Merge remote-tracking branch 'remotes/origin/develop' into feature/gfspbl_lpt

Author: BinLiu-NOAA

FV3

@@ -95,8 +95,6 @@ the data required to run the WM RTs are already available at the following ``DIS
      - /scratch2/NAGAPE/epic/UFS-WM_RT
    * - Hercules
      - /work/noaa/epic/hercules/UFS-WM_RT
-   * - Jet (Level 2)
-     - /mnt/lfs5/HFIP/hfv3gfs/role.epic/RT
    * - NOAA Cloud (Level 2)
      - /contrib/ufs-weather-model/RT
    * - Orion

doc/UsersGuide/source/BuildingAndRunning.rst

@@ -34,7 +34,7 @@ Users who have access to :term:`HPSS` can generate initial conditions (:term:`IC
 
    In order to generate all necessary configuration, data, input, and fix files to run a configuration similar to the July 2020 CAPE case for another date (still C48 resolution), the user first needs to run the base ``ufs_test.sh`` script for the default July 2020 CAPE case as described in :numref:`Section %s <run-2020-cape>`. 
 
-To generate coldstart ICs via the UFS_UTILS ``gdas_init``/``chgres_cube`` utilities on an :term:`RDHPCS` with :term:`HPSS` access (e.g., Hera or Jet), the user can run the following commands:
+To generate coldstart ICs via the UFS_UTILS ``gdas_init``/``chgres_cube`` utilities on an :term:`RDHPCS` with :term:`HPSS` access (e.g., Hera), the user can run the following commands:
 
 .. code-block:: console 
    
@@ -45,7 +45,7 @@ To generate coldstart ICs via the UFS_UTILS ``gdas_init``/``chgres_cube`` utilit
    ./build_all.sh
    cd util/gdas_init
 
-where ``<platform>`` is Hera or Jet. 
+where ``<platform>`` is Hera.
 
 Then, users will need to edit the ``config`` file to: 
 

doc/UsersGuide/source/CAPE2020.rst

@@ -13,6 +13,7 @@ This chapter provides instructions for building and running the Unified Forecast
 
    * The :ref:`July 2020 CAPE Case <cape-2020>`
    * The :ref:`Baroclinic Instability Case <baroclinic-wave>`
+   * The :ref:`Idealized, Regional Tropical Cyclone Case <idealized-tc>`
 
 .. attention::
 
@@ -108,47 +109,45 @@ On many NOAA :term:`RDHPCS`, a container named ``ubuntu22.04-intel-wm-dev-hsd-te
    +--------------------+--------------------------------------------------------+
    | Machine            | File location                                          |
    +====================+========================================================+
-   | Gaea               | /gpfs/f5/epic/world-shared/containers                  |
+   | Gaea               | /gpfs/f6/bil-fire8/world-shared/containers             |
    +--------------------+--------------------------------------------------------+
    | Hera               | /scratch1/NCEPDEV/nems/role.epic/containers            |
    +--------------------+--------------------------------------------------------+
-   | Jet                | /mnt/lfs5/HFIP/hfv3gfs/role.epic/containers            |
-   +--------------------+--------------------------------------------------------+
    | NOAA Cloud [#fn]_  | /contrib/EPIC/containers                               |
    +--------------------+--------------------------------------------------------+
    | Orion/Hercules     | /work/noaa/epic/role-epic/contrib/containers           |
    +--------------------+--------------------------------------------------------+
 
-.. [#fn] The CAPE case can run on the NOAA Cloud ParallelWorks (PW) platforms, but the baroclinic wave case cannot.
+.. [#fn] The CAPE case can run on the NOAA Cloud ParallelWorks (PW) platforms, but the baroclinic wave and tropical cyclone cases cannot.
 
 Users can simply set an environment variable to point to the container: 
 
 .. code-block:: console
 
    export img=path/to/ubuntu22.04-intel-wm-dev-hsd-test.img
 
-If users prefer, they may copy the container to their local working directory. For example, on Jet:
+If users prefer, they may copy the container to their local working directory. For example, on Gaea
 
 .. code-block:: console
 
-   cp /mnt/lfs5/HFIP/hfv3gfs/role.epic/containers/ubuntu22.04-intel-wm-dev-hsd-test.img .
+   cp /gpfs/f6/bil-fire8/world-shared/containers/ubuntu22.04-intel-wm-dev-hsd-test.img .
 
 Other Systems
 ----------------
 
-On other systems, users can build the Singularity container from a public Docker :term:`container` image or download the ``ubuntu22.04-intel-wm-dev-hsd-test.img`` container from the `UFS Hierarchical Testing Framework (HTF) Data Bucket <https://registry.opendata.aws/noaa-ufs-htf-pds/>`_. Downloading may be faster depending on the download speed on the user's system. Note that the container in the data bucket is from the November 20, 2024 ``develop`` branch.
+On other systems, users can build the Singularity container from a public Docker :term:`container` image or download the ``ubuntu22.04-intel-wm-dev-hsd-test.img`` container from the `UFS Hierarchical Testing Framework (HTF) Data Bucket <https://registry.opendata.aws/noaa-ufs-htf-pds/>`_. Downloading may be faster depending on the download speed on the user's system. Note that the container in the data bucket is from the May 30, 2025 ``develop`` branch.
 
 To download from the data bucket, users can run:
 
 .. code-block:: console
 
-   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20241115/ubuntu22.04-intel-wm-dev-hsd-test.img
+   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20250530/ubuntu22.04-intel-wm-dev-hsd-test.img
 
 To build the container from a Docker image, users can run:
 
 .. code-block:: console
 
-   singularity build --force ubuntu22.04-intel-wm-dev-hsd-test.img docker://noaaepic/ubuntu22.04-intel21.10-wm:ue160-fms202401-dev
+   singularity build --force ubuntu22.04-intel-wm-dev-hsd-test.img docker://noaaepic/ubuntu22.04-intel21.10-wm:ue160-fms202401-dev-tc
 
 This process may take several hours depending on the system. 
 
@@ -168,7 +167,7 @@ Users on any system may download and untar the data from the `UFS Hierarchical T
 .. code-block:: console
 
    cd $HSD
-   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20241115/HSD_fix_files_and_case_data.tar.gz
+   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20250530/HSD_fix_files_and_case_data.tar.gz
    tar xvfz HSD_fix_files_and_case_data.tar.gz
 
 .. _RunContainer:
@@ -234,9 +233,9 @@ Run the ``stage-rt.sh`` script with the proper arguments.
 
 where:
 
-   * ``-c`` is the compiler on the user's local machine (e.g., ``intel/2022.1.2``)
-   * ``-m`` is the :term:`MPI` on the user's local machine (e.g., ``impi/2022.1.2``)
-   * ``-p`` refers to the local machine/platform (e.g., ``hera``, ``jet``, ``gaea``, ``noaacloud``). Required for Gaea and Jet only. 
+   * ``-c`` is the compiler on the user's local machine (e.g., ``intel/2022.1.2``, ``intel-oneapi-compilers/2022.2.1``, ``intel/2023.2.0``)
+   * ``-m`` is the :term:`MPI` on the user's local machine (e.g., ``impi/2022.1.2``, ``intel-oneapi-mpi/2021.7.1``, ``cray-mpich/8.1.28``)
+   * ``-p`` refers to the local machine/platform (e.g., ``hera``, ``gaea``, ``noaacloud``). Required for Gaea, Hercules, and Orion only.
    * ``-i`` is the full path to the container image (e.g., ``$img`` or ``$HSD/ubuntu22.04-intel-wm-dev-hsd-test.img``).
 
 .. note::
@@ -259,9 +258,8 @@ Additionally, the user should see the ``ufs-weather-model`` directory in the ``$
 
 .. note::
 
-   Gaea and Jet:
+   Gaea:
       * Gaea uses a different compiler and MPI to run with the container: ``-c=intel-classic/2023.2.0 -m=cray-mpich/8.1.28``
-      * On Jet, ``cd`` to ``/mnt`` first before navigating to individual user workspaces to use the container.
 
 .. _ConfigureExptC:
 
@@ -287,6 +285,7 @@ Additional configuration may be needed for the specific test the user plans to r
 
    * The :ref:`July 2020 CAPE Test Configuration <cape-config>`
    * The :ref:`Baroclinic Instability Test Configuration <bw-config>`
+   * The :ref:`Idealized, Regional Tropical Cyclone Test Configuration <idealized-config>`
 
 .. _RunExptC:
 
@@ -303,7 +302,7 @@ To start the experiment, run:
 where:
 
 * ``<ACCOUNT>``: Account/project number for batch jobs.
-* ``<CASE_NAME>``: Name of the test case (e.g., ``2020_CAPE`` or ``baroclinic_wave``).
+* ``<CASE_NAME>``: Name of the test case (e.g., ``2020_CAPE``, ``baroclinic_wave``, or ``tropical_cyclone``).
 * ``<COMPILER>``: Compiler used for the tests (``intel`` or ``gnu``).
 
 The script will loop until it runs both tasks or crashes. ``rococtostat`` can be used to track its progress; see the :ref:`Track Progress <TrackProgress>` section for details.

doc/UsersGuide/source/HSDcontainer.rst

@@ -7,7 +7,7 @@
 Idealized, Regional Tropical Cyclone Case
 **************************************
 
-The idealized, regional tropical cyclone case is derived from the I-HAFS configuration (:cite:t:`Wang2024`) and is designed to support controlled studies of tropical cyclone dynamics and forecast development. This configuration removes real-world data assimilation and ocean coupling, focusing solely on atmospheric forecasts using idealized inputs.
+The idealized, regional tropical cyclone case is derived from the I-HAFS configuration (:cite:t:`Wang2024`) and is designed to support controlled studies of tropical cyclone dynamics and forecast development. It uses the ``FV3_HAFS_v1_thompson_nonsst`` physics suite, which is documented in the `DTC UFS HAFS v1 Scientific Documentation <https://dtcenter.ucar.edu/GMTB/UFS_SRW_HSD_TC/scidoc/_h_a_f_sv1_page.html>`_. The configuration used in this case removes real-world data assimilation and ocean coupling, focusing solely on atmospheric forecasts using idealized inputs.
 
 The case is configured to run at 4-km resolution, with 81 vertical levels. The forecast is initialized on 24 August 2019, and initial/lateral boundary conditions are provided for up to a five-day forecast duration. Initial and lateral boundary conditions (ICs/LBCs) are derived from a large-scale, idealized global FV3-based atmospheric forecast. The initial vortex is constructed using the Reed and Jablonowski (2011) method, introducing a weak, balanced storm into an environment favorable for rapid intensification. 
 

doc/UsersGuide/source/IdealizedTC.rst

@@ -55,17 +55,6 @@ It is recommended that users adjust certain values in the baroclinic wave case.
 
 In general, it is preferable to make ``FHMAX`` a multiple of 24. 
 
-.. note:: 
-
-   On Jet, users will also need to adjust ``${UFS_WM}/tests/fv3_conf/compile_slurm.IN_jet`` in order to manage memory requirements for longer runs of the ``baroclinic_wave`` test. Users will need to change the number of tasks per node from 8 to 6 and add ``#SBATCH --mem=0``. 
-
-   The file should include: 
-
-   .. code-block:: console 
-      
-      #SBATCH --ntasks-per-node=6
-      #SBATCH --mem=0
-
 Baseline Configuration
 ----------------------
 

doc/UsersGuide/source/baroclinic_wave.rst

@@ -2,5 +2,5 @@ Data for the HSD cases is already staged on Tier-1 platforms at the ``INPUTDATA_
 
 .. code-block:: console 
 
-   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20241115/HSD_fix_files_and_case_data.tar.gz
+   wget https://noaa-ufs-htf-pds.s3.amazonaws.com/develop-20250530/HSD_fix_files_and_case_data.tar.gz
    tar xvfz HSD_fix_files_and_case_data.tar.gz

doc/UsersGuide/source/doc-snippets/hsd_data.rst

@@ -1,10 +1,10 @@
-To run multiple cases at once, modify ``ufs_test.yaml`` to contain only a subset of tests (e.g., ``2020_CAPE`` and ``baroclinic_wave``) and use the ``-l`` argument:
+To run multiple cases at once, modify ``ufs_test.yaml`` to contain only a subset of tests (e.g., ``2020_CAPE``, ``baroclinic_wave``, ``tropical_cyclone``) and use the ``-l`` argument:
 
 .. code-block:: console
 
    ./ufs_test.sh -a epic -s -c -k -r -l ufs_test.yaml
 
-Alternatively, users may copy the sections for ``2020_CAPE``/``baroclinic_wave`` tests into a new YAML file (e.g., ``my_test_cases.yaml``) to call via ``ufs_test.sh``:
+Alternatively, users may copy the sections for ``2020_CAPE``/ ``baroclinic_wave``/ ``tropical_cyclone`` tests into a new YAML file (e.g., ``my_test_cases.yaml``) to call via ``ufs_test.sh``:
 
 .. code-block:: console
 

doc/UsersGuide/source/doc-snippets/hsd_run_multiple.rst

@@ -1 +1 @@
-export BL_DATE=20250528
+export BL_DATE=20250612

tests/bl_date.conf

@@ -1157,7 +1157,7 @@ export_ugwpv1() {
       export K_SPLIT=2
       export N_SPLIT=4
       export TAU=3.0
-      export RF_CUTOFF=100.0
+      export RF_CUTOFF=300.0
       export FV_SG_ADJ=450
       ;;
     "C1152")
@@ -1169,7 +1169,7 @@ export_ugwpv1() {
       export K_SPLIT=2
       export N_SPLIT=6
       export TAU=2.5
-      export RF_CUTOFF=100.0
+      export RF_CUTOFF=300.0
       export FV_SG_ADJ=450
       ;;
     "C3072")
@@ -1181,7 +1181,7 @@ export_ugwpv1() {
       export K_SPLIT=4
       export N_SPLIT=5
       export TAU=0.5
-      export RF_CUTOFF=100.0
+      export RF_CUTOFF=300.0
       export FV_SG_ADJ=300
       ;;
     *)