Squashed commit of the following:

commit f234a3e
Author: Ufuk Turunçoğlu <[email protected]>
Date:   Tue Apr 30 11:35:25 2024 -0600

    Fix for land component model (ufs-community#2191)

    * UFSWM - fix fully coupled land component configuration
      * NOAHMP - get fixed information from surface file

commit 04bbc15
Author: jiandewang <[email protected]>
Date:   Thu Apr 25 14:52:00 2024 -0400

    update MOM6 to its main repo. 20240401 commit (ufs-community#2241)

    * UFSWM -
      * MOM6 - update MOM6 to its main repo. 20240401 commit (NCAR-candidate-20240319)

commit b6c576d
Author: Daniel Sarmiento <[email protected]>
Date:   Tue Apr 23 12:24:22 2024 -0400

    Merged global namelist (ufs-community#2173)

    * UFSWM - global_control.nml_IN has been added as the new regression test namelist template for all global regression tests. The namelist now uses pointers (i.e. @[abc]) for variables and default values have been added to the default_vars.sh script. A new section in default_vars.sh has been added (export_tiled) to account for tiled RTs that pulls the correct parameter files using the ATMRES variable.
    Regression tests have been modified to account for these changes. Tests that were not compatible with the GFSv17_p8 core have been disabled for now. They will be turned on as they are updated from GFSv16 to GFSv17.

commit 5d2ca19
Author: WenMeng-NOAA <[email protected]>
Date:   Fri Apr 19 13:59:12 2024 -0400

    Update upp submodule (ufs-community#2213)

    * UFSWM - Update inline post
      * FV3 - Update upp submodule for inline post

commit 47c0099
Author: Brian Curtis <[email protected]>
Date:   Wed Apr 17 15:59:48 2024 -0400

    Add bash linting to CI. Cleanup .sh scripts a bit. Address .sh bugs. Adds -v Verbose option. (ufs-community#2218)  Remove nowarn Intel compiler flag (ufs-community#2225)

    * UFSWM
    - Add bash linting to CI:
      - uses superlinter to check for consistent bash code writing
    - Cleans up .sh scripts to comply with superlinter
    - Cleans up .sh scripts to be more consistent, easier to read.
    - Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's.
    - Addresses smaller bugs
      - quota/timeout search logic adjusted.
      - check for dirs existing (DISKNM, STMP, PTMP) before starting.
      - adjustments/cleanup to ecflow/rocoto sections
      - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh.
      - fix for issue where run_dir will not delete properly.
    * FV3: Address compiler warnings
      * atmos_cubed_sphere: Address compiler warnings.

commit 4f32a4b
Author: Rick Grubin <[email protected]>
Date:   Mon Apr 15 07:21:08 2024 -0600

    Document ATMW / ATMAERO / HAFS WM configurations (ufs-community#2160)

    * UFSWM
      * doc/Userguide
        * source
          * conf.py
          * Configurations.rst
          * FAQ.rst
          * InputsOutputs.rst
          * Introduction.rst

commit ac4445d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 15 08:59:42 2024 -0400

    Bump idna from 3.6 to 3.7 in /doc/UsersGuide (ufs-community#2234)

    *doc/UserGuide
       *requirements.txt - updates inda version from 3.6 to 3.7

commit 281b32f
Author: Samuel Trahan (NOAA contractor) <[email protected]>
Date:   Mon Apr 15 08:38:01 2024 -0400

    bug fixes: kchunk3d ignored, hailwat uninitialized in dycore, tile_num wrong for nests (ufs-community#2201)

    * UFSWM - None.
      * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP.
        * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.

commit 8a5f711
Author: Denise Worthen <[email protected]>
Date:   Thu Apr 11 13:32:26 2024 -0400

    Add PIO namelist control for CICE (ufs-community#2145)

    Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE

commit 45c8b2a
Author: JONG KIM <[email protected]>
Date:   Thu Apr 4 19:49:13 2024 -0400

    Hotfix/cubed sphere hash fix: HAILCAST diagnostic code (units issue) (ufs-community#2223)

    cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)

commit 26e6db6
Author: Denise Worthen <[email protected]>
Date:   Wed Apr 3 19:57:08 2024 -0400

    Enable cpl_scalars export from ATM and NoahMP for use by CMEPS (ufs-community#2175)

      * CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files
      * CMEPS - fix mapping mask for lnd->atm
      * FV3 - add export of cpl_scalars
      * NOAHMP - add export of cpl_scalars

commit 1411b90
Author: Dusan Jovic <[email protected]>
Date:   Mon Apr 1 18:04:44 2024 -0400

    Update module_write_netcdf to avoid hangs in RRFS runs (ufs-community#2193)

    * UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs
      * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs

commit 87c27b9
Author: Matthew Masarik <[email protected]>
Date:   Fri Mar 29 15:23:42 2024 -0400

    WW3 feature:  Langmuir turbulence parameterization (ufs-community#2195)

      * WW3 - Langmuir turbulence parameterization

commit c54e986
Author: Samuel Trahan (NOAA contractor) <[email protected]>
Date:   Wed Mar 27 16:11:03 2024 -0400

    regression test system bug fixes, eliminate MOM6 warnings (ufs-community#2197), add xr_cnvcld flag to FV3 (ufs-community#2185) (ufs-community#2202)

    * UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh.
      * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite
        * ccpp - physics-level changes to implement new namelist variable
      * MOM6 - update MOM6 code to eliminate all compiler warnings

.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

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

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)
 
 #------------------------------------------------------------------------------

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/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()

doc/UsersGuide/requirements.txt

@@ -18,7 +18,7 @@ docutils==0.20.1
     #   sphinx
     #   sphinx-rtd-theme
     #   sphinxcontrib-bibtex
-idna==3.6
+idna==3.7
     # via requests
 imagesize==1.4.1
     # via sphinx