Documentation

Access to HPC

Quick Start Guide

Kay User Guide

Tutorials

Videos

Advanced Documentation

Quick Start Guide

This provides some basic guidelines on getting started with Kay. New users to Kay (or to HPC systems in general) should read this documentation first.

Setting up an Account and Access

To become a user on Kay, you need to:

  • Register an account in here

Then you can:

  • Apply for a new National Service project
  • Join an existing project
  • Gain access through your institution condominium

Please refer to the Access to HPC section for more details.

All use of Kay is subject to the ICHEC Acceptable Usage Policy (AUP).

Connecting to Kay

You can connect to Kay using a SSH client.

On Unix-like systems (e.g. Linux, MacOS), SSH clients are usually pre-installed. You can access these through the Terminal (or any other command line interface).

ssh {{userName}}@kay.ichec.ie

Note: In the code examples like this, curly braces (and text inside it) are placeholders and should be replaced with the relevant text by you. For example, if your user name is jsmith, then replace {{userName}} in the code examples with jsmith

On Windows, you need to install a SSH client such as PuTTY or MobaXterm.

Note: Our firewall policy allows SSH access (using password authentication) only from an IP address in our member university's network. Users may configure key-authenticated SSH access that will enable access to Kay from the wider internet. Please note that the latter requires that you generate SSH public-private key pairs on another system other than Kay for security reasons (e.g. ssh-keygen for Linux/Mac, PuTTYgen and Pageant for Windows; DO NOT store your private key on Kay). Contact us at the ICHEC Helpdesk if you need help.

File Storage

We provide two locations for storing files on Kay

Home: /ichec/home/users/{{userName}}

Work: /ichec/work/{{projectName}}

They differ in few ways

Name Home Work
Purpose Store personal file or source code Store simulation data
Quota Smaller Limit: 25GB Larger Limit (see Class Projects Limits
Access Only to you To all users in the project
Backup Yes, backed up to tape No

Note: The data is backed up to protect against system failure. We cannot recover data, if it is accidentally deleted by any user.

Data Transfer

On Unix-like systems, you can use command line applications such as scp or sftp

Using scp

scp {{localFilePath}} {{userName}}@kay.ichec.ie:{{remoteFilePath}}

Using sftp

sftp {{userName}}@kay.ichec.ie

put {{localFilePath}}

On Windows, you can use graphical applications such as WinSCP.

Software Packages

We use environment modules (or commonly known as modules) to organise all the software packages we provide on Kay including scientific applications, compilers and development libraries. To start using the package of interest, you should load the corresponding module. You can list all the available modules on the system by:

module avail

To load the module:

module load intel/2019

To check the loaded modules in your environment:

module list

Job Submission

We use a batch system (SLURM) to allocate resources on Kay to users. For compute-intensive workloads, you should always use the compute nodes by submitting a batch job to SLURM. Please refer to Slurm Workload Manager, PBS to Slurm, and Slurm Commands pages for more detailed documentation.

To submit a job, create a submission script:

mybatchjob.sh

using emacs, nano or vim with the following text as an example (for a MPI application):

#!/bin/sh 

#SBATCH --time=00:20:00
#SBATCH --nodes=2
#SBATCH -A {{myProjectID}}
#SBATCH -p DevQ


module load intel/2019

srun -n 80 mpi-benchmarks/src/IMB-MPI1

Submit the job using:

sbatch mybatchjob.sh

You can check the progress of any jobs you have submitted by using:

squeue -u {{userName}}