How-To: Access Hellbender Command Line?

Open on Demand is a very convenient way to use Hellbender, but we encourage you to also learn how to use the cluster through terminal access. One reason is that Open On Demand is an additional layer on cluster service – requiring a web server to be up and running and during an outage you can still use the cluster via terminal. Not all HPC facilities use OOD, so having knowledge of terminal-based interface will assist you in accessing HPC in future environments.

 

To connect to Hellbender from your computer/laptop you will need to open a terminal application first (Mac and Linux machines have a native terminal application, while in Windows there are several options and we recommend using MobaXterm which we will use here to demonstrate terminal usage).

When you are installing MobaXterm on your Windows machine – make sure that you download the installer version (Green button in the figure below) of MobaXterm NOT the Portable version! 

Also, when the installer versions downloads it will be a zip file – unzip it first before starting installation. Do not click install executable within the zip file as that will lead to problems later when you try to run MobaXterm.

In MobaXterm after opening the app click the Start Local Terminal button:

To connect to Hellbender, type the following command:

ssh -X <pawprint/sso>@hellbender.rnet.missouri.edu

Replace the "bjmfg8" with your pawprint i.e. your SSO username on the Hellbender cluster.

The option -X means that ssh connection requires the so-called X tunnelling which will enable you to use even software with some graphical user interface elements (GUI). If you have a MAC you should use either the -X or the -Y option, and you should have XQuartz installed to use graphics. If you just installed XQuartz you will need to restart your Mac. 

You should get prompted for your password now:

Read carefully what it says – in this case it is asking for the password for my ssh key which was setup previously. If you do not have a ssh key setup you will be prompted for your regular password – i.e. the password that you use for your UM system account (SSO) – when you login for your university email or similar services if you are coming from a different institution. 

IMPORTANT – if you have the ssh key setup this connection should work regardless of which network your computer is connected to the Internet. However, if you do not have an SSH key setup, but rely on your SSO password to work, your computer must be on a UM campus network, or you must have a VPN connection active.

Open On Demand works regardless of the nature of your Internet connection – any connection should work.

After successfully typing in your password, you should be on the Hellbender login node:

 
It should be clearly visible in the command prompt that you are on a login node.

Warning – do not run any software while on the login node! It might lead to your account being locked until you attend the office hours training on how to properly run an interactive session.

You can edit text files, or submit your jobs, from the login node. Also, for downloading files to Hellbender using commands such as wget, rsync or scp - please do not use the login node - use the so-called data transfer node DTN.

To request an interactive session, you would execute the following command:

Where the options are: 
-N 1 - requesting one node
-n 8 - requesting 8 tasks (i.e. 8 CPUs)
--mem=20G requesting 20 GB of RAM
--time =4:00:00 requesting 4 hours of session time
-p general requesting resources on the general partition
--x11 is the option that should be given if you intend to run a software with GUI (graphics) – for this to work you must have had the -X option with your ssh command when connecting to the cluster.

Once the resources are allocated for your job/interactive session you should see a prompt like this:

Notice that we are not on a login node any longer but rather on one of the compute nodes (in this case c028). Now you can load the modules with software that you want to run and run the software. 

The important part of the salloc parameters is specifying the partition as general, which cannot be requeued by preemption. The same is true with the partition called gpu. You do not want to request requeue or gpu_requeue as a partition for your interactive session because it could get terminated while you are in the middle of your work. Be careful if you do not specify a partition name explicitly; the requeue will be used as the default option! 

If you want to get maximum amount of memory on the node you should specify --mem=0G rather than trying to figure out what is the maximum number you can use for the amount of ram.

 

In case you would like to get some GPU resources for your interactive session you can do the following command:

 

Hint – Use the screen command to save your interactive session in case of Internet connection loss.

It would be very frustrating if you were several hours into your interactive session and your Internet connection gets interrupted and you lose all your work. Notice that this is not a problem if your session is started via Open On Demand in which case you should always be able to reconnect to it through a web interface – as long as the session did not expire – i.e. ran out of its allocated time. This article refers to the case of a terminal-based interactive session.

To prevent this, you should prepend the salloc command with the command screen – like this (from the Hellbender login node):

 
 

Now imagine that your computer shuts down because your battery ran out, or you lost an Internet connection. After fixing the problem - connect to Hellbender login node again.

And type the command:

 
This should show you all the screen sessions (can be more than one screen sessions – notice the Detached status)

To reconnect the session, give the following command:

 
 

And you should be back where you were when your session was interrupted. This might not work well for sessions where you had GUI running via X-tunnel – i.e. if you used some kind of graphical user interface in your session. 

 

For additional assistance please e-mail itrss@missouri.edu or open a general support ticket via TDX.