https://github.com/bu-isciii/introduction_to_hpc
In this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.
https://github.com/bu-isciii/introduction_to_hpc
Last synced: 4 months ago
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In this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.
- Host: GitHub
- URL: https://github.com/bu-isciii/introduction_to_hpc
- Owner: BU-ISCIII
- License: gpl-3.0
- Created: 2025-07-20T14:14:40.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2025-09-10T08:22:57.000Z (9 months ago)
- Last Synced: 2025-09-10T11:59:03.963Z (9 months ago)
- Language: Shell
- Size: 5.01 MB
- Stars: 0
- Watchers: 0
- Forks: 2
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Introduction to High-Performance Computing (HPC) environment
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.
## Slides
### Day 1
- **Talk 1:** [Introduction to High-Performance Computing and its components. Identifying problems that can be addressed using a computing cluster](slides/talk1_introduction_hpc.pdf)
- **Talk 2:** [Introduction to the Linux environment. Using the shell and basic commands](slides/linux_intro.pdf).
- **Exercise 1:** [Linux basic commands](exercises/01_handson_linux/handson_linux1_BasicCommands.md) -- [Download pdf](exercises/01_handson_linux/handson_linux1_BasicCommands.pdf)
### Day 2
- **Exercise 2:** [Filesystem](exercises/01_handson_linux/handson_linux2_FileProcessing.md) -- [Download pdf](exercises/01_handson_linux/handson_linux2_FileProcessing.pdf)
- **Exercise 3:** [Users and privileges](exercises/01_handson_linux/handson_linux3_Privileges.md) -- [Download pdf](exercises/01_handson_linux/handson_linux3_Privileges.pdf)
- **Talk 3:** [Accessing, connecting to, and transferring data to an HPC environment](slides/talk3_access_connection_datatransfer.pdf)
- **Exercise 4:** [Accessing, connecting to, and transferring data to an HPC environment](exercises/04_access/handson_access.md) -- [Download pdf](exercises/xxx.pdf)
### Day 3
- **Talk 4:** [Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols](slides/talk4_filesystems_slurm.pdf)
- **Exercise 5:** [Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols](exercises/05_srun/handson_srun.md) -- [Download pdf](exercises/xxx.pdf)
- **Talk 5:** [Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC.](slides/talk5_SoftwareManagement_and_ContainersinHPC.pdf)
- **Exercise 6:** [Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC](exercises/06_software_management_hpc/handson_software_management.md) -- [Download pdf](exercises/xxxx.pdf)
### Day 4
- **Talk 6:** [Scripting and parallelization](slides/Talk6_Scripting_and_Parallelization.pdf)
- **Exercise 7:** [Scripting and parallelization](exercises/07_handson_scripting_and_parallelization/handson_scripting_and_parallelization.md) -- [Download pdf](exercises/xxxx.pdf)
- **Talk 7:** [Building a reliable and reproducible scientific workflow using Nextflow](slides/talk7_ReliableReproducible_ScientificWorkflows_Nextflow.pdf)
- **Exercise 8:** [Building a reliable and reproducible scientific workflow using Nextflow](exercises/08_handson_scientific_workflows_nextflow/handson_scientificworkflows_nextflow.md) -- [Download pdf](exercises/xxx.pdf)
### Day 5
- **Exercise 9:** [Practical cases and common issue](exercises/09_usecase_issues/handson_usecase_issues1.md) -- [Download pdf](exercises/xxx.pdf)