System Access
New HPC Documentation Website!
New documentation is coming that will replace our current Confluence website (the one you're viewing right now). We will be sending an announcement on when the site will go live. Interested in taking a peek? Check out this page for the beta version. Note: the URL is likely to change.
New GPUs on Ocelote!
We have recently added 22 new P100 GPUs to Ocelote. Need to request multiple GPUs on a node and you're finding Puma queue times too slow? You can now request two GPUs per node on Ocelote using --gres=gpu:2.
Web Access
The web interface, Open OnDemand, provides access to HPC's three clusters. More comprehensive information on this service can be found on our Open On Demand page.
Terminal Access
Users can gain command line access to HPC through our OOD web interface as an alternative to using a local SSH Client. To use this interface:
- Log into https://ood.hpc.arizona.edu/
- Go to the dropdown menu at the top of the screen and select Clusters
- Click Shell
- This will put you on the command line on one of the login nodes where you may perform regular housekeeping work, submit jobs, or request an interactive session.. By default, you will automatically be connected to Puma. To navigate to a different cluster, use the displayed shortcuts.
Virtual Desktop
Users may also interact with a cluster using a virtual desktop interface. To do this:
- Log into https://ood.hpc.arizona.edu/ and, under My Interactive Sessions, select Interactive Desktop under Desktops on the left-hand side of the page.
- A form will appear where you will select the target cluster, enter the amount of time you'd like to be allotted (in hours), the number of cores you need, your PI Group (if you are unsure what your group name is, you can check in https://portal.hpc.arizona.edu/portal/), and the queue. Once you've filled in your request, click Launch.
- A window will appear with the status of your request. It will start in a Pending state and will switch to Running when your desktop session is ready. Click Launch Interactive Desktop to access your session.
- That's it! You can now use the cluster with a Desktop interface
Command Line/Terminal Access
- All the integration on UArizona HPC supercomputers is done with the "bash” shell which means to get consistent results, bash must be your shell. New HPC users automatically are set to the bash shell unless they already are using a different shell.
When using SSH, if you leave out the netid@ then it may default to your workstation username, which may not be valid; on Linux and MacOS you can override this via a ~/.ssh/config "User netid" config line. On Windows, there may be an application-specific way to set the username for hpc.arizona.edu connections.
- If you try to log in and get a continuous prompt of "password" and nothing else, you are probably not registered for NetID+.
To log into HPC, you will need NetID+ enabled, an HPC account, and internet access. Because we require Duo-authentication to access the system, no VPN is required.
Logging in will first connect you to something called the bastion host, a computer that provides a gateway to our three clusters: Ocelote, ElGato, and Puma. This is the only function the bastion host serves. It is not for storing files, running programs, or accessing software.
Mac Access
Mac systems provide a built-in SSH client, so there is no need to install any additional software. You will find the terminal application under Applications → Utilities → Terminal.
Open the terminal and enter:
$ ssh netid@hpc.arizona.edu
where netid is your UArizona NetID. When you press enter, you will be prompted for your university password. Note: you will not see any characters appear on the screen while typing during this step. This is normal and everything is working as it should. After successfully entering your password, you will be prompted to Duo Authenticate. If everything is successful, you will be connected to the bastion host.
Windows Access
Windows systems do not have any built-in support for using SSH, so you will have to download a software package to do so. There are several available for Windows workstations. Free SSH clients are available for download from the University of Arizona's Site License website.
PuTTY
PuTTY is the most popular open source SSH Windows client. To use it: download, install, and open the Putty client. Next, open a connection and enter hpc.arizona.edu under Host Name and press Open
This will open a terminal. At the prompt, enter the following, replacing <netid> with your own NetID:
Login as: <netid>
You will then be prompted to Duo-Authenticate. If the process is successful, you will be connected to the bastion host.
MobaXterm
MobaXterm is another available SSH Windows client. To connect to HPC, download and install MobaXterm, open the software, select Session → SSH and enter hpc.arizona.edu under Remote host. Next, select the box next to Specify username and enter your UArizona NetID. To connect, click OK at the bottom of the screen:
This will open a terminal and will prompt you for your UArizona password. You will then need to Duo-authenticate. If everything is successful, you will be connected to the bastion host.
Once you reach the bastion host, regardless of method, you should see the following:
Success. Logging you in... Last login: This is a bastion host used to access the rest of the RT/HPC environment. Type "shell" to access the job submission hosts for all environments -----------------------------------------
From there, type shell to connect to the login nodes that will provide access to our three clusters. On the login nodes, you should see:
*** The default cluster for job submission is Puma *** Shortcut commands change the target cluster ----------------------------------------- Puma: $ puma (puma) $ Ocelote: $ ocelote (ocelote) $ ElGato: $ elgato (elgato) $ -----------------------------------------
By default, you will be connected to Puma when you first log in. To access the other clusters, follow the shortcut commands.
X11 Forwarding
X11 forwarding is a mechanism that allows a user to start up a remote application (e.g. VisIt or Matlab) and forward the application display to their local machine. The key to make forwarding work successfully is to include the -X flag at each login step. To check whether X11 forwarding is active, you may run the command:
$ echo $DISPLAY
If it comes back blank, something has gone wrong.
X11 Forwarding on Windows
To use X11 forwarding on a Windows system, you will need to download an X11 display server such as Xming.
PuTTY
To enable X11 forwarding in PuTTY, go to SSH → X11 and select the box next to Enable X11 forwarding.
Once you've connected to the bastion host, connect to the login nodes with the an additional flag -X:
$ shell -X
MobaXterm
To enable X11 forwarding in MobaXterm, open a new session, select SSH, and open Advanced SSH settings. Select the option below called X11-Forwarding.
Once you've connected to the bastion host, connect to the login nodes with the an additional flag -X:
$ shell -X
SSH Keys
Why Use SSH Keys?
The Bastion Host uses two-factor authentication and will, by default, prompt you for a password and 2nd factor when you attempt to log in. As an alternative, you can use PKI (Public Key Authentication). This means you will not have to provide a password or Duo-authenticate for any future sessions. To do this, you will need to create an SSH Key on your local workstation and copy the public key to the ~/.ssh/authorized_keys file in your HPC account on the bastion host.
Using SSH Keys for file transfers
Note that SSH Keys can also be used to avoid entering a password and 2nd factor when transferring files to to the cluster via the file transfer node (filexfer.hpc.arizona.edu) using command line programs like scp or sftp. Follow the steps above (2-4 under the Mac and Linux instructions), except use filexfer.hpc.arizona.edu instead of hpc.arizona.edu. Note that you only need to generate the keys in Step 1 once. The same ~/.ssh/id_rsa.pub file may be used to identify yourself to multiple hosts.