Basic Knot Usage


The hardware

There are over 1,000 cores for MPI jobs in 126 nodes. Each 'regular' node is 12 processing cores/node and the nodes have 48 GB or 64GB of RAM. There are 12 general purpose GPUs in 6 nodes (2/node). There are 4 'fat nodes' with either 512GB or 1TB of RAM. While you don't actually need to know the names of any of the nodes, you'll sometimes notice the names of nodes various places, so if you're interested, here's what they are:

List of Nodes:

  • node1-node42 and node46-87 are the regular MPI nodes, each with 12 cores.
  • node43-45 and node88-90 at GPU nodes.
  • node91-node93 are the 1TB and 32cores nodes while node94 is a 512GB and 32 core node.
  • node95 is 'knot' itself (the login node). node139 is knot-gpu (the login node for GPU and Xeon Phi development work)
  • node101-116 and node131-146 are regular MPI nodes with 64GB of RAM each.

Your files live in a directory /home which all of the nodes have access to. See the quick start guide for jumping into computation.

How to login:

There are actually two nodes you login to directly - you don't login to compute nodes - the login nodes are '' (the main login node) and '' (the login node for GPU and Xeon Phi development work)

To access the system you have several choices:

  • Command line:

login with your favorite terminal/SSH program to either (the main head node, or If you're logging in from a *nix type of desktop, you can launch X based applications back to your desktop (if you login with 'ssh -X')

  • Graphical interface:

Linux or Mac users can simply use their built in X-windows to directly send graphical output back to their computers by logging in with 'ssh -X'. Note if you're using a newer Mac (e.g. OS-X 10.9) you may have to install X-quartz for this to work, but it works seamlessly once you do.

Windows (and Mac, or even Linux) Use the NX or X2Go client. They are quite fast and works from Windows, Mac, or Linux.

Logging in from outside of campus

If you are connecting from a computer outside of campus, you need to setup a VPN to login to Knot.

How to transfer files to/from your computer

You can either use:

  • simple scp or rsync commands
  • a SFTP client, such as WinSCPCyberDuck,, FileZilla, or any other SFTP program that you like
  • GlobusOnline which offers some nice automatic restart and background transfer abilities

Running jobs

You can debug jobs on the head node, but for running large jobs, they need to be run from the queue. This way the node(s) are dedicated to working on YOUR job, and you can also submit lots of jobs at once and check back in later to see if they're all done - not like waiting on your desktop to finish one job so you can submit the next.