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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
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
Using Allas with bio data
Part 2
8. Working efficiently with data
Using Allas in batch jobs
Using Allas with local rclone
I/O intensive computing
9. 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 using CMake
Optimizing compiler options
10. Containers and Apptainer
Apptainer tutorial 1
Apptainer tutorial 2
Running containerized applications
How to get containers
Replicating a Conda environment
Creating Apptainer containers
11. How to speed up jobs
Performing a simple scaling test
Processing many files with HyperQueue
High-throughput Snakemake workflows
Running Gaussian with sbatch-hq
Application performance
View on GitHub
Part 2
11. How to speed up jobs
11. How to speed up jobs
11.1 Slides
11.2 Tutorials and exercises
Essential tutorial - Perform a simple scalability test
Tutorial - Processing many files in parallel with HyperQueue
Tutorial - Running Snakemake workflows on Puhti
Optional tutorial - Farming Gaussian jobs with HyperQueue
Exercise - Tune performance of a hybrid MPI/OpenMP application