SOURCE "../sorc/mom6" )
   ecbuild_bundle( PROJECT soca SOURCE "../sorc/soca" )
 
   # Build JEDI/DA or other peripherals
   ecbuild_bundle( PROJECT gdas-utils SOURCE "../utils" )
+  ecbuild_bundle( PROJECT da-utils SOURCE "../sorc/da-utils" )
 
 # Build IODA converters
   option(BUILD_IODA_CONVERTERS "Build IODA Converters" ON)

bundle/fv3-interface.cmake

@@ -0,0 +1,18 @@
+# FV3 dycore
+set(OPENMP                ON )
+set(32BIT                 OFF)
+set(DEBUG                 OFF)
+set(MOVING_NEST           OFF)
+set(MULTI_GASES           OFF)
+set(USE_GFSL63            ON )
+set(NO_PHYS               ON )
+set(GFS_PHYS              OFF)
+set(GFS_TYPES             OFF)
+set(use_WRTCOMP           OFF)
+set(INTERNAL_FILE_NML     ON )
+set(ENABLE_QUAD_PRECISION ON )
+
+add_library(fv3dycore IMPORTED SHARED)
+set_target_properties(fv3dycore PROPERTIES IMPORTED_LOCATION ${CMAKE_CURRENT_BINARY_DIR}/fv3/libfv3.${CMAKE_SHARED_LIBRARY_SUFFIX})
+
+message(WARN "WE ARE USING fv3-interface.cmake")

ci/driver.sh

@@ -60,11 +60,32 @@ repo_url="https://github.com/NOAA-EMC/GDASApp.git"
 for pr in $open_pr_list; do
   gh pr edit $pr --remove-label $CI_LABEL --add-label ${CI_LABEL}-Running
   echo "Processing Pull Request #${pr}"
+
+  # get the branch name used for the PR
+  gdasapp_branch=$(gh pr view $pr --json headRefName -q ".headRefName")
+
+  # get the fork information
+  pr_details=$(gh pr view $pr --repo ${repo_url} --json headRepository,headRepositoryOwner,headRefName)
+
+  # extract the necessary info
+  fork_owner=$(gh pr view $pr --repo ${repo_url} --json headRepositoryOwner --jq '.headRepositoryOwner.login')
+  fork_name=$(gh pr view $pr --repo ${repo_url} --json headRepository --jq '.headRepository.name')
+
+  # construct the fork URL
+  gdasapp_url="https://github.com/$fork_owner/${fork_name}.git"
+
+  echo "Fork URL: $gdasapp_url"
+  echo "Branch Name: $gdasapp_branch"
+
+  # create PR specific directory
+  if [ -d $GDAS_CI_ROOT/PR/$pr ]; then
+      rm -rf $GDAS_CI_ROOT/PR/$pr
+  fi
   mkdir -p $GDAS_CI_ROOT/PR/$pr
   cd $GDAS_CI_ROOT/PR/$pr
 
   # clone copy of repo
-  git clone --recursive $repo_url
+  git clone --recursive --jobs 8 --branch $gdasapp_branch $gdasapp_url
   cd GDASApp
 
   # checkout pull request
@@ -94,11 +115,11 @@ for pr in $open_pr_list; do
   # run build and testing command
   $my_dir/run_ci.sh -d $GDAS_CI_ROOT/PR/$pr/GDASApp -o $GDAS_CI_ROOT/PR/$pr/output_${commit}
   ci_status=$?
-  gh pr comment $pr --body-file $GDAS_CI_ROOT/PR/$pr/output_${commit}
+  gh pr comment $pr --repo ${repo_url} --body-file $GDAS_CI_ROOT/PR/$pr/output_${commit}
   if [ $ci_status -eq 0 ]; then
-    gh pr edit $pr --remove-label ${CI_LABEL}-Running --add-label ${CI_LABEL}-Passed
+    gh pr edit $pr --repo ${repo_url} --remove-label ${CI_LABEL}-Running --add-label ${CI_LABEL}-Passed
   else
-    gh pr edit $pr --remove-label ${CI_LABEL}-Running --add-label ${CI_LABEL}-Failed
+    gh pr edit $pr --repo ${repo_url} --remove-label ${CI_LABEL}-Running --add-label ${CI_LABEL}-Failed
   fi
 done
 

ci/gw_driver.sh

@@ -61,11 +61,36 @@ workflow_url="https://github.com/NOAA-EMC/global-workflow.git"
 for pr in $open_pr_list; do
   gh pr edit $pr --remove-label $CI_LABEL --add-label ${CI_LABEL}-Running
   echo "Processing Pull Request #${pr}"
+
+  # get the branch name used for the PR
+  gdasapp_branch=$(gh pr view $pr --json headRefName -q ".headRefName")
+
+  # check for a companion PR in the global-workflow
+  companion_pr_exists=$(gh pr list --repo ${workflow_url} --head ${gdasapp_branch} --state open)
+  if [ -n "$companion_pr_exists" ]; then
+    # get the PR number
+    companion_pr=$(echo "$companion_pr_exists" | awk '{print $1;}')
+
+    # extract the necessary info
+    fork_owner=$(gh pr view $companion_pr --repo $workflow_url --json headRepositoryOwner --jq '.headRepositoryOwner.login')
+    fork_name=$(gh pr view $companion_pr --repo $workflow_url --json headRepository --jq '.headRepository.name')
+
+    # Construct the fork URL
+    workflow_url="https://github.com/$fork_owner/$fork_name.git"
+
+    echo "Fork URL: $workflow_url"
+    echo "Branch Name: $gdasapp_branch"
+  fi
+
+  # create PR specific directory
+  if [ -d $GDAS_CI_ROOT/workflow/PR/$pr ]; then
+      rm -rf $GDAS_CI_ROOT/workflow/PR/$pr
+  fi
   mkdir -p $GDAS_CI_ROOT/workflow/PR/$pr
   cd $GDAS_CI_ROOT/workflow/PR/$pr
-
+  
   # clone global workflow develop branch
-  git clone --recursive $workflow_url
+  git clone --recursive --jobs 8 --branch dev/gdasapp $workflow_url
 
   # checkout pull request
   cd $GDAS_CI_ROOT/workflow/PR/$pr/global-workflow/sorc/gdas.cd

ci/hera.sh

@@ -1,8 +1,8 @@
-export GDAS_CI_ROOT=/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp
+export GDAS_CI_ROOT=/scratch1/NCEPDEV/da/role.jedipara/CI/GDASApp
 export GDAS_CI_HOST='hera'
 export GDAS_MODULE_USE=$GDAS_CI_ROOT/repo/modulefiles
 export SLURM_ACCOUNT=da-cpu
 export SALLOC_ACCOUNT=$SLURM_ACCOUNT
 export SBATCH_ACCOUNT=$SLURM_ACCOUNT
 export SLURM_QOS=debug
-export PATH=$PATH:/scratch1/NCEPDEV/da/Cory.R.Martin/CI/gh/gh_2.46.0_linux_amd64/bin
+export PATH=$PATH:/home/role.jedipara/bin

mains/gdas.cc

@@ -14,6 +14,7 @@
 #include "ufo/instantiateObsFilterFactory.h"
 #include "ufo/ObsTraits.h"
 
+#include "oops/runs/ConvertToStructuredGrid.h"
 #include "oops/runs/ConvertState.h"
 #include "oops/runs/HofX4D.h"
 #include "oops/runs/LocalEnsembleDA.h"
@@ -52,6 +53,9 @@ int runApp(int argc, char** argv, const std::string traits, const std::string ap
   // Define a map from app names to lambda functions that create unique_ptr to Applications
   std::map<std::string, std::function<std::unique_ptr<oops::Application>()>> apps;
 
+  apps["converttostructuredgrid"] = []() {
+      return std::make_unique<oops::ConvertToStructuredGrid<Traits>>();
+  };	
   apps["convertstate"] = []() {
       return std::make_unique<oops::ConvertState<Traits>>();
   };
@@ -96,6 +100,7 @@ int main(int argc,  char ** argv) {
   // Check that the application is recognized
   // ----------------------------------------
   const std::set<std::string> validApps = {
+    "converttostructuredgrid",
     "convertstate",
     "hofx4d",
     "localensembleda",

modulefiles/GDAS/gaea.intel.lua

@@ -43,6 +43,7 @@ load("fftw/3.3.10")
 load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
+load("fms/2023.04")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
@@ -74,9 +75,6 @@ load("py-xarray/2023.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 
--- hack for wxflow
---prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")
-
 setenv("CC","cc")
 setenv("CXX","CC")
 setenv("FC","ftn")

modulefiles/GDAS/hera.intel.lua

@@ -43,6 +43,7 @@ load("fftw/3.3.10")
 load("fckit/0.11.0")
 load("fiat/1.2.0")
 --load("ectrans/1.2.0")
+load("fms/2023.04")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
@@ -73,9 +74,7 @@ load("py-scipy/1.11.3")
 load("py-xarray/2023.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
-
--- hack for wxflow
-prepend_path("PYTHONPATH", "/scratch1/NCEPDEV/da/python/gdasapp/wxflow/20240307/src")
+load("py-click/8.1.7")
 
 setenv("CC","mpiicc")
 setenv("FC","mpiifort")
@@ -86,9 +85,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/data/test")
+setenv("CRTM_FIX","/scratch1/NCEPDEV/da/role.jedipara/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/scratch1/NCEPDEV/da/role.jedipara/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/scratch1/NCEPDEV/da/role.jedipara/GDASApp/unittestdata")
 --prepend_path("PATH","/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/intel-18.0.5.274/prod_util/1.2.2/bin")
 
 whatis("Name: ".. pkgName)

modulefiles/GDAS/hercules.intel.lua

@@ -40,6 +40,7 @@ load("fftw/3.3.10")
 load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
+load("fms/2023.04")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
@@ -60,7 +61,7 @@ load("py-pybind11/2.11.0")
 --load("crtm/v2.4_jedi")
 load("contrib/0.1")
 load("noaatools/3.1")
-load("rocoto/1.3.5")
+load("rocoto/1.3.7")
 
 load("hpc/1.2.0")
 unload("python/3.10.13")
@@ -79,9 +80,9 @@ local mpinproc = '-n'
 setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
-setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm/2.4.0")
-setenv("GDASAPP_TESTDATA","/work2/noaa/da/cmartin/CI/GDASApp/data")
-setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/cmartin/CI/GDASApp/data/test/")
+setenv("CRTM_FIX","/work2/noaa/da/role-da/GDASApp/fix/crtm/2.4.0")
+setenv("GDASAPP_TESTDATA","/work2/noaa/da/role-da/GDASApp/testdata")
+setenv("GDASAPP_UNIT_TEST_DATA_PATH", "/work2/noaa/da/role-da/GDASApp/unittestdata")
 prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")
 
 execute{cmd="ulimit -s unlimited",modeA={"load"}}

modulefiles/GDAS/noaacloud.intel.lua

@@ -41,6 +41,7 @@ load("fftw/3.3.10")
 load("fckit/0.11.0")
 load("fiat/1.2.0")
 load("ectrans/1.2.0")
+load("fms/2023.04")
 load("atlas/0.35.1")
 load("sp/2.5.0")
 load("gsl-lite/0.37.0")
@@ -72,9 +73,6 @@ load("py-xarray/2023.7.0")
 load("py-f90nml/1.4.3")
 load("py-pip/23.1.2")
 
--- hack for wxflow
---prepend_path("PYTHONPATH", "/contrib/Wei.Huang/data/glopara/data/gdasapp-wxflow-20240307/src/wxflow")
-
 setenv("CC","mpiicc")
 setenv("FC","mpiifort")
 setenv("CXX","mpiicpc")