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CSC Computing Environment
Home
Part 1
1. Prerequisites
CSC account and project
Login to Puhti
Basic Linux commands
Basic file editing
Using SSH keys
2. Introduction to the HPC environment
3. Disk areas
Main disk areas
Finding where you have lots of data
Fast disk areas
I/O intensive computing
4. Module system
Modules in Puhti
Biosoftware in Puhti
5. Batch queue system and interactive use
Serial batch jobs
Parallel batch jobs
Interactive batch jobs
Retrieving data from bio data repositories
6. Batch job resource usage
Understanding resource usage with sacct and seff
Find resource usage of recent jobs
7. Allas
Basic usage of Allas
File backup with Allas
Allas in batch jobs
Using Allas with bio data
Part 2
8. Installing own software
Installing binary applications
Installing Python packages and environments
Installing R application and libraries
Installing a simple C code from source
Installing Perl applications and libraries
Installing Java applications
Installing own C, C++ or Fortran programs
9. Containers and Apptainer
Apptainer tutorial 1
Apptainer tutorial 2
Running containerized applications
How to get containers
Replicating a Conda environment
Creating Apptainer containers
10. How to speed up jobs
Performing a simple scaling test
Processing many files with HyperQueue
Running Gaussian with sbatch-hq
View on GitHub
Part 2
9. Containers and Apptainer
9. Containers and Apptainer
9.1 Slides
9.2 Video: Containers
9.3 Tutorials and exercises
Essential tutorial - Introduction to Apptainer
Tutorial - Apptainer introduction continued
Tutorial - Running containerized applications
Advanced tutorial - How to get containers
Exercise - Replicating a Conda environment
Exercise - Creating Apptainer containers