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  • Numerical Ocean Modeling

Getting Started

  • Installing Python and Jupyter
  • Setting up a Github Repository
  • Getting Familiar with Jupyter Notebooks
  • Installing a compiler with MPI
  • Getting Familiar with Unix Environments

Oceanography

  • Overview
  • Wind-Driven Circulation
  • Thermohaline Circulation
  • Primitive Equations
  • Momentum
  • Thermodynamics
  • Equation of State

Numerical Modeling

  • Model Grids
  • Difference Methods

MITgcm

  • Getting Started with MITgcm
  • File Layout
  • Choosing an optfile
  • Defining the Model Grid
  • Initial Conditions
  • External Forcing
  • Boundary Conditions
  • Diagnosing Issues

Computing Clusters

  • Navigating an HPC
  • Running jobs on an HPC
  • conda Environments

Model Analysis

  • Volume Budgets
  • Heat Budgets
  • Salt Budgets

A Regional Model Example

  • Configuration Overview
  • Model Grid
  • Bathymetry
  • Initial Conditions
  • External Forcing Conditions
  • Boundary Conditions
  • Choosing Packages
  • Running the Model

State Estimation

  • Green’s Functions

Documentation

  • Contributions
  • References
  • Repository
  • Open issue
  • .md

Navigating an HPC

Contents

  • Directory Structure
    • The Home Directory
    • The Scratch Directory

Navigating an HPC#

This page outline how to navigate a high performance computing environment.

Directory Structure#

In a typical HPC environment, each user is provided with two main directories – a home directory and a scratch or directory.

The Home Directory#

The home directory on a cluster is the first directory you will land in when you log into the computing cluster. Typically, many users will have a home directory on the same node with shared – and therefore limited – storage. Since storage is limited, your home directory should not be used to store any large files or data. Instead, it should be used to manage configuration files, such as a .bash_profile, or perhaps a small installation of miniconda in the case that Python is not available on your HPC. You may also choose to keep a few simple scripts, such as example scripts for loading modules or submitting jobs.

Note

You should never submit a job from your home directory.

The Scratch Directory#

The scratch directory – sometimes called a nobackup directory – is used to store code and data, and submit jobs. These directories are connected to large storage systems and you can check your storage allocation which is typically on the order of 1 TB or more. However, since the storage system is large, these directories are not typically backed up so you should be sure to copy inportant files to your local machine to ensure you don’t lose any crucial data. In your scratch directory, you are free to upload data and manage codes and files as you see fit. Your scratch directory is yours and can’t be edited by other users unless you give them permission.

Note

You should never run codes on an HPC without submitting job. Simple tasks are ok - such as moving or zipping files – but all computations should be managed in a job.

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Diagnosing Issues

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Running jobs on an HPC

Contents
  • Directory Structure
    • The Home Directory
    • The Scratch Directory

By Mike Wood

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