PRACE Spring School "HPC for Life Sciences" in collaboration with BioExcel
Time: Mon 2017-04-10 09.00 - Thu 2017-04-13 17.00
Location: KTH main campus, Stockholm
Contact:
Overview
BioExcel Center of Excellence is bringing together for the first time the main developers of four of the major and most popular codes for molecular modelling and simulations - GROMACS , AMBER , NAMD and VMD . This is a great opportunity for novice and experienced users to learn from the very authors of the software. The 2017 Spring School is organized jointly with PRACE , the main HPC resource provider in Europe. The school program will allow participants to get a comprehensive introduction to the different codes; to understand their scalability and performance, as well as ways to avoid potential issues; to learn the best practices about using them on HPC systems. Extensive hands-on sessions will cover more than half of time during the school. The course will take place at the computer laboratories of PDC Center for High Performance Computing at KTH Royal Institute of Technology in Stockholm. Participants will be able to run on the PRACE Tier‐1 system Beskow, the largest Tier-1 system within the Nordic countries. The school is also supported by the Swedish National Infrastructure for Computing (SNIC) .
Lecturers
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Prof. Thomas CHEATHAM (University Information Technology, University of Utah) - main developer of AMBER |
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Jim PHILLIPS (University of Illinois, Urbana-Champaign) - main developer of NAMD |
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Prof. Erik LINDAHL (Stockholm University) - main developer of GROMACS |
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John STONE (University of Illinois, Urbana-Champaign) - main developer of VMD |
Preliminary Programme
| Time | Topic | Trainer |
| Day 1 - Monday 10th April 2017 | ||
| 08:30-09:00 | Registration | |
| 09:00-09:15 | Welcome | Michaela Barth |
| 09:15-10:00 | BioExcel Center of Excellence - Training Programme | Vera Matser |
| 10:00-10:30 | Coffee break | |
| 10:30-12:00 | Molecular visualisations with VMD | John Stone |
| 12:00-13:00 | Lunch | |
| 13:00-13:45 | How to use the PDC Supercomputing systems | Henrik Zazzi |
| 13:45-15:00 | Hands-on VMD | |
| 15:00-15:30 | Coffee break | |
| 15:30-17:30 | Hands-on VMD | |
| Day 2 - Tuesday 11th April 2017 | ||
| 09:30 - 10:30 | HPC Simulations with NAMD | Jim Phillips |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | HPC Simulations with NAMD | |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:30 | Hands-on NAMD | |
| 14:30 - 15:00 | Coffee Break | |
| 15:00 - 17:00 | Hands-on NAMD | |
| Day 3 - Wednesday 12th April 2017 | ||
| 09:30 - 10:30 | HPC Simulations with GROMACS | Erik Lindahl |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | HPC Simulations with GROMACS | |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:30 | Hands-on GROMACS | |
| 14:30 - 15:00 | Coffee Break | |
| 15:00 - 17:00 | Hands-on GROMACS | |
| 18:00 | Social Event Dinner | |
| Day 4 - 13th April 2017 | ||
| 09:30 - 10:30 | HPC Simulations with AMBER | Tom Cheatham |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | HPC Simulations with AMBER | |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:30 | Hands-on AMBER | |
| 14:30 - 15:00 | Coffee Break | |
| 15:00 - 17:00 | Hands-on AMBER | |
How to apply
The course is free of charge (though you are responsible for your own travel and accommodation costs). For the hands-on sessions, participants can bring their own laptops, in that case you have to make sure that all the required software (a detailed list including expected versions will be communicated in advance) is installed once the course starts.
Full details and registration via the PRACE website .
For more information on the BioExcel travel grant, please email Vera Matser .