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Introduction to Using the Shell in a High-Performance Computing Context

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Connecting to the remote HPC system

Overview

Teaching: 25 min
Exercises: 10 min
Questions

  • How do I open a terminal?

  • How do I connect to a remote computer?

  • What is an SSH key?

Objectives

  • Connect to a remote HPC system.

Prerequisites

To access the Greene HPC cluster, you must be connected to the NYU network. If you are physically on campus and connected via a wired connection in your office or through NYU’s WiFi, you can directly SSH into the clusters without any additional steps. However, if you are off-campus or working remotely, connecting through the NYU VPN or using the gateway servers is required to establish a secure connection to the HPC systems.

Remote Connections with the NYU VPN & HPC Gateway Server

If you are connecting from a remote location that is not on the NYU network (your home for example), you have two options:

  1. VPN Option: set up your computer to use the NYU VPN. Once you’ve created a VPN connection, you can proceed as if you were connected to the NYU net.

  2. Gateway Option: go through our gateway servers (example below). Gateways are designed to support only a very minimal set of commands and their only purpose is to let users connect HPC systems without needing to first connect to the VPN.

Log into the Greene Cluster

NYU Campus: From within the NYU network, that is, from an on-campus location, or after you VPN inside NYU’s network, you can login to the HPC clusters directly.

Off-campus: The host name of Greene is ‘greene.hpc.nyu.edu’. Logging in to Greene is the two-stage process. The HPC clusters (Greene) are not directly visible to the internet (outside the NYU Network). If you are outside NYU’s Network (off-campus) you must first login to a bastion host named gw.hpc.nyu.edu.

From within the NYU network, that is, from an on-campus location, or after you VPN inside NYU’s network, you can log in to the HPC clusters directly. You do not need to log in to the bastion host.

To log in to the HPC cluster (Greene), simply use:

ssh <NYUNetID>@greene.hpc.nyu.edu

For access from Windows stations using PuTTY, please click here.

To connect to VPN from Linux/MAC, please click here.

From an off-campus location (outside NYU-NET), logging in to the HPC clusters is a two-step process:

  1. First, log in to the bastion host, gw.hpc.nyu.edu. From a Mac or Linux workstation, this is a simple terminal command (replace <NYUNetID> with your NetID). Your password is the same password you use for NYU Home:
ssh <NYUNetID>@gw.hpc.nyu.edu

Windows users will need to use PuTTY, see here for instructions.

  1. Next, log in to the cluster. For Greene, this is done with:
ssh <NYUNetID>@greene.hpc.nyu.edu

Opening a Terminal

Accessing the Greene HPC cluster is primarily done through the Command Line Interface (CLI). A CLI provides a text-based environment that allows users to manage files, run programs, and navigate directories via command input. On macOS, the built-in CLI tool is Terminal, while Windows 10 users can leverage the Windows Subsystem for Linux (WSL) for similar functionality. Additionally, a popular tool for connecting to Linux servers from Windows is PuTTY, a free SSH client.

Connecting to an HPC system is most often done through a tool known as “SSH” (Secure SHell) and usually SSH is run through a terminal. So, to begin using an HPC system we need to begin by opening a terminal. Different operating systems have different terminals, none of which are exactly the same in terms of their features and abilities while working on the operating system. When connected to the remote system the experience between terminals will be identical as each will faithfully present the same experience of using that system.

Here is the process for opening a terminal in each operating system.

Linux

There are many different versions (aka “flavours”) of Linux and how to open a terminal window can change between flavours. Fortunately most Linux users already know how to open a terminal window since it is a common part of the workflow for Linux users. If this is something that you do not know how to do then a quick search on the Internet for “how to open a terminal window in” with your particular Linux flavour appended to the end should quickly give you the directions you need.

To connect to the gateway servers, simply open a terminal application and enter the following command:

ssh <NetID>@gw.hpc.nyu.edu

After typing in your password you will be logged in to the cluster. Once this connection is established, you can make one more hop and connect to one of the HPC clusters:

# this will connect you to Greene HPC cluster
ssh <NetID>@greene.hpc.nyu.edu

Mac

Macs have had a terminal built in since the first version of OS X since it is built on a UNIX-like operating system, leveraging many parts from BSD (Berkeley Software Distribution). The terminal can be quickly opened through the use of the Searchlight tool. Hold down the command key and press the spacebar. In the search bar that shows up type “terminal”, choose the terminal app from the list of results (it will look like a tiny, black computer screen) and you will be presented with a terminal window. Alternatively, you can find Terminal under “Utilities” in the Applications menu.

To connect to the gateway servers, simply open a terminal application and enter the following command:

ssh <NetID>@gw.hpc.nyu.edu

After typing in your password you will be logged in to the cluster. Once this connection is established, you can make one more hop and connect to one of the HPC clusters:

# this will connect you to Greene HPC cluster
ssh <NetID>@greene.hpc.nyu.edu

Windows

While Windows does have a command-line interface known as the “Command Prompt” that has its roots in MS-DOS (Microsoft Disk Operating System) it does not have an SSH tool built into it and so one needs to be installed. There are a variety of programs that can be used for this; a few common ones we describe here, as follows:

Git BASH

Git BASH gives you a terminal like interface in Windows. You can use this to connect to a remote computer via SSH. It can be downloaded for free from here.

Windows Subsystem for Linux

The Windows Subsystem for Linux also allows you to connect to a remote computer via SSH. Instructions on installing it can be found here.

MobaXterm

MobaXterm is a terminal window emulator for Windows and the home edition can be downloaded for free from mobatek.net. If you follow the link you will note that there are two editions of the home version available: Portable and Installer. The portable edition puts all MobaXterm content in a folder on the desktop (or anywhere else you would like it) so that it is easy to add plug-ins or remove the software. The installer edition adds MobaXterm to your Windows installation and menu as any other program you might install. If you are not sure that you will continue to use MobaXterm in the future, the portable edition is likely the best choice for you. MobaKeyGen, see the MoabXterm documentation

Download the version that you would like to use and install it as you would any other software on your Windows installation. Once the software is installed you can run it by either opening the folder installed with the portable edition and double-clicking on the executable file named MobaXterm_Personal_11.1 (your version number may vary) or, if the installer edition was used, finding the executable through either the start menu or the Windows search option.

Once the MobaXterm window is open you should see a large button in the middle of that window with the text “Start Local Terminal”. Click this button and you will have a terminal window at your disposal.

PuTTY

It is strictly speaking not necessary to have a terminal running on your local computer in order to access and use a remote system, only a window into the remote system once connected. PuTTY is likely It is, strictly speaking, not necessary to have a terminal running on your local computer in order to access and use a remote system, only a window into the remote system once connected. PuTTY is likely the oldest, most well-known, and widely used software solution to take this approach.

PuTTY is available for free download from https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html. Download the version that is correct for your operating system and install it as you would other software on your Windows system. Once installed it will be available through the start menu or similar. puttygen, see the Putty documentation

Running PuTTY will not initially produce a terminal but instead a window full of connection options. Putting the address of the remote system in the “Host Name (or IP Address)” box and either pressing enter or clicking the “Open” button should begin the connection process.

If this works you will see a terminal window open that prompts you for a username through the “login as:” prompt and then for a password. If both of these are passed correctly then you will be given access to the system and will see a message saying so within the terminal. If you need to escape the authentication process you can hold the Control (Ctrl) key and press the c key to exit and start again.

Note that you may want to paste in your password rather than typing it. Use Ctrl plus a right-click of the mouse to paste content from the clipboard to the PuTTY terminal.

For those logging in with PuTTY it would likely be best to cover the terminal basics already mentioned above before moving on to navigating the remote system.

Open OnDemand (Web-based Graphical User Interface)

Open OnDemand is an open source project funded by the National Science Foundation (NSF). Open OnDemand is designed to create easier access to users to interface with HPC systems. Originally developed by Ohio Supercomputer Center (OSC), used by many universities around the world, and now servicing the NYU Greene HPC cluster.

Open OnDemand has a variety of convenient tools to manage files, access the command line, manage and monitor jobs, and launch interactive applications, such as Jupyter Notebooks, RStudio sessions, and even full Linux Desktops.

Features Include:

Easy file management - upload and download files, view HTML and pictures without downloading

Command-line shell access without any SSH client locally installed

Job management and monitoring

Full Linux desktop experience without X11

Interactive Apps such as JupyterHub and RStudio without the need for port forwarding

Open OnDemand (OOD) is accessible to all users with a valid NYU HPC account while on-campus network or through a VPN.

To access OOD visit: https://ood.hpc.nyu.edu (VPN Required)

Access the Shell

Under the clusters menu you can select the Greene Shell Access option to access the Linux shell. No local SSH client is required.

Interactive Applications

GUI based applications are accessible without the need for port or X11 forwarding. Select the Interactive Apps menu, select the desired application, and submit the job based on required resources and options.

Troubleshooting Connections to Open OnDemand

A common issue that can occur is receiving an error that the Open OnDemand page cannot be reached. Sometimes this can indicate that the service is down, but often this is an issue with the the local browser cache. You can test this by opening a private browser window and seeing if https://ood.hpc.nyu.edu will load. If it does, try deleting the cache for https://ood.hpc.nyu.edu in your browser history to resolve this issue.

In Chrome, this can be done by navigating to this page in your settings:

chrome://settings/content/all?searchSubpage=ood.hpc.nyu.edu&search=site+data

The link above will automatically search for the Open OnDemand site data and cookies. You can then simply click on the trashcan icon to delete the site cache.

Once done, try navigating again to https://ood.hpc.nyu.edu and the site should load. For other issues please email hpc@nyu.edu.

Creating an SSH key

SSH keys are an alternative method for authentication to obtain access to remote computing systems. They can also be used for authentication when transferring files or for accessing version control systems. In this section you will create a pair of SSH keys, a private key which you keep on your own computer and a public key which is placed on the remote HPC system that you will log in to.

Linux, Mac and Windows Subsystem for Linux

Once you have opened a terminal check for existing SSH keys and filenames since existing SSH keys are overwritten,

$ ls ~/.ssh/

then generate a new public-private key pair,

$ ssh-keygen -t ed25519 -a 100 -f ~/.ssh/id_Graham_ed25519

If ed25519 is not available, use the older (but strong and trusted) RSA cryptography:

$ ls ~/.ssh/
$ ssh-keygen -o -a 100 -t rsa -b 4096 -f ~/.ssh/id_Graham_rsa

The flag -b sets the number of bits in the key. The default is 2048. EdDSA uses a fixed key length, so this flag would have no effect.

When prompted, enter a strong password that you will remember. Cryptography is only as good as the weakest link, and this will be used to connect to a powerful, precious, computational resource.

Take a look in ~/.ssh (use ls ~/.ssh). You should see the two new files: your private key (~/.ssh/key_Graham_ed25519 or ~/.ssh/key_Graham_rsa) and the public key (~/.ssh/key_Graham_ed25519.pub or ~/.ssh/key_Graham_rsa.pub). If a key is requested by the system administrators, the public key is the one to provide.

Private keys are your private identity

A private key that is visible to anyone but you should be considered compromised, and must be destroyed. This includes having improper permissions on the directory it (or a copy) is stored in, traversing any network in the clear, attachment on unencrypted email, and even displaying the key (which is ASCII text) in your terminal window.

Protect this key as if it unlocks your front door. In many ways, it does.

Further information

For more information on SSH security and some of the flags set here, an excellent resource is Secure Secure Shell.

Logging onto the system

With all of this in mind, let’s connect to a remote HPC system. In this workshop, we will connect to Graham — an HPC system located at the University of Waterloo. Although it’s unlikely that every system will be exactly like Graham, it’s a very good example of what you can expect from an HPC installation. To connect to our example computer, we will use SSH (if you are using PuTTY, see above).

SSH allows us to connect to UNIX computers remotely, and use them as if they were our own. The general syntax of the connection command follows the format ssh -i ~/.ssh/key_for_remote_computer <NetID>@greene.hpc.nyu.edu when using SSH keys and ssh yourUsername@some.computer.address if only password access is available. Let’s attempt to connect to the HPC system now:

ssh -i ~/.ssh/key_Graham_ed25519 yourUsername@graham.computecanada.ca

or

ssh -i ~/.ssh/key_Graham_rsa yourUsername@graham.computecanada.ca

or if SSH keys have not been enabled

ssh yourUsername@graham.computecanada.ca


The authenticity of host 'graham.computecanada.ca (199.241.166.2)' can't be established.
ECDSA key fingerprint is SHA256:JRj286Pkqh6aeO5zx1QUkS8un5fpcapmezusceSGhok.
ECDSA key fingerprint is MD5:99:59:db:b1:3f:18:d0:2c:49:4e:c2:74:86:ac:f7:c6.
Are you sure you want to continue connecting (yes/no)?  # type "yes"!
Warning: Permanently added the ECDSA host key for IP address '199.241.166.2' to the list of known hosts.
yourUsername@graham.computecanada.ca's password:  # no text appears as you enter your password
Last login: Wed Jun 28 16:16:20 2017 from s2.n59.queensu.ca

Welcome to the ComputeCanada/SHARCNET cluster Graham.

If you’ve connected successfully, you should see a prompt like the one below. This prompt is informative, and lets you grasp certain information at a glance. (If you don’t understand what these things are, don’t worry! We will cover things in depth as we explore the system further.)

[yourUsername@gra-login1 ~]$

Telling the Difference between the Local Terminal and the Remote Terminal

You may have noticed that the prompt changed when you logged into the remote system using the terminal (if you logged in using PuTTY this will not apply because it does not offer a local terminal). This change is important because it makes it clear on which system the commands you type will be run when you pass them into the terminal. This change is also a small complication that we will need to navigate throughout the workshop. Exactly what is reported before the $ in the terminal when it is connected to the local system and the remote system will typically be different for every user. We still need to indicate which system we are entering commands on though so we will adopt the following convention:

Being certain which system your terminal is connected to

If you ever need to be certain which system a terminal you are using is connected to then use the following command: $ hostname.

Keep two terminal windows open

It is strongly recommended that you have two terminals open, one connected to the local system and one connected to the remote system, that you can switch back and forth between. If you only use one terminal window then you will need to reconnect to the remote system using one of the methods above when you see a change from [local]$ to [yourUsername@gra-login1 ~]$ and disconnect when you see the reverse.

Key Points

  • To connect to a remote HPC system using SSH and a password, run ssh <NetID>@greene.hpc.nyu.edu.

  • To connect to a remote HPC system using SSH and an SSH key, run ssh -i ~/.ssh/key_for_remote_computer <NetID>@greene.hpc.nyu.edu.

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