SCHISM-ecFLOW

Overview

SCHISM-ecFLOW is an automated workflow system for the SCHISM using ecFlow. This project aims to streamline the preprocessing steps, job setup, execution of SCHISM model runs and post-processing steps.

Features

• Automated preprocessing steps
  • Namelist generation
  • Boundary condition generation (bctides.in)
  • Time-varying water elevation generation
  • Atmospheric forcing
  • Generation of various .gr3 files (roughness, windrot, diffmin, diffmax)
• Automated job setup
  • Run directory creation
  • Copying of fixed input files
• ecFlow-based workflow management

Directory Structure

.
├── LICENSE
├── README.md
├── ecf/                  # ecFlow task scripts
├── preprocess/           # Duplicate of ecf scripts (to be consolidated)
├── pyschism_suite/
│   ├── fix/              # Symlink to fixed input files
│   ├── job_submission/   # Job submission task outputs
│   ├── preprocess/       # Preprocessing task outputs
│   ├── scripts/          # Python scripts for preprocessing tasks
│   └── workdir/          # Working directory for generated input files
├── pyschism_suite.def    # ecFlow suite definition file
└── scripts/              # Duplicate of pyschism_suite/scripts (to be consolidated)

Key Components

1. Boundary Conditions: scripts/Bnd/gen_bctides.py
2. Elevation: scripts/Elev/ (includes OTPS data and scripts)
3. Job Card Generation: scripts/Job_card/gen_jobcard.py
4. Run Directory Setup: scripts/Job_dir/gen_rundir.py
5. Manning Coefficient: scripts/Manning/gen_gr3_input.py
6. Surface Flux: scripts/Sflux/gen_sflux_era5.py
7. Namelist Generation: scripts/namelist/gen_namelist.py

Prerequisites

• ecFlow (please see installation instructions here https://github.com/mansurjisan/ecflow-setup-test-hercules)
• Python 3.9.1
• SCHISM model

Installation

1. Clone this repository:

   git clone https://github.com/mansurjisan/SCHISM-ecFLOW.git
   cd SCHISM-ecFLOW
   

2. [Add any additional installation steps, such as setting up a Python virtual environment or installing dependencies]

Usage

1. Configure the ecFlow suite:

   ecflow_client --port 3141 --load=/home/mjisan/pyschism_suite.def
   

2. Start the ecFlow suite:

   ecflow_client --port 3141 --begin=/pyschism_suite.def
   

3. Monitor the workflow:

   ecflow_client --port 3141 --get_state=/pyschism_suite
   

Workflow Diagram

The following diagram illustrates the SCHISM-ecFLOW workflow: