Hands On Introduction to HPC for Life Scientists
Dates: 30 October - 1 November 2019
Location: EPCC at University of Birmingham
Lecture Slides
Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.
Day 1
- Introduction BioExcel
- PRACE, ARCHER and EPCC training
- Course Overview, Syllabus and Timetable
- Why HPC?
- Parallel Programming Patterns
- Measuring Parallel Performance
- Building Blocks: Software (Operating Systems, Processes, Threads)
- Building Blocks: Hardware (Processors, Cores, Memory, and Accelerators)
Day 2
- Parallel Programming Models
- HPC Architectures
- Batch Systems & Parallel Application Launchers
- Compilers and Building Software
- Parallel Libraries
Day 3
- Pipelines and Workflows
- The UK HPC and European HPC landscapes
- HPC Europa
- The Future of HPC
- Conclusions
Course Chat
https://paper.dropbox.com/doc/Hands-on-Introduction-to-HPC-for-Life-Scientists--AiWIz4Y9lhGjLVhIzGx3kcoDAg-fwondyFx2HL5ijFV14izvThe Chat page is a live collaborative online document, hosted by Dropbox, which we will use to share links, information and comments. All course participants are encouraged to contribute.
Exercise Material
Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.
Practical 1: Sequence Alignment using HMMER
Practical 2: Molecular Dynamics using GROMACS
- Reference: MD with GROMACS
- Reference: GROMACS Performance Tuning and Optimisation
- Reference: GROMACS Manual - Getting good performance from mdrun
- Reference: GROMACS Manuel - Domain decomposition & dynamic load balancing
- Instructions
Practical 3: QM/MM simulation using CP2K
Interactive Access
If you are having to wait a long time for jobs to run, you can try following these instructions to gain direct interactive access to an ARCHER node.
