UFS Short-Range Weather App Users Guide

• 1. Introduction
  • 1.1. How to Use This Document
  • 1.2. Prerequisites for Using the SRW Application
    • 1.2.1. Background Knowledge Prerequisites
    • 1.2.2. Software/Operating System Requirements
  • 1.3. SRW App Components Overview
    • 1.3.1. Pre-processor Utilities and Initial Conditions
    • 1.3.2. Forecast Model
    • 1.3.3. Unified Post-Processor (UPP)
    • 1.3.4. METplus Verification Suite
    • 1.3.5. Visualization Example
    • 1.3.6. Build System and Workflow
  • 1.4. Code Repositories and Directory Structure
    • 1.4.1. Hierarchical Repository Structure
    • 1.4.2. Directory Structure
    • 1.4.3. Experiment Directory Structure
  • 1.5. User Support, Documentation, and Contributions to Development
  • 1.6. Future Direction
• 2. Quick Start Guide
  • 2.1. Install the HPC-Stack
  • 2.2. Building and Running the UFS SRW Application
• 3. Container-Based Quick Start Guide
  • 3.1. Download the Container
    • 3.1.1. Prerequisites: Install Singularity
    • 3.1.2. Working in the Cloud or on HPC Systems
    • 3.1.3. Build the Container
    • 3.1.4. Allocate a Compute Node
    • 3.1.5. Start Up the Container
  • 3.2. Set up the Build Environment
  • 3.3. Download and Stage the Data
  • 3.4. Generate the Forecast Experiment
    • 3.4.1. Set the Experiment Parameters
    • 3.4.2. Activate the Regional Workflow
    • 3.4.3. Generate the Regional Workflow
  • 3.5. Run the Workflow Using Stand-Alone Scripts
  • 3.6. New Experiment
  • 3.7. Plot the Output
• 4. Building and Running the SRW App
  • 4.1. Install the HPC-Stack
    • 4.1.1. Background
    • 4.1.2. Instructions
  • 4.2. Download the UFS SRW Application Code
  • 4.3. Check Out External Components
  • 4.4. Set Up the Environment and Build the Executables
    • 4.4.1. devbuild.sh Approach
    • 4.4.2. CMake Approach
    • 4.4.3. Additional Details for Building on MacOS
  • 4.5. Download and Stage the Data
  • 4.6. Grid Configuration
  • 4.7. Generate the Forecast Experiment
    • 4.7.1. Set Experiment Parameters
    • 4.7.2. Set Up the Python and Other Environment Parameters
    • 4.7.3. Generate the Regional Workflow
    • 4.7.4. Description of Workflow Tasks
  • 4.8. Run the Workflow Using Rocoto
    • 4.8.1. Launch the Rocoto Workflow Using a Script
    • 4.8.2. Launch the Rocoto Workflow Manually
    • 4.8.3. Automated Option
  • 4.9. Plot the Output
• 5. SRW Application Components
  • 5.1. Pre-processor Utilities and Initial Conditions
  • 5.2. Forecast Model
  • 5.3. Post-processor
  • 5.4. METplus Verification Suite
  • 5.5. Visualization Example
  • 5.6. Build System and Workflow
• 6. Install and Build the HPC-Stack
  • 6.1. Install and Build the HPC-Stack in a Singularity Container
    • 6.1.1. Install Singularity
    • 6.1.2. Build and Run the Container
    • 6.1.3. Build the HPC-Stack
  • 6.2. Non-Container HPC-Stack Installation and Build (General/Linux)
    • 6.2.1. Install Prerequisites
    • 6.2.2. Configure the Build
    • 6.2.3. Set Up Compiler, MPI, Python & Module System
    • 6.2.4. Build the HPC-Stack
  • 6.3. Install and Build HPC-Stack on MacOS
    • 6.3.1. Prerequisites for Building HPC-Stack
    • 6.3.2. Building HPC-Stack
  • 6.4. Installation of the HPC-Stack Prerequisites
  • 6.5. Build Parameters
    • 6.5.1. Compiler & MPI
    • 6.5.2. Other Parameters
  • 6.6. HPC-Stack Components
  • 6.7. HPC-Stack Additional Notes
    • 6.7.1. Setting Compiler Flags and Other Options
    • 6.7.2. Adding a New Library or Package
    • 6.7.3. Configuring for a new HPC
    • 6.7.4. Using the DOWNLOAD_ONLY Option
    • 6.7.5. Using the HPC-Stack
    • 6.7.6. Known Workaround for Certain Installations of Lmod
    • 6.7.7. Known Issues
• 7. Input and Output Files
  • 7.1. Input Files
    • 7.1.1. Initial and Boundary Condition Files
    • 7.1.2. Pre-processing (UFS_UTILS)
    • 7.1.3. UFS Weather Model
    • 7.1.4. Unified Post Processor (UPP)
    • 7.1.5. Workflow
  • 7.2. Output Files
    • 7.2.1. Initial and boundary condition files
    • 7.2.2. Pre-processing (UFS_UTILS)
    • 7.2.3. UFS Weather Model
    • 7.2.4. Unified Post Processor (UPP)
  • 7.3. Downloading and Staging Input Data
    • 7.3.1. Static Files
    • 7.3.2. Initial Condition/Lateral Boundary Condition File Formats and Source
    • 7.3.3. Initial and Lateral Boundary Condition Organization
    • 7.3.4. Default Initial and Lateral Boundary Conditions
    • 7.3.5. Running the App for Different Dates
    • 7.3.6. Staging Initial Conditions Manually
    • 7.3.7. Coexistence of Multiple Files for the Same Date
    • 7.3.8. Best Practices for Conserving Disk Space and Keeping Files Safe
• 8. Limited Area Model (LAM) Grids: Predefined and User-Generated Options
  • 8.1. Predefined Grids
    • 8.1.1. Predefined 3-km CONUS Grid
    • 8.1.2. Predefined SUBCONUS Grid Over Indianapolis
    • 8.1.3. Predefined 13-km Grid
    • 8.1.4. Predefined 25-km Grid
  • 8.2. Creating User-Generated Grids
    • 8.2.1. Code Example
• 9. Workflow Parameters: Configuring the Workflow in config.sh and config_defaults.sh
  • 9.1. Platform Environment
    • 9.1.1. Machine-Dependent Parameters:
  • 9.2. Parameters for Running Without a Workflow Manager
  • 9.3. Cron-Associated Parameters
  • 9.4. Directory Parameters
  • 9.5. NCO Mode Parameters
  • 9.6. Pre-Processing File Separator Parameters
  • 9.7. File Name Parameters
  • 9.8. Forecast Parameters
  • 9.9. Model Configuration Parameters
  • 9.10. METplus Parameters
  • 9.11. Initial and Lateral Boundary Condition Generation Parameters
  • 9.12. Base Directories for External Model Files
  • 9.13. User-Staged External Model Directory and File Parameters
  • 9.14. NOMADS Parameters
  • 9.15. CCPP Parameter
  • 9.16. Stochastic Physics Parameters
    • 9.16.1. Specific Humidity (SHUM) Perturbation Parameters
    • 9.16.2. Stochastically Perturbed Physics Tendencies (SPPT) Parameters
    • 9.16.3. Stochastic Kinetic Energy Backscatter (SKEB) Parameters
    • 9.16.4. Parameters for Stochastically Perturbed Parameterizations (SPP)
    • 9.16.5. Land Surface Model (LSM) SPP
  • 9.17. Predefined Grid Parameters
  • 9.18. Grid Generation Parameters
    • 9.18.1. ESGgrid Settings
    • 9.18.2. GFDLgrid Settings
  • 9.19. Computational Forecast Parameters
  • 9.20. Write-Component (Quilting) Parameters
  • 9.21. Pre-existing Directory Parameter
  • 9.22. Verbose Parameter
  • 9.23. Debug Parameter
  • 9.24. Rocoto Workflow Tasks
  • 9.25. Workflow Task Parameters
  • 9.26. Pre-Processing Parameters
    • 9.26.1. Baseline Workflow Tasks
    • 9.26.2. Verification Tasks
  • 9.27. Aerosol Climatology Parameter
  • 9.28. Surface Climatology Parameter
  • 9.29. Fixed File Parameters
  • 9.30. Subhourly Forecast Parameters
  • 9.31. Customized Post Configuration Parameters
  • 9.32. Community Radiative Transfer Model (CRTM) Parameters
  • 9.33. Ensemble Model Parameters
  • 9.34. Halo Blend Parameter
  • 9.35. FVCOM Parameter
  • 9.36. Thread Affinity Interface
• 10. Rocoto Introductory Information
  • 10.1. rocotorun
  • 10.2. rocotostat
  • 10.3. rocotocheck
  • 10.4. rocotorewind
  • 10.5. rocotoboot
• 11. Workflow End-to-End (WE2E) Tests
  • 11.1. Supported Tests
  • 11.2. Running the WE2E Tests
  • 11.3. The WE2E Test Information File
  • 11.4. Checking Test Status
  • 11.5. Modifying the WE2E System
    • 11.5.1. Modifying an Existing Test
    • 11.5.2. Adding a New Test
    • 11.5.3. Adding a New WE2E Test Category
    • 11.5.4. Creating Alternate Names for a Test
• 12. Graphics Generation
  • 12.1. Loading the Environment
  • 12.2. Cartopy Shape Files
  • 12.3. Running the Plotting Scripts
    • 12.3.1. Plotting Output from One Experiment
    • 12.3.2. Plotting Differences from Two Experiments
  • 12.4. Submitting Plotting Scripts Through a Batch System
• 13. SRW App Contributor’s Guide
  • 13.1. Background
    • 13.1.1. Authoritative branch
    • 13.1.2. Code Management Team
  • 13.2. Contribution Process
    • 13.2.1. Opening an Issue
    • 13.2.2. Making a Pull Request
  • 13.3. Code and Configuration Standards
    • 13.3.1. General
    • 13.3.2. SRW Application
    • 13.3.3. Regional Workflow
  • 13.4. Contributor Requirements
    • 13.4.1. Preparing Code for Contribution to the UFS SRW Application
  • 13.5. Testing
• 14. FAQ
  • 14.1. How do I turn on/off the cycle-independent workflow tasks?
  • 14.2. How do I define an experiment name?
  • 14.3. How do I change the Physics Suite Definition File (SDF)?
  • 14.4. How do I restart a DEAD task?
  • 14.5. How do I change the grid?
• 15. Glossary