Logging in to Bert
Overview
Teaching: 20 min
Exercises: 15 minQuestions
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
AVAIL
tells us if the partition is available.TIMELIMIT
tells us if there’s a time limit for jobsNODES
is the number of nodes in this partition in this particular state.STATE
describes what these nodes are doing:drain
means that the node will become unavailable once the jobs currently running on it complete.down
means that the node is is powered off or otherwise unavailable for use.alloc
means that the node is fully allocated; all CPU cores are in use running users’ software.mix
means that some of the CPU cores on a node are allocated to a user, and others are available for use.idle
means that the node is not currently allocated, and is available for use.
Exercises
Logging into Bert
If you haven’t already:
- In your web browser go to the account request page and enter your details.
- Log in to
bert.ibers.aber.ac.uk
using your SSH client.- Run the
sinfo
command to see how busy things are.- 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.