Course/Event Essentials
Training Content and Scope
Other Information
In the wake of collaborations between national European research centers, a new course promoted by EuroCC Italy and EuroCC Lithuania has been established: “HPC Molecular Modelling“, scheduled from November 6th to 8th, 2024, in streaming mode.
The course is dedicated to professionals who want to deepen their understanding of supercomputing applied to molecular modeling programs: the aim of the course is to provide researchers with the tools to run simulations as efficiently as possible on current and future supercomputers.
Pre-requisites:
Research interest in classical molecular dynamics with a focus on the simulation of biomolecular systems.
Basic knowledge of Unix is essential, and some experience of Python is recommended.
“HPC Molecular Modelling”
November 6th-8th, 2024
Program
► Day 1 — November 6th, 2024
Vilnius Time
Bologna Time
Activity
10:00 - 10:30
9:00 - 9:30
Registration
10:30 - 11:15
9:30 - 10:15
Introduction to HPC architectures and parallelism
11:15 - 11:30
10:15 - 10:30
Coffee break
11:30 - 12:30
10:30 - 11:30
Introduction to Classic Molecular Dynamics
12:30 - 14:00
11:30 - 13:00
Lunch Break
14:00 - 15:00
13:00 - 14:00
Parallel Molecular Dynamics
15:00 - 15:30
14:00 - 14:30
Coffee Break
15:30 - 17:30
14:30 - 16:30
Hands-On: Introduction to CINECA HPC
► Day 2 — November 7th, 2024
Vilnius Time
Bologna Time
Activity
10:00 - 10:45
9:00 - 9:45
MD on GPU Architectures
10:45 - 11:30
9:45 - 10:30
Hands-On: Strong scaling MD with large systems
11:30 - 11:45
10:30 - 10:45
Coffee Break
11:45 - 12:45
10:45 - 11:45
Hands-On: Strong scaling (continue)
12:45 - 14:15
11:45 - 13:15
Lunch Break
14:15 - 16:15
13:15 - 15:15
Hands-on: Teamwork – job optimization for a long trajectory on Leonardo. using ligand-protein complexes from LIGATE
16:15 - 16:30
15:15 - 15:30
Coffee Break
16:30 - 17:15
15:30 - 16:15
Hands on: High-throughput MD
17:15 - 17:45
16:15 - 16:45
Hands on: Common errors in MD simulations
► Day 3 — November 8th, 2024
Vilnius Time
Bologna Time
Activity
10:00 - 11:30
9:00 - 10:30
Analysis of MD trajectories
11:30 - 12:00
10:30 - 11:00
Coffee Break
12:00 - 13:30
11:00 - 12:30
Hands-on. Analysis of MD simulations with Python Notebooks on Galileo100
13:30 - 15:00
12:30 - 14:00
Lunch Break
15:00 - 15:45
14:00 - 14:45
Invited speaker: to be announced