UFS Short-Range Weather App Users Guide

• 1. Introduction
  • 1.1. How to Use This Document
  • 1.2. SRW App Components Overview
    • 1.2.1. Pre-processor Utilities and Initial Conditions
    • 1.2.2. Forecast Model
    • 1.2.3. Unified Post-Processor (UPP)
    • 1.2.4. Visualization Example
    • 1.2.5. Build System and Workflow
  • 1.3. Code Repositories and Directory Structure
    • 1.3.1. Hierarchical Repository Structure
    • 1.3.2. Directory Structure
    • 1.3.3. Experiment Directory Structure
  • 1.4. User Support, Documentation, and Contributions to Development
  • 1.5. Future Direction
• 2. Container-Based Quick Start Guide
  • 2.1. Building the UFS SRW Application
    • 2.1.1. Prerequisites: Install Singularity
    • 2.1.2. Working in the Cloud
    • 2.1.3. Working on HPC Systems
    • 2.1.4. Set Up the Container
  • 2.2. Set up the Build Environment
  • 2.3. Build the Executables
  • 2.4. Download and Stage the Data
  • 2.5. Generate the Forecast Experiment
    • 2.5.1. Set the Experiment Parameters
    • 2.5.2. Activate the Regional Workflow
    • 2.5.3. Generate the Regional Workflow
  • 2.6. Run the Workflow Using Stand-Alone Scripts
  • 2.7. Plot the Output
• 3. Building and Running the SRW App
  • 3.1. Install the HPC-Stack
    • 3.1.1. Background
    • 3.1.2. Instructions
  • 3.2. Download the UFS SRW Application Code
  • 3.3. Check Out External Components
  • 3.4. Set up the Build Environment
  • 3.5. Build the Executables
  • 3.6. Download and Stage the Data
  • 3.7. Grid Configuration
  • 3.8. Generate the Forecast Experiment
    • 3.8.1. Set Experiment Parameters
    • 3.8.2. Default configuration: config_defaults.sh
    • 3.8.3. User-specific configuration: config.sh
    • 3.8.4. Set up the Python and other Environment Parameters
    • 3.8.5. Generate the Regional Workflow
    • 3.8.6. Description of Workflow Tasks
  • 3.9. Run the Workflow Using Rocoto
    • 3.9.1. Launch the Rocoto Workflow Using a Script
    • 3.9.2. Launch the Rocoto Workflow Manually
    • 3.9.3. Automated Option
  • 3.10. Plot the Output
• 4. SRW Application Components
  • 4.1. Pre-processor Utilities and Initial Conditions
  • 4.2. Forecast Model
  • 4.3. Post-processor
  • 4.4. Visualization Example
  • 4.5. Build System and Workflow
• 5. Install and Build the HPC-Stack
  • 5.1. Install and Build the HPC-Stack in a Singularity Container
    • 5.1.1. Install Singularity
    • 5.1.2. Build and Run the Container
    • 5.1.3. Build the HPC-Stack
  • 5.2. Non-Container HPC-Stack Installation and Build
    • 5.2.1. Install Prerequisites
    • 5.2.2. Configure the Build
    • 5.2.3. Set Up Compiler, MPI, Python & Module System
    • 5.2.4. Build the HPC-Stack
  • 5.3. Installation of the HPC-Stack Prerequisites
  • 5.4. Build Parameters
    • 5.4.1. Compiler & MPI
    • 5.4.2. Other Parameters
  • 5.5. HPC-Stack Components
  • 5.6. HPC-Stack Additional Notes
    • 5.6.1. Setting Compiler Flags and Other Options
    • 5.6.2. Adding a New Library or Package
    • 5.6.3. Configuring for a new HPC
    • 5.6.4. Using the DOWNLOAD_ONLY Option
    • 5.6.5. Using the HPC-Stack
    • 5.6.6. Known Workaround for Certain Installations of Lmod
    • 5.6.7. Known Issues
• 6. Input and Output Files
  • 6.1. Input Files
    • 6.1.1. Initial and Boundary Condition Files
    • 6.1.2. Pre-processing (UFS_UTILS)
    • 6.1.3. UFS Weather Model
    • 6.1.4. Unified Post Processor (UPP)
    • 6.1.5. Workflow
  • 6.2. Output Files
    • 6.2.1. Initial and boundary condition files
    • 6.2.2. Pre-processing (UFS_UTILS)
    • 6.2.3. UFS Weather Model
    • 6.2.4. Unified Post Processor (UPP)
  • 6.3. Downloading and Staging Input Data
    • 6.3.1. Static Files
    • 6.3.2. Initial Condition Formats and Source
    • 6.3.3. Initial and Lateral Boundary Condition Organization
    • 6.3.4. Default Initial and Lateral Boundary Conditions
    • 6.3.5. Running the App for Different Dates
    • 6.3.6. Staging Initial Conditions Manually
    • 6.3.7. Coexistence of Multiple Files for the Same Date
    • 6.3.8. Best Practices for Conserving Disk Space and Keeping Files Safe
• 7. Configuring the Workflow: config.sh and config_defaults.sh
  • 7.1. Platform Environment
  • 7.2. Parameters for Running Without a Workflow Manager
  • 7.3. Cron-Associated Parameters
  • 7.4. Directory Parameters
  • 7.5. NCO Mode Parameters
  • 7.6. Pre-Processing File Separator Parameters
  • 7.7. File Name Parameters
  • 7.8. Forecast Parameters
  • 7.9. Initial and Lateral Boundary Condition Generation Parameters
  • 7.10. User-Staged External Model Directory and File Parameters
  • 7.11. CCPP Parameter
  • 7.12. Grid Generation Parameters
  • 7.13. Computational Forecast Parameters
  • 7.14. Write-Component (Quilting) Parameters
  • 7.15. Predefined Grid Parameters
  • 7.16. Pre-existing Directory Parameter
  • 7.17. Verbose Parameter
  • 7.18. Pre-Processing Parameters
  • 7.19. Surface Climatology Parameter
  • 7.20. Fixed File Parameters
  • 7.21. Workflow Task Parameters
  • 7.22. Customized Post Configuration Parameters
  • 7.23. Halo Blend Parameter
  • 7.24. FVCOM Parameter
  • 7.25. Compiler Parameter
• 8. Limited Area Model (LAM) Grids: Predefined and User-Generated Options
  • 8.1. Predefined Grids
  • 8.2. Creating User-Generated Grids
• 9. Configuring a New Platform
  • 9.1. Installing NCEPLIBS-external
  • 9.2. Installing NCEPLIBS
  • 9.3. Building the UFS SRW Application
  • 9.4. Setting Up Your Python Environment
  • 9.5. Running Without a Workflow Manager: Generic Linux and macOS Platforms
  • 9.6. Running on a New Platform with Rocoto Workflow Manager
  • 9.7. Software/Operating System Requirements
• 10. Workflow End-to-End (WE2E) Tests
• 11. Graphics Generation
  • 11.1. Plotting output from one experiment
  • 11.2. Plotting differences from two experiments
  • 11.3. Submitting plotting scripts through a batch system
• 12. SRW App Contributor’s Guide
  • 12.1. Background
    • 12.1.1. Authoritative branch
    • 12.1.2. Code Management Team
  • 12.2. Contribution Process
    • 12.2.1. Opening an Issue
    • 12.2.2. Making a Pull Request
  • 12.3. Code and Configuration Standards
    • 12.3.1. General
    • 12.3.2. SRW Application
    • 12.3.3. Regional Workflow
  • 12.4. Contributor Requirements
    • 12.4.1. Preparing Code for Contribution to the UFS SRW Application
  • 12.5. Testing
• 13. FAQ
  • 13.1. How do I turn on/off the cycle-independent workflow tasks?
  • 13.2. How do I define an experiment name?
  • 13.3. How do I change the Physics Suite Definition File (SDF)?
  • 13.4. How do I restart a DEAD task?
  • 13.5. How do I change the grid?
• 14. Additional Rocoto Information
  • 14.1. rocotorun
  • 14.2. rocotostat
  • 14.3. rocotocheck
  • 14.4. rocotorewind
  • 14.5. rocotoboot
• 15. Glossary