Access#

SMU HPC systems are directly accessible on campus via Ethernet, excluding dorms, and PerunaNet. All other networks require using the SMU VPN. Instructions for setting up and using the VPN can be found here.

HPC OnDemand Web Portal#

SMU HPC clusters can be accessed directly from a browser via the HPC OnDemand Web Portal, which provides access to files, remote desktops, JupyterLab, and RStudio.

Terminal Access via SSH#

Secure shell access via SSH is available for SMU HPC systems. There are many SSH clients available for different operating systems.

The following instructions are for standard OpenSSH installations such as those found in Linux, macOS, and Windows (>=10) including WSL.

  1. Open a terminal

  2. Type ssh <your_username>@<m3|superpod>.smu.edu where <your_username> is your username, which is usually the first part of your SMU email address, and <m3|superpod> is either m3 or superpod.

  3. Type a Duo passcode or 1 for a Duo push. The passcode can come from the Duo app or from an OIT procured hardware token (faculty and staff only).

PuTTY requires the one-time installation of this SSH client and X11.

  1. PuTTY is the most popular (and free) SSH client available. Download and install the newest version.

  2. In order to view graphics from ManeFrame, you will also need to install an X-server. The most popular, again free, X11 implementation on Windows is Xming. To install Xming, download and install the newest versions of both the Xming X server and the Xming Fonts.

Once these two programs are installed, you can then log into SMU HPC systems:

  1. Start the Xming program in the Start Menu. The Xming program runs from the System Tray.

  2. Start the PuTTY program in the Start Menu.

  3. In the PuTTY window:

    1. In the “Category” box:

      1. Scroll to the bottom and select “+” next to “SSH”.

      2. Select “X11”.

    2. In the “X11 forwarding” section, select “Enable X11 forwarding”.

    3. In the “Category” box, scroll to the top and select “Session”.

    4. In the “Host Name” field, type “<m3|superpod>.smu.edu” where <m3|superpod> is either m3 or superpod.

    5. In the “Saved Sessions” field, type “M3” or “SuperPOD”, respectively.

    6. Press “Save”.

    7. Press “Open”. Select “Yes” if you presented with a “PuTTY Security Alert” window.

    8. At the command prompt, type your username, which is the first part of your SMU email address, followed by enter.

    9. At the command prompt, type your SMU password followed by enter.

Graphical Applications via X11-Forwarding#

No additional softare needed. Add the -X flag, e.g. ssh -X ... when logging in.

macOS requires the one-time installation of XQuartz to provide X11 for graphical applications.

  1. Install XQuartz

  2. Log out and back into the Mac or reboot

  3. Open the Terminal app at /Applications/Utilities/Terminal.app

  4. Run the command defaults write org.macosforge.xquartz.X11 enable_iglx -bool true to enable indirect GLX, which is disabled by default

After XQuartz is installed add the -X flag, e.g. ssh -X ... when logging in.

Windows SSH via OpenSSH or PuTTY, requires Xming. To install Xming, download and install the newest versions of both the Xming X server and the Xming Fonts.

Setting Up Key-Based Authentication#

Key-based authentication can be used to log into SMU HPC clusters without needing to input a password, but you still will need to go through Duo.

Warning

The commands given below are to be run from your computer and not on the clusters themselves.

Run the following commands from a terminal on the local computer that you want to have key-based access to SMU HPC resources:

  1. u=<your SMU HPC username> <your SMU HPC username> is set to your SMU HPC username to be used for the subsequent commands.

  2. c=<SMU HPC cluster>, where <SMU HPC cluster> is either m3 or superpod

  3. ssh-keygen -q -t ecdsa -f ~/.ssh/id_ecdsa_${c} You will need to press enter twice.

  4. cat ~/.ssh/id_ecdsa_${c}.pub | ssh ${u}@${c}.smu.edu "mkdir -p ~/.ssh && chmod 0700 ~/.ssh && touch ~/.ssh/authorized_keys && chmod 0700 ~/.ssh/authorized_keys && cat >> ~/.ssh/authorized_keys && chmod 0400 ~/.ssh/authorized_keys" Press enter and you will be prompted for your SMU password.

  5. printf "Host *${c}.smu.edu\n   User %s\n   IdentityFile ~/.ssh/id_ecdsa_${c}\n" "${u}" >> ~/.ssh/config

  6. ssh-add -k ~/.ssh/id_ecdsa_${c}

Run the following commands from a terminal on the local computer that you want to have key-based access to SMU HPC resources:

  1. u=<your SMU HPC username> <your SMU HPC username> is set to your SMU HPC username to be used for the subsequent commands.

  2. c=<SMU HPC cluster>, where <SMU HPC cluster> is either m3 or superpod

  3. ssh-keygen -q -t ecdsa -f ~/.ssh/id_ecdsa_${c} You will need to press enter twice.

  4. cat ~/.ssh/id_ecdsa_${c}.pub | ssh ${u}@${c}.smu.edu "mkdir -p ~/.ssh && chmod 0700 ~/.ssh && touch ~/.ssh/authorized_keys && chmod 0700 ~/.ssh/authorized_keys && cat >> ~/.ssh/authorized_keys && chmod 0400 ~/.ssh/authorized_keys" Press enter and you will be prompted for your SMU password.

  5. printf "Host *${c}.smu.edu\n   User %s\n   IdentityFile ~/.ssh/id_ecdsa_${c}\n" "${u}" >> ~/.ssh/config

  6. ssh-add --apple-use-keychain ~/.ssh/id_ecdsa_${c} You will be asked for the key’s password, if present.

  1. Open PuTTYgen.

  2. Press “Generate”.

  3. Move mouse around blank area in window as instructed until key has been generated.

  4. Select the “Conversions” menu and then “Export OpenSSH key”.

  5. Press “Yes” at the warning prompt.

  6. Type “<cluster>_ssh_key_private” for the file name, where “<cluster>” is either “m3” or “superpod”

  7. Press “Save”.

  8. Leaving the “PuTTY Key Generator” window open, open the PuTTY application.

  9. Type “<cluster>.smu.edu” into the “Host Name” field, where “<cluster>” is either “m3” or “superpod”

  10. Press “Open”.

  11. Enter your SMU username (first part of your SMU email address).

  12. Enter your SMU password.

  13. At the command prompt type echo " (note the single double quote at the end).

  14. From the “PuTTY Key Generator” window, copy all the text in the “Public key for pasting into OpenSSH authorized_keys file:” section (select all the text, right-click, and select “Copy”).

  15. Select PuTTY window and right-click at the prompt to paste the copied text.

  16. At the command prompt type " >> ~/.ssh/authorized_keys (note the single double quote at the beginning).

  17. Press the “Enter (return)” key.

  18. At the command prompt type exit to log out of the cluster.

  19. Close the “PuTTY Key Generator” window.

Accessing Files via SFTP#

SFTP Clients#

There are several popular SFTP clients available and any file transfer client that supports SFTP will work with SMU HPC clusters. Several popular SFTP clients include WinSCP (Windows) and CyberDuck (Windows, macOS). These clients generally display two panes with the left side being your local files and the right side being your files on the cluster. When setting up access in these clients, SFTP must be chosen and your credentials will be your normal SMU HPC credentials.

Users using SFTP clients such as Transmit and Cyberduck on macOS or Cyberduck and WinSCP on Windows will be prompted by the application for their password, if not saved, followed by a request for a Duo passcode or 1 for a Duo push. The passcode can come from the Duo app or from an OIT procured hardware token (faculty and staff only).

Reducing the Number of Duo Authentications#

An initial SSH/SFTP connection can be reused for subsequent connections, which allows for multiple connections without being prompted by Duo repeatedly.

SSH#

For those using OpenSSH (macOS, Linux, and Windows WSL), add the following to your local computer’s SSH ~/.ssh/config file:

Host *
  ControlMaster auto
  ControlPath ~/.ssh/sockets/ssh_mux_%C
  ControlPersist 600

Then make the sockets directory via mkdir -p ~/.ssh/sockets.

PuTTY#

For those using PuTTY on Windows, check the box “Share SSH connection if possible” under “Category”; “Connection”; “SSH”; “Sharing an SSH connection between PuTTY tools”.

Cyberduck#

Cyberduck does not use SSH configurations, therefore the following setting can be used to enable connection persistence. Within Cyberduck:

  1. Select Edit, Preferences, Transfers, and then General.

  2. Under “Transfers”, use the “Transfer Files” drop-down to select “Use browser connection”.

Port Forwarding#

Note

These instructions assume you are using an OpenSSH client. This is the default on Mac and Linux terminals. On Windows systems, WSL is OpenSSH based.

You can use forwarding to utilize some HPC resources from your own computer (typically over a web browser.)

You should not run programs on the login nodes, so it is necessary to use a login node as a “jump” between your computer and the compute node(s) you are using.

The basic procedure is:

  1. Log in to a HPC machine

  2. Request compute resuorces using srun, sbatch, salloc, or similar

  3. Start your program and get port information

  4. ssh into the compute node you got using a login node as a jump host and forward the appropriate port

For example, you might want to port forward JupyterLab:

  1. login, e.g. ssh username@m3.smu.edu

  2. Request resources, in this case, an interactive shell session using 1 core and 4GB of memory for 1 hour:

srun -p dev -c 1 --mem=4GB -t 60 --pty $SHELL
  1. Start JupyterLab (note you will need to setup JupyterLab in a Python or Conda environment see: conda example

jupyter lab --ip 0.0.0.0 --no-browser

Once Jupyter Lab starts, you should see something like

[C 2023-06-08 12:06:31.942 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///users/username/.local/share/jupyter/runtime/jpserver-952278-open.html
    Or copy and paste one of these URLs:
        http://c002:8888/lab?token=b93c756f0f3026f816bf9bcee417b77fd4dcc75b3a38ebdc
     or http://127.0.0.1:8888/lab?token=b93c756f0f3026f816bf9bcee417b77fd4dcc75b3a38ebdc

We need two pieces of information: the compute node and the port. These can be read off the link http://c002:8888/lab?token=b93c756f0f3026f816bf9bcee417b77fd4dcc75b3a38ebdc. The format is http:://node:port/lab... so in this case, the node is c002 and the port is 8888. Note that these may be different each time you run.

  1. Keeping your original terminal open and running, open a new terminal (or new terminal tab) and run ssh username@node -J username@m3.smu.edu -L port:node:port. So in this case, we should run ssh username@c002 -J username@m3.smu.edu -L 8888:c002:8888. After this connects and you login (twice, once for the login node and once for the compute node) you should be able to use the link http://127.0.0.1:8888/... from your prefered web browser.

SSH Host Key Changes#

Occationally the SSH host keys will change SMU HPC systems. When this happens you may get a message such as the one below:

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@                              
@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @                              
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@                              
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!                                    
Someone could be eavesdropping on you right now (man-in-the-middle attack)!              
It is also possible that a host key has just been changed.                               
The fingerprint for the ED25519 key sent by the remote host is                           
SHA256:4242424242424242424242424242424242424242424.                                      
Please contact your system administrator.                                                
Add correct host key in /Users/adent/.ssh/known_hosts to get rid of this message.    
Offending ED25519 key in /Users/adent/.ssh/known_hosts:42                            
Host key for superpod.smu.edu has changed and you have requested strict checking.
Host key verification failed.                                                            

To resolve the issue the offending key needs to be removed on your local machine.

OpenSSH#

On macOS, Linux, and Windows using the Command Prompt, PowerShell, WSL, or MobaXterm, the offending key can be removed via:

ssh-keygen -R superpod.smu.edu

Please note that the specific host, e.g. superpod.smu.edu, may be different. See the specific host in the second to last line of the error message (highlighted above).

PuTTY on Windows#

  1. Open the “Registry Editor”.

  2. Browse to “HKEY_CURRENT_USER\SOFTWARE<Your Windows User Name>\PuTTY\SshHostKeys”.

  3. Right-click on the offending key and select delete.

Accessing SMU HPC Systems Using the Bastion Hosts#

The bastion hosts provide an alternative to using the VPN to access SMU HPC systems via SSH. Access to the bastion hosts can be requested by emailing help@smu.edu with “[HPC]” in the subject line.

There are two ways to setup access to SMU HPC systems through the bastion hosts. The first is manually and the second is via script that will automate the setup procedure including the setup of SSH keys. In both cases the VPN is no longer needed for SSH access.

Manual Setup#

The manual procedure will work on any operating system using OpenSSH, which includes Linux, macOS, and Windows.

The bastion hostnames are:

  • sjump7ap01.smu.edu

  • sjump7ap02.smu.edu

Accessing M3 then done via:

ssh -l <your_hpc_username> -J sjump7ap01.smu.edu m3.smu.edu

While accessin the SuperPOD is done via:

ssh -l <your_hpc_username> -J sjump7ap01.smu.edu m3.smu.edu

In both cases <your_hpc_username> should be replaced with your SMU HPC username.

Automated Setup#

The automated script will guide you through setting up your SSH configuration such that you can access M3 and the NVIDIA SuperPOD (MP) without need of the SMU VPN nor passwords. This is accomplished using SSH keys and SMU’s HPC bastion hosts.

The script makes only single one-line edit to ~/.ssh/config with all other files contained in ~/.ssh/smu_hpc_ssh.

Note that if something goes wrong during the setup process you can simply restart this script to try again.

Begin by copying and pasting the command below into a UNIX terminal, e.g. Linux, macOS, or Windows WSL, on your own computer, i.e. not logged into M3 nor the NVIDIA SuperPOD (MP).

curl -fsSL https://raw.githubusercontent.com/SouthernMethodistUniversity/smu_hpc_ssh/main/setup.sh | sh

After following the scripts prompts you can access the SuperPOD via ssh mp and M3 via ssh m3. Note the same command is used both on and off campus. The SSH setup made by the script will automatically determine if the bastion hosts are needed and use them if so.