Learning how to use HPC infrastructure (part IV: Submitting jobs, using containers, checkpointing, workflows)

Thursday 17 Oct 2024, 09:30 → 16:15 Europe/Brussels

CYCL09b (Louvain-La-Neuve)

We will continue to learn the fundamental tool needed to use a cluster. We will learn how to submit a job to the cluster with SLURM, how to beat the walltime and how to make your code portable and fully automated.
Contents: Preparing, submitting and managing jobs with Slurm Using a Checkpoint/restart program to overcome time limits Workflows Container	Prerequisite: Being able to use SSH with private keys
	Type: Lecture Hands-on Target audience: Rookie Must: This session is a must-have for anyone.

1 Preparing, submitting and managing jobs with Slurm

Slurm is the job manager installed on all CÉCI clusters. The session teaches attendees how to prepare a submission script, how to submit, monitor, and manage jobs on the clusters.

 

Contents: Role of a job scheduler  Creating and submitting a job  Setting job constraints and parameters  Managing and monitoring jobs  Working interactively  Getting accounting information  How priorities are computed  Creating basic submission scripts Best practice	Prerequisite: Being able to use SSH with private keys  Being familiar with a text editor  Mastering the Linux command line and the GNU utilities Follow-up: Checkpointing to make jobs fit maximum allowed time Workflows to organise jobs and experiments Advanced Slurm to write more complex parallel submission scripts.
Type: Hands-on Target audience: Everyone Must: This session is mandatory.

Speaker: Damien François (UCLouvain/CISM)

slurm2024-1.pdf

2 HPC program portability with Singularity/Apptainer

Singularity is a container solution for HPC. Containers help with reproducibility as they nicely package software and data dependencies, along with libraries that are needed. It allows users to install and run software that required root access to be installed on clusters where they only have regular user permissions. The rationale is to perform all the software installation in a container image (a kind of lightweight virtual machine, that can use a different Linux distribution than the one on the compute nodes!) on a machine where you have root access and then transfer and run that image on the machine on which you do not have root access. Images can be built from recipes shared by others, and from recipes made for Docker, the leader container solution outside the HPC world.
Contents: Container concepts and benefits Starting a Singularity container on the cluster Accessing the cluster filesystems Building a container image from a recipe Building a container image from scratch Singularity hub	Prerequisite: Being able to use SSH with private keys  Being familiar with a text editor  Mastering the Linux command line and the GNU utilities (mkdir, cp, scp, etc.) Basic knowledge of Linux system administration
Type: Hands-on Target audience: Advanced user Must: This session is a must-have for anyone dealing with software that only installs on Ubuntu...

Speaker: Dr Olivier Mattelaer (UCLouvain/CISM)

23_10_25_Singularity_CISM.pdf

3 Using a Checkpoint/restart program to overcome time limits

Checkpointing and Restarting, or the art of stopping some computations to continue them later, or on another computer, is a very convenient way to get past time limits set on the clusters, and to protect against hardware or software failure on the compute nodes.
Contents: Use and challenges of checkpointing The different approaches Checkpointing in Slurm Using DMTCP for checkpointing	Prerequisite: Being able to use SSH with private keys  Being familiar with a text editor  Mastering the Linux command line and the GNU utilities (mkdir, cp, scp, etc.) Passive knowledge of either C, Fortran, Octave, Python or R
Type: Hands-on Target audience: Everyone Must: This session is a must-have for anyone feeling oppressed by time limits.

Speaker: Olivier Mattelaer (UCLouvain/CISM)

24_10_checkpointing.pdf

CHECKPOINT.tgz

4 Workflow management systems

Whenever one has to deal with multiple jobs on a HPC system, the idea of automating parts or all of the job management process involves describing and implementing so-called 'workflows'. Options for managing workflows are numerous and range from using basic scheduler features such as job arrays and job dependencies, up to using a complex system managed by a central, multi-user, database. This session aims at guiding participants towards the right tool for their use and help them reduce the time they spend managing their jobs by automating what can be automated and follow best practices.

 

Contents: Introduction to workflows  Types of workflow management systems  Choosing a workflow management system  An example with Maestro	Prerequisite: Being able to use SSH with private keys  Being familiar with a text editor  Mastering the Linux command line and the GNU utilities Working knowledge of Slurm
Type: Hands-on Target audience: Everyone Must: This session is useful.

Speaker: Damien François (UCLouvain/CISM)

Workflows-2024-1.pdf

Workflows-2024-2.pdf