Connect to the HPC

Overview

Teaching: 10 min
Exercises: 5 min

Questions

• How do I connect to an HPC system?

Objectives

• Be able to connect to a remote HPC system

Opening a Terminal

Connecting to an HPC system is most often done with a program known as “SSH” (Secure SHell) which is accessed through a Terminal. Linux and Mac users will find a Terminal program already installed on their computers. Windows PC users will need to install a Terminal emulator, I suggest using PuTTY. If you haven’t done so, please download the appropriate version for your 32bit or 64bit OS.

32 bit or 64 bit OS?

Visit this website for instructions on determining if your Windows 7,8 or 10 is 32 or 64 bit.

Connecting with SSH

The SSH program needs atleast one parameter to connect to a remote server:

• Server Address The web address of the server to connect to

Additional parameters may also be necessary:

• Port Number The specific port used to connect to the server
• User ID Your user ID on the HPC system

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Basic SSH Connection

Open your terminal, and input the following command.

ssh login.marcc.jhu.edu -l username  # username is an email-style name like jhedid@jhu.edu

If you’ve never connected to this particular server before you’ll encounter a message similar to this:

The authenticity of host 'login.marcc.jhu.edu' can't be established.
RSA key fingerprint is 2a:b6:f6:8d:9d:c2:f8:2b:8c:c5:03:06:a0:f8:59:12.
Are you sure you want to continue connecting (yes/no)?

This is your computer warning you that you’re about to connect to another computer, type "yes" to proceed. This will add the HPC to your "known hosts", and you shouldn’t see the message again the future.

Warning: Permanently added 'login.marcc.jhu.edu' (RSA) to the list of known hosts.

Two factor authentication is used at MARCC so you should be prompted to enter your verification code:

Verification code:

You should now be prompted to input your password. Type it in carefully (no characters will appear on the screen), then press ENTER.

username@login.marcc.osc.edu's password: 

If you entered your password appropriately, congratulations, you’re now connected.

The Command Prompt

The command prompt is the symbol or series of characters which precedes each shell command, and lets the user know the shell is ready to receive commands. For example, when you initially login to the HPC you command prompt should resemble -bash-4.2. If your command prompt changes to >, the shell is expecting further input. Use the key-binding CTRL+C to escape shell commands, returning your prompt from > to -bash-4.2.

Let’s all change our command prompts to something more useful, input the command PS1='\W\n $ '. Our command prompt is now our current working directory followed by a "$".

On MARCC systems, the PS1 is predefined: [kmanalo@bc-login01 ~]$ echo $PS1 [\u@\h \W]\$. This just means that [username@hostname current-working-directory] is the default prompt.

Key Points

• We connect to remote servers using the terminal

• SSH is a secure protocol for connecting to remote servers

• To connect to a server, you need it’s address, an open port (usually 22 for ssh), and your user ID