Merge from upstream develop

.github/workflows/aux.yml

@@ -1,9 +1,12 @@
-name: Helpers
+name: Repo Check
 on:
-  workflow_run:
-    workflows: ["Pull Request Tests"]
-    types:
-      - requested
+  #workflow_run:
+  #  workflows: ["Pull Request Tests"]
+  #  types:
+  #    - requested
+  pull_request:
+    branches:
+      - develop
 env:
   app: Accept:application/vnd.github.v3+json
   base_url: $GITHUB_API_URL/repos/$GITHUB_REPOSITORY/actions/runs
@@ -30,24 +33,28 @@ jobs:
     steps:
     - name: Check up-to-dateness and post comment
       run: |
-        head_sha=${{ github.event.workflow_run.head_sha }}
-        git clone -q ${{ github.event.workflow_run.head_repository.html_url }} .
+        trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
+        head_sha=${{ github.event.pull_request.head.sha }}
+        head_brc=${{ github.event.pull_request.head.ref }}
+        head_url=${{ github.event.pull_request.head.repo.html_url }}
+        git clone -q -b $head_brc $head_url .
         git checkout -q $head_sha
         git submodule -q update --init --recursive
         cd ${{ github.workspace }}/tests/ci
         url=$GITHUB_API_URL/repos/$GITHUB_REPOSITORY
         pr_number=$(curl -sS -H $app $url/pulls \
           | jq -r '.[] | select(.head.sha == "'"$head_sha"'") | .number')
         echo "pr_number is $pr_number"
-        pr_uid=${{ github.event.workflow_run.head_repository.owner.login }}
+        pr_uid=${{ github.event.pull_request.head.repo.owner.login }}
         echo "pr_uid is $pr_uid"
-        comment="$(./repo_check.sh $pr_uid 2>/dev/null)"
-        echo "comment is $comment"
-        if [[ -n $comment ]]; then
-          curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-            $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
-          echo -n "failure" >~/repocheck_file
-        else
-          echo -n "success" >~/repocheck_file
-        fi
+        ./repo_check.sh
+        #comment="$(./repo_check.sh 2>/dev/null)"
+        #echo "comment is $comment"
+        #if [[ -n $comment ]]; then
+        #  curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+        #    $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
+        #  echo -n "failure" >~/repocheck_file
+        #else
+        #  echo -n "success" >~/repocheck_file
+        #fi
         

.github/workflows/superlinter.yml

@@ -0,0 +1,37 @@
+---
+name: Super-Linter
+
+on:
+  push: null
+  pull_request: null
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Super-Linter
+        uses: super-linter/[email protected]
+        env:
+          LINTER_RULES_PATH: /
+          DEFAULT_BRANCH: origin/develop
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          FILTER_REGEX_EXCLUDE: .*(tests/fv3_conf/.*|tests/ci/.*|tests/auto/.*|tests/auto-jenkins/.*|tests/opnReqTests/.*|tests/opnReqTest|tests/atparse.bash).*
+          VALIDATE_BASH: true
+          BASH_SEVERITY: style
+          #VALIDATE_GITHUB_ACTIONS: true
+          #VALIDATE_LUA: true
+          #VALIDATE_MARKDOWN: true
+          #VALIDATE_PYTHON_PYLINT: true
+          #VALIDATE_YAML: true

.shellcheckrc

@@ -0,0 +1,16 @@
+# Global settings for Shellcheck (https://github.com/koalaman/shellcheck)
+enable=all
+
+external-sources=true
+
+# Disable variable referenced but not assigned
+disable=SC2154
+
+# Disable following non-constant source
+disable=SC1090
+
+# Disable non-existent binary
+disable=SC1091
+
+# Disable -p -m only applies to deepest directory
+disable=SC2174

CDEPS-interface/cdeps_files.cmake

@@ -56,6 +56,7 @@ list(APPEND cdeps_datm_files
 list(APPEND cdeps_dice_files
   CDEPS/dice/dice_datamode_ssmi_mod.F90
   CDEPS/dice/dice_flux_atmice_mod.F90
+  CDEPS/dice/dice_datamode_cplhist_mod.F90
   CDEPS/dice/ice_comp_nuopc.F90
 )
 

CICE-interface/CMakeLists.txt

@@ -39,7 +39,7 @@ else()
 endif()
 
 # Configuration Options
-set(CICE_IO "NetCDF" CACHE STRING "CICE OPTIONS: Choose IO options.")
+set(CICE_IO "PIO" CACHE STRING "CICE OPTIONS: Choose IO options.")
 set_property(CACHE CICE_IO PROPERTY STRINGS "NetCDF" "PIO" "Binary")
 
 # Too many files to list, so include them via this file
@@ -51,7 +51,8 @@ list(APPEND lib_src_files
   ${cice_shared_files_c}
   ${icepack_files}
   ${cice_mpi_comm_files}
-  ${cice_nuopc_cmeps_driver_files})
+  ${cice_nuopc_cmeps_driver_files}
+  ${cice_cdeps_inline_files})
 
 list(APPEND _cice_defs FORTRANUNDERSCORE
                        coupled)
@@ -84,6 +85,11 @@ if(OpenMP_Fortran_FOUND)
   target_link_libraries(cice PRIVATE OpenMP::OpenMP_Fortran)
 endif()
 
+# ice prescribed
+add_dependencies(cice cdeps::cdeps)
+target_compile_definitions(cice PUBLIC "DISABLE_FoX")
+target_link_libraries(cice PUBLIC cdeps::cdeps)
+
 ###############################################################################
 ### Install
 ###############################################################################

CICE-interface/cice_files.cmake

@@ -150,3 +150,22 @@ list(APPEND cice_nuopc_cmeps_driver_files
   CICE/cicecore/drivers/nuopc/cmeps/ice_shr_methods.F90
   CICE/cicecore/drivers/nuopc/cmeps/ice_mesh_mod.F90
 )
+
+#-- Using ice prescribed ifndef cesmcoupled
+list(APPEND cice_cdeps_inline_files
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_orb_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_const_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_abort_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_strconvert_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_log_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_sys_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_kind_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_nl_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_cal_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_string_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/share/shr_timer_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/streams/dshr_strdata_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/streams/dshr_stream_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/streams/dshr_methods_mod.F90
+  ${PROJECT_SOURCE_DIR}/CDEPS-interface/CDEPS/dshr/dshr_mod.F90
+)

CMakeLists.txt

@@ -16,7 +16,7 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 ###############################################################################
 
 # Valid applications and choices
-list(APPEND VALID_APPS ATM ATMAERO ATMAQ ATMW ATMWM ATML LND LND-LM4 S2S S2SA S2SW S2SWA S2SWAL HAFS HAFSW HAFS-MOM6 HAFS-MOM6W HAFS-ALL NG-GODAS)
+list(APPEND VALID_APPS ATM ATMAERO ATMAQ ATMW ATMWM ATML LND LND-LM4 S2S S2SA S2SW S2SWA S2SWAL ATM_DS2S ATM_DS2S-PCICE HAFS HAFSW HAFS-MOM6 HAFS-MOM6W HAFS-ALL NG-GODAS)
 set(APP NONE CACHE BOOL "Application Name")
 if(NOT (APP IN_LIST VALID_APPS))
   message(FATAL_ERROR "${APP} is not a valid application.\nValid Applications are: ${VALID_APPS}")
@@ -75,6 +75,7 @@ set(JEDI_DRIVER     OFF CACHE BOOL "Enable JEDI as top level driver")
 set(CMEPS_AOFLUX    OFF CACHE BOOL "Enable atmosphere-ocean flux calculation in mediator")
 set(PDLIB           OFF CACHE BOOL "Enable Domain Decomposition in WW3 via PDLIB")
 set(CDEPS_INLINE    OFF CACHE BOOL "Enable CDEPS inline capability")
+set(HYDRO           OFF CACHE BOOL "Enable hydrostatic set")
 
 set(CMAKE_Platform $ENV{CMAKE_Platform})
 if(CMAKE_Platform)
@@ -124,6 +125,7 @@ message("PARALLEL_NETCDF .. ${PARALLEL_NETCDF}")
 message("JEDI_DRIVER ...... ${JEDI_DRIVER}")
 message("CMEPS_AOFLUX ..... ${CMEPS_AOFLUX}")
 message("CDEPS_INLINE ..... ${CDEPS_INLINE}")
+message("HYDRO  ........... ${HYDRO}")
 
 message("")
 
@@ -152,7 +154,7 @@ if(FMS)
   find_package(FMS 2022.04 REQUIRED COMPONENTS R4 R8)
   if(APP MATCHES "^(HAFSW)$")
     add_library(fms ALIAS FMS::fms_r4)
-  elseif (APP MATCHES "^(S2S|S2SA|S2SW|S2SWA|S2SWAL|NG-GODAS|HAFS-MOM6|HAFS-MOM6W)$")
+  elseif (APP MATCHES "^(S2S|S2SA|S2SW|S2SWA|S2SWAL|ATM_DS2S|ATM_DS2S-PCICE|NG-GODAS|HAFS-MOM6|HAFS-MOM6W)$")
     add_library(fms ALIAS FMS::fms_r8)
   endif()
   if(APP MATCHES "^(ATM|ATMAERO|ATMAQ|ATMWM|ATMW|ATML|ATML-LM4|LND-LM4|HAFS|HAFS-ALL)$")
@@ -340,6 +342,7 @@ if(CDEPS)
   add_dependencies(ufs cdeps::cdeps)
   list(APPEND _ufs_defs_private FRONT_CDEPS_DATM=cdeps_datm_comp)
   list(APPEND _ufs_defs_private FRONT_CDEPS_DOCN=cdeps_docn_comp)
+  list(APPEND _ufs_defs_private FRONT_CDEPS_DICE=cdeps_dice_comp)
   target_link_libraries(ufs PUBLIC cdeps::cdeps)
 endif()
 

NOAHMP-interface/CMakeLists.txt

@@ -8,9 +8,10 @@ list(APPEND _noahmp_cap_files noahmp/drivers/nuopc/lnd_comp_kind.F90
                               noahmp/drivers/nuopc/lnd_comp_domain.F90
                               noahmp/drivers/nuopc/lnd_comp_import_export.F90
                               noahmp/drivers/nuopc/lnd_comp_nuopc.F90
-                              noahmp/drivers/nuopc/lnd_comp_driver.F90)
+                              noahmp/drivers/nuopc/lnd_comp_driver.F90
+			      noahmp/drivers/nuopc/lnd_comp_cplscalars.F90)
 
-# CCPP interface 
+# CCPP interface
 list(APPEND _noahmp_ccpp_files noahmp/drivers/ccpp/noahmpdrv.F90
                                noahmp/drivers/ccpp/sfc_diff.f
                                noahmp/drivers/ccpp/machine.F
@@ -25,7 +26,7 @@ list(APPEND _noahmp_files noahmp/src/module_sf_noahmplsm.F90
                           noahmp/src/module_sf_noahmp_glacier.F90)
 
 #------------------------------------------------------------------------------
-# Set CCPP flags for C/C++/Fortran preprocessor 
+# Set CCPP flags for C/C++/Fortran preprocessor
 add_definitions(-DCCPP)
 
 #------------------------------------------------------------------------------
@@ -55,8 +56,10 @@ endif()
 
 #------------------------------------------------------------------------------
 # Add model-specific flags for C/C++/Fortran preprocessor
-add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
-add_definitions(-DINTERNAL_FILE_NML)
+if (NOT HYDRO)
+add_definitions(-DMOIST_CAPPA -DUSE_COND)
+endif()
+add_definitions(-DINTERNAL_FILE_NML -DNEMS_GSM)
 
 #------------------------------------------------------------------------------
 # NOAHMP

build.sh

@@ -1,21 +1,29 @@
 #!/bin/bash
 set -eu
-
-if [[ $(uname -s) == Darwin ]]; then
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+uname_s=$(uname -s)
+if [[ ${uname_s} == Darwin ]]; then
+  UFS_MODEL_DIR=$(greadlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 else
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+  UFS_MODEL_DIR=$(readlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 fi
+echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
+readonly UFS_MODEL_DIR
 
 export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
 export FC=${FC:-mpif90}
 
 BUILD_DIR=${BUILD_DIR:-${UFS_MODEL_DIR}/build}
-mkdir -p ${BUILD_DIR}
+mkdir -p "${BUILD_DIR}"
 
-cd ${BUILD_DIR}
-cmake ${UFS_MODEL_DIR} ${CMAKE_FLAGS}
+cd "${BUILD_DIR}"
+ARR_CMAKE_FLAGS=()
+for i in ${CMAKE_FLAGS}; do ARR_CMAKE_FLAGS+=("${i}") ; done
+cmake "${UFS_MODEL_DIR}" "${ARR_CMAKE_FLAGS[@]}"
 # Turn off OpenMP threading for parallel builds
 # to avoid exhausting the number of user processes
-OMP_NUM_THREADS=1 make -j ${BUILD_JOBS:-4} VERBOSE=${BUILD_VERBOSE:-}
+OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"

cmake/GNU.cmake

@@ -1,18 +1,22 @@
-set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ggdb -fbacktrace -cpp -fcray-pointer -ffree-line-length-none -fno-range-check")
-
-if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+# https://github.com/ufs-community/ufs-weather-model/issues/2159
+if(MOVING_NEST)
+  message(FATAL_ERROR "Option MOVING_NEST not compatible with ${CMAKE_Fortran_COMPILER_ID}}")
 endif()
 
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ggdb -fbacktrace -cpp -fcray-pointer -ffree-line-length-none -fno-range-check")
+
 if(NOT 32BIT)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8 -fdefault-double-8")
 endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
     set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check")
-    if(CMAKE_Platform STREQUAL "hercules.gnu")
-      set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -mcmodel=medium")
+    # https://github.com/ufs-community/ufs-weather-model/issues/2155
+    if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin" AND ${CMAKE_HOST_SYSTEM_PROCESSOR} MATCHES "arm64")
+      set( CMAKE_Fortran_FLAGS_DEBUG     "${CMAKE_Fortran_FLAGS_DEBUG} -mcmodel=small" )
+    else()
+      set( CMAKE_Fortran_FLAGS_DEBUG     "${CMAKE_Fortran_FLAGS_DEBUG} -mcmodel=medium" )
     endif()
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
 else()

cmake/Intel.cmake

@@ -1,6 +1,15 @@
-set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -nowarn -sox -align array64byte -qno-opt-dynamic-align")
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -sox -align array64byte -qno-opt-dynamic-align")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qno-opt-dynamic-align -sox -fp-model source")
 
+# warning #5462: Global name too long.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 5462")
+
+# remark #7712: This variable has not been used.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 7712")
+
+# remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 8291")
+
 if(CMAKE_Platform STREQUAL "derecho.intel")
   set(CMAKE_Fortran_LINK_FLAGS "-Wl,--copy-dt-needed-entries")
 endif()

cmake/configure_apps.cmake

@@ -57,6 +57,7 @@ if(APP MATCHES "^(S2S|S2SA|S2SW|S2SWA|S2SWAL)$")
   set(FV3        ON  CACHE BOOL "Enable FV3"                 FORCE)
   set(MOM6       ON  CACHE BOOL "Enable MOM6"                FORCE)
   set(CICE6      ON  CACHE BOOL "Enable CICE6"               FORCE)
+  set(CDEPS      ON  CACHE BOOL "Enable CDEPS"               FORCE)
   set(STOCH_PHYS ON  CACHE BOOL "Enable Stochastic Physics"  FORCE)
   if(APP MATCHES "^(S2SW|S2SWA|S2SWAL)")
     set(WW3      ON  CACHE BOOL "Enable WAVEWATCH III"       FORCE)
@@ -72,6 +73,20 @@ if(APP MATCHES "^(S2S|S2SA|S2SW|S2SWA|S2SWAL)$")
   message("${APP_MSG} mode")
 endif()
 
+if(APP MATCHES "^(ATM_DS2S|ATM_DS2S-PCICE)$")
+  set(APP_MSG "Configuring UFS app in ATM_DS2S with CDEPS data")
+  set(CMEPS      ON  CACHE BOOL "Enable CMEPS"               FORCE)
+  set(FMS        ON  CACHE BOOL "Enable FMS"                 FORCE)
+  set(FV3        ON  CACHE BOOL "Enable FV3"                 FORCE)
+  set(STOCH_PHYS ON  CACHE BOOL "Enable Stochastic Physics"  FORCE)
+  set(CDEPS      ON  CACHE BOOL "Enable CDEPS"               FORCE)
+  if (APP MATCHES  "^(ATM_DS2S-PCICE)$")
+    set(CICE6      ON  CACHE BOOL "Enable CICE6"               FORCE)
+    string(CONCAT APP_MSG ${APP_MSG} " with prescribed ice sea ice")
+  endif()
+  message("${APP_MSG} mode")
+endif()
+
 if(APP MATCHES "^(HAFS|HAFSW|HAFS-MOM6|HAFS-MOM6W|HAFS-ALL)$")
   set(CMEPS      ON  CACHE BOOL "Enable CMEPS"               FORCE)
   set(CDEPS      ON  CACHE BOOL "Enable CDEPS"               FORCE)

cmake/configure_noaacloud.intel.cmake

@@ -0,0 +1 @@
+set(PARALLEL_NETCDF ON CACHE BOOL "Enable parallel NetCDF" FORCE)