Accessing the Palmetto Cluster

Overview

Teaching: 15 min
Exercises: 0 min
Questions
  • How can I access the Palmetto cluster from my local machine?

Objectives
  • Logging into Palmetto from a local Mac / Windows computer.

For this workshop, we will utilize Palmetto’s new browser-based interface. This interface includes a directory navigation interface and a browser-based terminal.

OpenOnDemand Interface

Visit the following URL from your browser:

https://openod.palmetto.clemson.edu

You will need to login with your Clemson username and password, and perform a DUO check.

Open OnDemand Dashboard

On the top menu bar, click on Clusters, then Palmetto Shell Access

Open OnDemand Shell Menu

Enter your account password, then DUO information to log in to the browser-based terminal

Open OnDemand Shell Menu

When logged in, you are presented with a welcome message and the following “prompt”:

[username@login001 ~]$

The prompt in a bash shell usually consists of a dollar ($) sign, and shows that the shell is waiting for input. The prompt may also contain other information: this prompt tells you your username and which node you are connected to - login001 is one of the “login” nodes. It also tells you your current directory, i.e., ~, which, as you will learn shortly, is short for your home directory. We will mostly refer to the prompt as just $, i.e.,

$

Let’s enter our first command! Type the command whoami, then press the Enter key (sometimes marked Return) to send the command to the shell. The command’s output is the ID of the current user.

$ whoami

Basic structure of the cluster

Structure of the Palmetto Cluster

The Palmetto cluster has several “compute” nodes that can perform fast calculations on large amounts of data. It also has a few so-called “service” nodes, that are not meant for this purpose. Instead, they are meant to help users perform other actions such as transfering code and data to and from the cluster.

Remote login (for reference purpose)

To be able to run commands on the Palmetto cluster from your own machine, you will first need to be able to log in to the Palmetto. This is known as a remote login.

For Mac OS X, you can open the Terminal Application (which is usually in Applications → Utilities folder) and run the following:

ssh <your Palmetto username>@login.palmetto.clemson.edu

For Windows, first you need to download and install MobaXterm Home Edition.

It is important that you unzip the downloaded installer prior to installation. The zipped installer file contains an additional data file besides the installer executable. This data file is not accessible if the installer executable is called from insize the zipped file (something Windows allows you to do).

After MobaXterm starts, click the Session button.

Main MobaXterm Windows

Select SSH session and use the following parameters (whichever required), then click OK:

MobaXterm SSH Session

At this stage, for both Mac and Windows, you will be asked to enter your username and password, then DUO option.

Login interface

For MobaXterm, please select No when asked if you want to save your password. Password saving selection

When logged in, you are presented with a welcome message and the following “prompt”:

[username@login001 ~]$

Key Points