Documentation

Quick Start Guide

This provides some basic guidelines on getting started with Kay. If you are a new user to the Kay National HPC System (or to HPC systems in general), you should read this documentation first.

Setting up an Account and Access

To become a user on Kay, you must:

  • Register an account in here

Then you will need to do one of the following:

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

SSH Keys 

  • All users must initially configure an SSH key on each device they use to connect to Kay. Please note that the latter requires that you generate SSH public-private key pair on each local workstation (and not on Kay) for security reasons (e.g. ssh-keygen for Linux/Mac, MobaXterm for Windows; DO NOT store your private key on Kay). Check out our tutorial - Setting up SSH Keys - for more details. As a new user, you will need to send us your public key before you can connect to Kay.
  • You will need to login using your central ICHEC account username. You will be requested to authenticate using both your central ICHEC account password and SSH key-based authentication.

Logging in

You can connect to Kay using a SSH client:

  • 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

  • Windows: You need to install a SSH client. We recommend MobaXterm.

 

      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: Data is backed up to protect against system failure. We cannot recover data if you accidentally delete it.

      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
      
      mpirun -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}}

      Need help?

      If you get stuck, you can check our: