Logging in to Bert

Overview

Teaching: 20 min
Exercises: 15 min
Questions
Objectives
  • Understand the difference between the login node and compute nodes.

  • Understand how to log in to Bert

Logging in

Before we can log in to Bert, we need to have an account.

We can then log in to the system by typing:

$ ssh username@bert.ibers.aber.ac.uk

If you use Windows and haven’t installed the Git bash shell, you can instead use PuTTY and enter either bert.ibers.aber.ac.uk in the hostname box.

What’s available?

Bert’s Nodes

These figures may still be subject to some change.

Partition Number of Nodes Cores per node RAM Other
AMD 4 32 256GB  
Intel 5* 8 96GB 3 nodes are broken
Highmem 1 32 512GB  
Fat 1 16 1TB  
GPU 1 32 768GB Has a GPU Accelerator

Slurm

Slurm is the management software used on Bert. It lets you submit (and monitor or cancel) jobs to the cluster and chooses where to run them.

Other clusters might run different job management software such as LSF, Sun Grid Engine or Condor, although they all operate along similar principles.

How busy is the cluster?

The sinfo command tells us the state of the cluster. It lets us know what nodes are available, how busy they are and what state they are in.

Clusters are sometimes divided up into partitions. This might separate some nodes which are different to the others (e.g. they have more memory, GPUs or different processors).

PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
gpu          up   infinite      1   idle gpu01
intel        up   infinite      1    mix node003
intel        up   infinite      1   idle node004
amd          up   infinite      4    mix node[008-011]
highmem      up   infinite      1   idle node012
fat          up   infinite      1   idle node002

Exercises

Logging into Bert

If you haven’t already:

  1. In your web browser go to the account request page and enter your details.
  2. Log in to bert.ibers.aber.ac.uk using your SSH client.
  3. Run the sinfo command to see how busy things are.
  4. Try sinfo --long, what extra information does this give?

Key Points

  • ssh bert.ibers.aber.ac.uk to log in to the system

  • sinfo shows partitions and how busy they are.