Krakow Conference on Computational Medicine 2025

Your Journey to HPC and Beyond. A Guide to Research at Scale with the Model Execution Environment

Date and time: 

15 October 2025 at 15:30 pm 

Place:  

Academic Computer Centre CYFRONET
of the AGH University of Krakow
Nawojki 11 street
30-950 Kraków

Maximum number of participants: 20

Duration: 2h

---

Marek Kasztelnik², Piotr Nowakowski^1,2, and Piotr Połeć²

¹Sano Centre for Computational Medicine, Czarnowiejska 36, 30-054 Kraków, Poland
²ACC Cyfronet AGH, ul. Nawojki 11, 30-950 Kraków, Poland
{p.nowakowski}@sanoscience.org, {m.kasztelnik,p.polec}@cyfronet.pl

Keywords: modelling, simulation, HPC, SLURM, Model Execution Environment

 

1. Introduction

 

This tutorial provides an introduction to High-Performance Computing (HPC) and its application in scientific research. Participants will be guided through the fundamental concepts of HPC, learning how to leverage powerful computing resources for their research needs. The tutorial will feature the Model Execution Environment (MEE), a platform designed to simplify the execution of complex simulations and data analysis pipelines on HPC infrastructure. We will explore how MEE supports the integration and execution of scientific applications, drawing on real-world examples from European research projects.

 

2. Description of the tutorial

 

This 2-hour tutorial will be a blend of lectures and live demonstrations. The session will cover the following topics:

• Introduction to HPC and the SLURM queuing system: We will begin with an overview of HPC concepts and a practical guide to using the SLURM workload manager for submitting and managing jobs on a cluster.
• API-driven job submission: This segment will focus on programmatic job submission. Participants will learn how to use an API to submit jobs to the HPC cluster and how to integrate this functionality with an external web application.
• Introduction to the Model Execution Environment (MEE): The final part of the tutorial will introduce the MEE. We will showcase how MEE streamlines the process of running scientific applications. This will involve:
  • an overview of how to define and manage complex computational workflows.
  • a case study from the InSilicoWorld project, demonstrating how MEE was used to store cohort data and run hundreds of simulations as part of a large-scale computational campaign.

3. Knowledge and skills to be gained

 

Upon completion of this tutorial, participants will be able to:

• Understand the fundamentals of High-Performance Computing,
• Submit and manage computational jobs on an HPC cluster using the SLURM scheduler,
• Programmatically submit jobs to an HPC cluster via an API,
• Understand the purpose and benefits of the Model Execution Environment (MEE).

 

Acknowledgements: This tutorial is made possible by the contributions and results from the following projects: EDITH (grant agreement no. 101083771), InSilicoWorld (grant agreement no. 101016503), GEMINI (grant agreement no. 101083771).

 

References:

1. InSilicoWorld project: https://insilico.world/
2. EDITH project: https://www.edith-csa.eu
3. GEMINI project: https://dth-gemini.eu
4. Sano seminar: Composing Applications In The Model Execution Environment: https://www.youtube.com/watch?v=hFM1jPVAhtg
5. Kasztelnik, M. et al. (2023). Digital Twin Simulation Development and Execution on HPC Infrastructures. In: Mikyška, J., de Mulatier, C., Paszyński, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M. (eds) Computational Science – ICCS 2023. ICCS 2023. Lecture Notes in Computer Science, vol 14074. Springer, Cham. https://doi.org/10.1007/978-3-031-36021-3_2