add tests on Gaea.

.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/super-linter@v6.3.0
+        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

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 +1,12 @@
-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")
+
 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

doc/UsersGuide/source/FAQ.rst

@@ -166,7 +166,7 @@ options:
 MOM6, CICE6 and CMEPS restart files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In ``nems.configure``, set the ALLCOMP_attribute ``restart_n`` to a
+In ``ufs.configure``, set the ALLCOMP_attribute ``restart_n`` to a
 value greater than the forecast length.
 
 MOM6 history files
@@ -229,11 +229,11 @@ How do I set the total number of tasks for my job?
 In the UFS WM, each component's MPI task information, including the
 starting and ending tasks and the number of threads, are specified
 using the component-specific ``petlist_bounds`` and
-``omp_num_threads`` in ``nems.configure``. In general, the total
+``omp_num_threads`` in ``ufs.configure``. In general, the total
 number of MPI tasks required is the sum of all the sub-component
 tasks, as long as those components do not overlap (i.e., share the
 same PETs). An example of a global 5 component coupled configuration
-nems.configure at the end of this section.
+ufs.configure at the end of this section.
 
 FV3atm
 ^^^^^^
@@ -286,7 +286,7 @@ If ESMF-managed threading is used, the total number of PETs for the
 atmosphere component is given by the product of the number of threads
 requested and the total number of MPI ranks (both forecast and write
 grid component). If ``num_threads_atm`` is the number of threads
-specified for the FV3atm component, in ``nems.configure`` the ATM PET
+specified for the FV3atm component, in ``ufs.configure`` the ATM PET
 bounds are given by
 
 ::
@@ -295,7 +295,7 @@ bounds are given by
    ATM_omp_num_threads    num_threads_atm
 
 Note that in UWM, the ATM component is normally listed first in
-``nems.configure`` so that the starting PET for the ATM is 0.
+``ufs.configure`` so that the starting PET for the ATM is 0.
 
 GOCART
 ^^^^^^
@@ -330,7 +330,7 @@ MPI tasks for CMEPS is given by
 
    total_tasks_med = smaller of (300, FV3atm forecast tasks)
 
-and in ``nems.configure``
+and in ``ufs.configure``
 
 ::
 
@@ -342,7 +342,7 @@ MOM6
 
 For MOM6 the only restriction currently on the number of MPI ranks
 used by MOM6 is that it is divisible by 2. The starting PET in
-``nems.configure`` will be the last PET of the preceding component,
+``ufs.configure`` will be the last PET of the preceding component,
 incremented by one. Threading in MOM6 is not recommended at this time.
 
 ::
@@ -388,14 +388,14 @@ For the 1-deg CICE domain for example, ``ice_in`` would be
 
 
 In UFS, only a single thread is used for CICE so for ``nprocs`` set in
-``ice_in``, the tasks in ``nems.configure`` are set as:
+``ice_in``, the tasks in ``ufs.configure`` are set as:
 
 ::
 
    ICE_petlist_bounds:            starting_ICE_PET  nprocs+starting_ICE_PET-1
    ICE_omp_num_threads:           1
 
-The starting ICE PET in ``nems.configure`` will be the last PET of the
+The starting ICE PET in ``ufs.configure`` will be the last PET of the
 preceding component, incremented by one.
 
 WW3
@@ -409,20 +409,20 @@ for WW3 and the number of threads to be used.
    WAV_petlist_bounds:         starting_WAV_PET  num_tasks_wav*num_threads_wav+starting_WAV_PET-1
    WAV_omp_num_threads:        num_threads_wav
 
-The starting WAV PET in ``nems.configure`` will be the last PET of the
+The starting WAV PET in ``ufs.configure`` will be the last PET of the
 preceding component, incremented by one.
 
 
-Example: 5-component nems.configure
+Example: 5-component ufs.configure
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-For the fully coupled S2SWA application, a sample ``nems.configure`` is shown below :
+For the fully coupled S2SWA application, a sample ``ufs.configure`` is shown below :
 
 
 .. code-block:: console
 
 		#############################################
-		####  NEMS Run-Time Configuration File  #####
+		####  UFS Run-Time Configuration File  #####
 		#############################################
 
 		# ESMF #

doc/UsersGuide/source/InputsOutputs.rst

@@ -2288,7 +2288,7 @@ on the monthly, daily, hourly, yearly or timestep intervals set by the *histfreq
 *0* for both monthly and daily frequencies and neither yearly nor per-timestep output is requested, only 6-hour
 mean history files will be produced.
 
-Further details of the configuration of CICE model output can be found in the CICE documentation `Section 3.1.4 <https://cice-consortium-cice.readthedocs.io/en/main/user_guide/ug_implementation.html#model-output>`__.
+Further details of the configuration of CICE model output can be found in the CICE documentation `Section 3.1.4 <https://cice-consortium-cice.readthedocs.io/en/main/user_guide/ug_implementation.html#model-input-and-output>`__.
 
 .. _ww3-out:
 

doc/UsersGuide/source/Introduction.rst

@@ -47,7 +47,7 @@ The UFS WM code is portable and can be used with Linux or Mac operating systems
 
 Those wishing to contribute development to the UFS WM should become familiar with the procedures for running the model as a standalone component and for executing the regression tests described in the UFS WM GitHub `wiki <https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents>`__ to make sure no inadvertent changes to the results have been introduced during the development process.
 
-Support for the UFS WM is provided through the `UFS Forum <https://forums.ufscommunity.org/forum/ufs-weather-model>`__ by the Developmental Testbed Center (DTC) and other groups involved in UFS development, such as NOAA's Environmental Modeling Center (:term:`EMC`), NOAA research laboratories (GFDL, NSSL, ESRL, and AOML), and :term:`NCAR`. UFS users and developers are encouraged not only to post questions, but also to help address questions posted by other members of the community.
+Support for the UFS WM is provided through the `UFS Forum <https://github.com/ufs-community/ufs-weather-model/discussions>`__ by the Developmental Testbed Center (DTC) and other groups involved in UFS development, such as NOAA's Environmental Modeling Center (:term:`EMC`), NOAA research laboratories (GFDL, NSSL, ESRL, and AOML), and :term:`NCAR`. UFS users and developers are encouraged not only to post questions, but also to help address questions posted by other members of the community.
 
 This WM User's Guide is organized as follows:
 
@@ -57,6 +57,8 @@ This WM User's Guide is organized as follows:
 
    * :numref:`Chapter %s <InputsOutputs>` (Data: Input, Model Configuration, and Output Files) lists the model inputs and outputs and has a description of the key files.
 
+   * :numref:`Chapter %s <Configurations>` (Configurations) lists the currently supported configurations for the UFS WM.
+
    * :numref:`Chapter %s <ConfigParams>` (Configuration Parameters) lists the purpose and valid values for various configuration parameters.
 
    * :numref:`Chapter %s <AutomatedTesting>` (Automated Testing) describes UFS WM automated testing options.

doc/UsersGuide/source/conf.py

@@ -69,9 +69,12 @@
 # The master toctree document.
 master_doc = 'index'
 
-# The language for content autogenerated by Sphinx. 
-# Not set because default is 'en'.
-# language = 'en'
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

tests/bl_date.conf

@@ -1 +1 @@
-export BL_DATE=20240401
+export BL_DATE=20240419