Bay-Delta SCHISM User Guide

The following topical guides take you through what it takes to set up a basic model run using the Bay-Delta SCHISM toolchain. You won’t have action items on all the topics for every run, but the Bay-Delta SCHISM Essentials section will get you started on a basic hindcast and the Topical Guides describe numerous common modeling tasks and where the gotchas are.

See Installation And Getting Started for programatic setup and basic introductory materials.

Essentials for Running the Model

• Running a Preprepared Setup
• Overview of a Bay-Delta SCHISM Run
  • Grid and Spatial Data
    • Templates
    • Preprocessor
  • Time-dependent data
  • Files that Change with Both Mesh and Dates
  • Driver Files (param.tropic.nml, param.clinic.nml)
  • Other Nomenclature and Concepts
  • Organizing the Launch Directory
• Vignette: Hindcast Bay Delta SCHISM at Delta Modeling Section with Preprocessor
  • Windows
  • Linux
    • Barotropic
    • Baroclinic
• Required Files, Directory Structure and Recommended Study Practices
  • Required files and structure
    • SCHISM launch directory structure
    • Launch directory
    • Output directory
    • Atmospheric (sflux) directory
  • Study layout
• Grid, Spatial Data and Preprocessor
  • Do I need it? Copy existing run vs preprocess from template?
  • Running the preprocessor
    • Applying the template
    • Partial preprocessing for modification
  • Configuring the input (yaml)
  • Where to? Required files and directory structure
• Volumetric Refinement and Smoothing, Depth Enforcement
  • Overview
  • Mathematical Formulation
  • Depth Enforcement
  • Shoreline Discovery Seeds
  • Preprocessor Integration
  • Inline Parameters (Annotated)
  • Examples
    • Sacramento River and Threemile Slough
    • Middle River and northern Mildred Island

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Boundaries & Input Files

• Prepare Ocean Boundary (elev2D.th.nc)
• Inflow/Outflow Boundaries
• Atmospheric setup
• Ocean Boundary Stabilization: Barotropic Warmup
• Key Run Parameters and Gotchas
• Run Initialization and Restart (Hotstart)
• Nudging Files
• Vegetation

Inspection of Model Setup

• Checklists
• Test Suite for Prechecking Runs

Output Files

• Output

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Computing Resources

• Intro to Clusters and High Performance Computing
  • Anatomy of a Cluster
  • Figure: Cluster Components
  • Compilation
  • Job Submission
  • Compute Nodes and Message Passing
  • Input/Output and Scribes
  • Example Slurm Launch File
  • Example Shell Script to Run SCHISM
  • Intro to Batch Cloud Cluster
  • Figure: Azure Batch Cluster Components
• Running on Azure Batch
  • Setup Azure
    • Download Azure Utilities
    • Login
    • Register with Azure
      • Set Console Variables
      • Create Azure Accounts
      • Removing a Resource Group
    • Download azure_dms_batch
  • Upload Applications
    • SCHISM
    • Python Packages
  • File Transfer Commands
    • azcopy commands
      • Generating SAS Links
    • azcopy options
  • Ensure Batch Quota
  • References
• Step-by-step: HelloSCHISM on Azure
  • Initial Setup
  • Uploading Model Input Files
  • Set up Model Run Config
    • Spot Pricing Config
  • Run Simulation!
• Step-by-step: Bay-Delta SCHISM on Azure
  • Initial Setup
  • Uploading Model Input Files
  • Running Model Simulation
    • Simple Run Config
    • Spot Pricing Config

Advanced Tasks and Concepts

• Common Problems and Diagnosis
• Simulating water age
• Sea Level Rise
• Sources, Sinks, Delta Channel Depletions
• Hydraulic Structures
• Gridding the Horizontal Mesh
• Utilities and Scripts