In this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.
The material includes slides with theory concepts and practical exercises.
- Talk 1: Introduction to High-Performance Computing and its components. Identifying problems that can be addressed using a computing cluster
- Talk 2: Introduction to the Linux environment. Using the shell and basic commands.
- Exercise 1: Linux basic commands -- Download pdf
- Exercise 2: Filesystem -- Download pdf
- Exercise 3: Users and privileges -- Download pdf
- Talk 3: Accessing, connecting to, and transferring data to an HPC environment
- Exercise 4: Accessing, connecting to, and transferring data to an HPC environment -- Download pdf
- Talk 4: Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols
- Exercise 5: Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols -- Download pdf
- Talk 5: Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC.
- Exercise 6: Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC -- Download pdf
- Talk 6: Scripting and parallelization
- Exercise 7: Scripting and parallelization -- Download pdf
- Talk 7: Building a reliable and reproducible scientific workflow using Nextflow
- Exercise 8: Building a reliable and reproducible scientific workflow using Nextflow -- Download pdf
- Exercise 9: Practical cases and common issue -- Download pdf