leaving only env files changed from develop

docs/UsersGuide/source/ConfigNewPlatform.rst

@@ -4,7 +4,7 @@
 Configuring a New Platform
 ==========================
 
-The UFS SRW Application has been designed to work primarily on a number of Level 1 and 2 support platforms, as specified `here <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`_. However, it is also designed with flexibility in mind, so that any sufficiently up-to-date machine with a UNIX-based operating system should be capable of running the application. A full list of prerequisites for installing the UFS SRW App and running the Graduate Student Test can be found in :numref:`Section %s <SW-OS-Requirements>`.
+The UFS SRW Application has been designed to work primarily on a number of Level 1 and 2 support platforms, as specified `here <https://github.com/ufs-community/ufs-srweather-app/wiki/Supported-Platforms-and-Compilers>`__. However, it is also designed with flexibility in mind, so that any sufficiently up-to-date machine with a UNIX-based operating system should be capable of running the application. A full list of prerequisites for installing the UFS SRW App and running the Graduate Student Test can be found in :numref:`Section %s <SW-OS-Requirements>`.
 
 The first step to installing on a new machine is to install :term:`NCEPLIBS` (https://github.com/NOAA-EMC/NCEPLIBS), the NCEP libraries package, which is a set of libraries created and maintained by NCEP and EMC that are used in many parts of the UFS. NCEPLIBS comes with a large number of prerequisites (see :numref:`Section %s <SW-OS-Requirements>` for more info), but the only required software prior to starting the installation process are as follows:
 
@@ -57,7 +57,7 @@ However, it is also possible to install these utilities via Macports (https://ww
 
 Installing NCEPLIBS-external
 ============================
-In order to facilitate the installation of NCEPLIBS (and therefore, the SRW and other UFS applications) on new platforms, EMC maintains a one-stop package containing most of the prerequisite libraries and software necessary for installing NCEPLIBS. This package is known as NCEPLIBS-external, and is maintained in a git repository at https://github.com/NOAA-EMC/NCEPLIBS-external. Instructions for installing these will depend on your platform, but generally so long as all the above-mentioned prerequisites have been installed you can follow the proceeding instructions verbatim (in bash; a csh-based shell will require different commands). Some examples for installing on specific platforms can be found in the `NCEPLIBS-external/doc directory <https://github.com/NOAA-EMC/NCEPLIBS-external/tree/release/public-v2/doc>`.
+In order to facilitate the installation of NCEPLIBS (and therefore, the SRW App and other UFS applications) on new platforms, EMC maintains a one-stop package containing most of the prerequisite libraries and software necessary for installing NCEPLIBS. This package is known as NCEPLIBS-external, and is maintained in a git repository at https://github.com/NOAA-EMC/NCEPLIBS-external. Instructions for installing these will depend on your platform, but generally so long as all the above-mentioned prerequisites have been installed you can follow the proceeding instructions verbatim (in bash; a csh-based shell will require different commands). Some examples for installing on specific platforms can be found in the `NCEPLIBS-external/doc directory <https://github.com/NOAA-EMC/NCEPLIBS-external/tree/release/public-v2/doc>`.
 
 
 These instructions will install the NCEPLIBS-external in the current directory tree, so be sure you are in the desired location before starting.
@@ -126,8 +126,8 @@ Further information on including prerequisite libraries, as well as other helpfu
 
 Once the NCEPLIBS package has been successfully installed, you can move on to building the UFS SRW Application.
 
-Building the UFS Short-Range Weather Application (UFS SRW App)
-==============================================================
+Building the UFS SRW Application 
+=======================================
 Building the UFS SRW App is similar to building NCEPLIBS, in that the code is stored in a git repository and is built using CMake software. The first step is to retrieve the code from GitHub, using the variables defined earlier:
 
 .. code-block:: console
@@ -212,8 +212,9 @@ Once the data has been staged, setting up your experiment on a platform without
   These are the two ``MACHINE`` settings for generic, non-Rocoto-based platforms; you should choose the one most appropriate for your machine. ``MACOS`` has its own setting due to some differences in how command-line utilities function on Darwin-based operating systems.
 
 ``LAYOUT_X=2``
+
 ``LAYOUT_Y=2``
-  These are the settings that control the MPI decomposition when running the weather model. There are default values, but for your machine it is recommended that you specify your own layout to achieve the correct number of MPI processes for your application.  In total, your machine should be able to handle ``LAYOUT_X×LAYOUT_Y+WRTCMP_write_tasks_per_group`` tasks. ``WRTCMP_write_tasks_per_group`` is the number of MPI tasks that will be set aside for writing model output, and it is a setting dependent on the domain you have selected. You can find and edit the value of this variable in the file ``regional_workflow/ush/set_predef_grid_params.sh``.
+   These are the settings that control the MPI decomposition when running the weather model. There are default values, but for your machine it is recommended that you specify your own layout to achieve the correct number of MPI processes for your application. In total, your machine should be able to handle ``LAYOUT_X×LAYOUT_Y+WRTCMP_write_tasks_per_group`` tasks. ``WRTCMP_write_tasks_per_group`` is the number of MPI tasks that will be set aside for writing model output, and it is a setting dependent on the domain you have selected. You can find and edit the value of this variable in the file ``regional_workflow/ush/set_predef_grid_params.sh``.
 
 ``RUN_CMD_UTILS="mpirun -np 4"``
   This is the run command for MPI-enabled pre-processing utilities. Depending on your machine and your MPI installation, you may need to use a different command for launching an MPI-enabled executable.

docs/UsersGuide/source/ConfigWorkflow.rst

@@ -22,7 +22,7 @@ Platform Environment
    Setting ``RUN_ENVIR`` to “community” will use the standard directory structure and variable naming convention and is recommended in most cases for users who are not planning to implement their code into operations at NCO.
 
 ``MACHINE``: (Default: “BIG_COMPUTER”)
-   The machine (a.k.a. platform) on which the workflow will run.  Currently supported platforms include "WCOSS_CRAY," "WCOSS_DELL_P3," "HERA," "ORION," "JET," "ODIN," "CHEYENNE," "STAMPEDE,” “GAEA,” “MACOS,” and “LINUX."
+   The machine (a.k.a. platform) on which the workflow will run.  Currently supported platforms include "WCOSS_DELL_P3," "HERA," "ORION," "JET," "ODIN," "CHEYENNE," "STAMPEDE,” “GAEA,” “MACOS,” and “LINUX."
 
 ``ACCOUNT``: (Default: “project_name”)
    The account under which to submit jobs to the queue on the specified ``MACHINE``.

docs/UsersGuide/source/FAQ.rst

@@ -1,17 +1,26 @@
 .. _FAQ:
 
-***
+****
 FAQ
-***
+****
+
+* :ref:`How do I turn on/off the cycle-independent workflow tasks? <CycleInd>`
+* :ref:`How do I define an experiment name? <DefineExptName>`
+* :ref:`How do I change the Physics Suite Definition File (SDF)? <ChangePhysics>`
+* :ref:`How do I restart a DEAD task? <RestartTask>`
+* :ref:`How do I change the grid? <ChangeGrid>`
+
+.. _CycleInd:
+
+===========================================================
+How do I turn on/off the cycle-independent workflow tasks?
+===========================================================
 
-=========================================================
-How do I turn On/Off the Cycle-Independent Workflow Tasks
-=========================================================
 The first three pre-processing tasks ``make_grid``, ``make_orog``, and ``make_sfc_climo``
 are cycle-independent, meaning that they only need to be run once per experiment. If the
 grid, orography, and surface climatology files that these tasks generate are already 
 available (e.g. from a previous experiment that used the same grid as the current), then
-these tasks can be skipped by having the workflow use those pre-generated files.  This 
+these tasks can be skipped, and the workflow can use those pre-generated files. This 
 can be done by adding the following lines to the ``config.sh`` script before running 
 the ``generate_FV3LAM_wflow.sh`` script:
 
@@ -28,26 +37,36 @@ The ``RUN_TASK_MAKE_GRID``, ``RUN_TASK_MAKE_OROG``, and ``RUN_TASK_MAKE_SFC_CLIM
 disable their respective tasks, and ``GRID_DIR``, ``OROG_DIR``, and ``SFC_CLIMO_DIR``
 specify the directories in which the workflow can find the pre-generated grid, orography,
 and surface climatology files, respectively (these directories may be the same, i.e. all
-three sets of files may be placed in the same location).  By default, the ``RUN_TASK_MAKE_...`` 
+three sets of files may be placed in the same location). By default, the ``RUN_TASK_MAKE_...`` 
 flags are set to ``TRUE`` in ``config_defaults.sh``, i.e. the workflow will by default 
 run the ``make_grid``, ``make_orog``, and ``make_sfc_climo`` tasks.
 
+.. _DefineExptName:
+
 ===================================
 How do I define an experiment name?
 ===================================
+
 The name of the experiment is set in the ``config.sh`` file using the variable ``EXPT_SUBDIR``.
-See :numref:`Section %s <SetUpConfigFile>` for more details.
+See :numref:`Section %s <UserSpecificConfig>` for more details.
+
+
+.. _ChangePhysics:
+
+=========================================================
+How do I change the Physics Suite Definition File (SDF)?
+=========================================================
 
-================================================
-How do I change the Suite Definition File (SDF)?
-================================================
 The SDF is set in the ``config.sh`` file using the variable ``CCPP_PHYS_SUITE``.  When the
 ``generate_FV3LAM_wflow.sh`` script is run, the SDF file is copied from its location in the forecast
 model directory to the experiment directory ``EXPTDIR``.
 
+.. _RestartTask:
+
 =============================
 How do I restart a DEAD task?
 =============================
+
 On platforms that utilize Rocoto workflow software (such as NCAR’s Cheyenne machine), sometimes if
 something goes wrong with the workflow a task may end up in the DEAD state:
 
@@ -67,15 +86,18 @@ command:
 
 .. code-block:: console
 
-   rocotorewind -w FV3SAR_wflow.xml -d FV3SAR_wflow.db -v 10 -c 201905200000 -t get_extrn_ics
+   rocotorewind -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 201905200000 -t get_extrn_ics
 
 where ``-c`` specifies the cycle date (first column of rocotostat output) and ``-t`` represents the task name
-(second column of rocotostat output).  After using ``rocotorewind``, the next time ``rocotorun`` is used to
+(second column of rocotostat output). After using ``rocotorewind``, the next time ``rocotorun`` is used to
 advance the workflow, the job will be resubmitted.
 
+.. _ChangeGrid:
+
 ===========================
 How do I change the grid?
 ===========================
+
 To change the predefined grid, you need to modify the ``PREDEF_GRID_NAME`` variable in the
 ``config.sh`` script which the user has created to generate an experiment configuration and workflow.
 Users can choose from one of three predefined grids for the SRW Application:

docs/UsersGuide/source/Glossary.rst

@@ -7,38 +7,78 @@ Glossary
 .. glossary::
 
    CCPP
-      A forecast-model agnostic, vetted collection of codes containing atmospheric physical 
-      parameterizations and suites of parameterizations for use in Numerical Weather Prediction 
-      (NWP) along with a framework that connects the physics to the host forecast model.
+      The `Common Community Physics Package <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`_ is a forecast-model agnostic, vetted collection of codes containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (NWP) along with a framework that connects the physics to the host forecast model.
+
+   Component
+      A software element that has a clear function and interface. In Earth system models, components are often single portions of the Earth system (e.g. atmosphere, ocean, or land surface) that are assembled to form a whole.
+
+   Component Repository
+      A :term:`repository` that contains, at a minimum, source code for a single component.
+
+   Container
+      `Docker <https://www.docker.com/resources/what-container>`__ describes a container as "a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another."
+
+   CONUS
+      Continental United States
 
    chgres_cube
        The preprocessing software used to create initial and boundary condition files to 
        “coldstart” the forecast model.
 
+   dynamical core
+      Global atmospheric model based on fluid dynamics principles, including Euler's equations of motion.
+
+   EPIC
+      EPIC stands for the `Earth Prediction Innovation Center <https://epic.noaa.gov/>`__. EPIC seeks to accelerate scientific research and modeling contributions through continuous and sustained community engagement to produce the most accurate and reliable operational modeling system in the world. 
+
    FV3
       The Finite-Volume Cubed-Sphere dynamical core (dycore). Developed at NOAA's Geophysical 
       Fluid Dynamics Laboratory (GFDL), it is a scalable and flexible dycore capable of both 
       hydrostatic and non-hydrostatic atmospheric simulations.  It is the dycore used in the 
       UFS Weather Model.
 
+   GFS
+      `Global Forecast System <https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast>`_. The GFS is a National Centers for Environmental Prediction (NCEP) weather forecast model that generates data for dozens of atmospheric and land-soil variables, including temperatures, winds, precipitation, soil moisture, and atmospheric ozone concentration. The system couples four separate models (atmosphere, ocean model, land/soil model, and sea ice) that work together to accurately depict weather conditions.
+
    GRIB2 
       The second version of the World Meterological Organization's (WMO) standard for distributing gridded data.  
 
+   HPC-Stack
+      The `HPC-Stack <https://github.com/NOAA-EMC/hpc-stack>`__ is a repository that provides a unified, shell script-based build system for building the software stack required for numerical weather prediction (NWP) tools such as the `Unified Forecast System (UFS) <https://ufscommunity.org/>`__ and the `Joint Effort for Data assimilation Integration (JEDI) <https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/>`__ framework.
+
+   HRRR
+      `High Resolution Rapid Refresh <https://rapidrefresh.noaa.gov/hrrr/>`__. The HRRR is a NOAA real-time 3-km resolution, hourly updated, cloud-resolving, convection-allowing atmospheric model, initialized by 3km grids with 3km radar assimilation. Radar data is assimilated in the HRRR every 15 min over a 1-h period adding further detail to that provided by the hourly data assimilation from the 13km radar-enhanced Rapid Refresh.
+
+   IC/LBC
+      Initial conditions/lateral boundary conditions
+
+   LAM
+      Limited Area Model, formerly known as the "Stand-Alone Regional Model," or SAR. LAM grids use a regional (rather than global) configuration of the FV3 dynamical core. 
+
+   LBC
+      Lateral boundary conditions.
+
+   MPI
+      MPI stands for Message Passing Interface. An MPI is a standardized communication system used in parallel programming. It establishes portable and efficient syntax for the exchange of messages and data between multiple processors that are used by a single computer program. An MPI is required for high-performance computing (HPC).
+
+   NAM
+      `North American Mesoscale Forecast System <https://www.ncei.noaa.gov/products/weather-climate-models/north-american-mesoscale>`_. NAM generates multiple grids (or domains) of weather forecasts over the North American continent at various horizontal resolutions. Each grid contains data for dozens of weather parameters, including temperature, precipitation, lightning, and turbulent kinetic energy. NAM uses additional numerical weather models to generate high-resolution forecasts over fixed regions, and occasionally to follow significant weather events like hurricanes.
+
    NCEP
       National Centers for Environmental Prediction, an arm of the National Weather Service,
-      consisting of nine centers.  More information can be found at https://www.ncep.noaa.gov.
+      consisting of nine centers. More information can be found at https://www.ncep.noaa.gov.
 
    NCEPLIBS
       The software libraries created and maintained by :term:`NCEP` that are required for running 
-      :term:`chgres_cube`, the UFS Weather Model, and :term:`UPP`.
+      :term:`chgres_cube`, the UFS Weather Model, and :term:`UPP`. They are included in the `HPC-Stack <https://github.com/NOAA-EMC/hpc-stack>`__. 
 
    NCEPLIBS-external
       A collection of third-party libraries required to build :term:`NCEPLIBS`, :term:`chgres_cube`, 
-      the UFS Weather Model, and :term:`UPP`.
+      the UFS Weather Model, and :term:`UPP`. They are included in the `HPC-Stack <https://github.com/NOAA-EMC/hpc-stack>`__.  
 
    NCL
       An interpreted programming language designed specifically for scientific data analysis and 
-      visualization.  More information can be found at https://www.ncl.ucar.edu.
+      visualization. Stands for NCAR Command Language. More information can be found at https://www.ncl.ucar.edu.
 
    NEMS
       The NOAA Environmental Modeling System is a common modeling framework whose purpose is 
@@ -47,6 +87,18 @@ Glossary
    NEMSIO
       A binary format for atmospheric model output from :term:`NCEP`'s Global Forecast System (GFS).
 
+   NWP
+      Numerical Weather Prediction (NWP) takes current observations of weather and processes them with computer models to forecast the future state of the weather. 
+
+   Orography
+      The branch of physical geography dealing with mountains.
+
+   RAP
+      `Rapid Refresh <https://rapidrefresh.noaa.gov/>`__. The continental-scale NOAA hourly-updated assimilation/modeling system operational at NCEP. RAP covers North America and is comprised primarily of a numerical forecast model and an analysis/assimilation system to initialize that model. RAP is complemented by the higher-resolution 3km High-Resolution Rapid Refresh (HRRR) model.
+
+   Repository
+      A central location in which files (e.g., data, code, documentation) are stored and managed. 
+
    UFS
       The Unified Forecast System is a community-based, coupled comprehensive Earth modeling 
       system consisting of several applications (apps). These apps span regional to global 
@@ -60,10 +112,16 @@ Glossary
       and boundary condition generation codes used by the UFS Short-Range Weather App are all 
       part of this collection.
 
+   Umbrella repository
+      A repository that houses external code, or “externals,” from additional repositories.
+
    UPP
-      The Unified Post Processor is software developed at :term:`NCEP` and used operationally to 
+      The `Unified Post Processor <https://dtcenter.org/community-code/unified-post-processor-upp>`__ is software developed at :term:`NCEP` and used operationally to 
       post-process raw output from a variety of :term:`NCEP`'s NWP models, including the FV3.
 
+   Weather Enterprise
+      Individuals and organizations from public, private, and academic sectors that contribute to the research, development, and production of weather forecast products; primary consumers of these weather forecast products.
+
    Weather Model
       A prognostic model that can be used for short- and medium-range research and
       operational forecasts. It can be an atmosphere-only model or an atmospheric