Tutorials
General
- Getting started with Puhti
- Getting started with Mahti
- Getting started with Helmi
- Managing data on Puhti and Mahti scratch disks
- Conda best practices
- CSC Quick reference (pdf)
- How to run existing containers in Puhti
- Linux basics for CSC
- Interactive and batch job hands-on in Puhti
- Using csc-env command
- Developing scripts remotely
- Using CSC HPC environment efficiently
- Building Singularity containers from scratch
- Getting disk usage using Lue
- Installing software with Spack
- Running Julia jobs on Puhti and Mahti clusters
Performance and high-throughput workflows
- Optimising parallel I/O
- Dask & parallel Python
- General high-throughput guidelines
- Running Nextflow workflows using HyperQueue
- FireWorks workflow manager
- How to run many short jobs with GNU Parallel
- HyperQueue meta-scheduler
Allas
- Using Allas interactively in Puhti and Mahti
- Using Allas in batch jobs
- Using Allas to host a dataset for a research project
- Tools for client side encryption for Allas
- Using Allas from LUMI supercomputer
Bioinformatics
- Installing packages from Bioconda using Tykky
- Singularity applications on Puhti
- Running MaxQuant on Puhti
- Nextflow tutorial for Puhti (basic)
- Running Nextflow pipelines on Puhti (advanced)
- Running Snakemake pipelines on Puhti
- Schrödinger Maestro Puhti advanced tutorial
- Schrödinger GPU-powered screening of the Molport database
- Running your first job on Puhti
Chemistry
- Farming Gaussian jobs with HyperQueue
- Using Gabedit for Gaussian jobs on Puhti
- High-throughput computing with GROMACS
Data analysis and machine learning
- Data analysis guide
- Machine learning guide
- Using RStudio or Jupyter notebooks in Puhti
- Starting with parallel R
Geoinformatics
- Introduction to geocomputing in CSC computing environment
- Earth Observation (EO) guide
- Using geospatial files directly from cloud, inc Allas
- GDAL tutorial
- Virtual rasters
- For software specific tutorials and examples, see the respective software pages
Pouta - cloud
- cPouta and ePouta related videos
- Learn cloud computing by developing and deploying a web application
- Orchestration with Heat
- Create a jumphost in cPouta
- SSH Key-pair
Rahti - container cloud
- Accessing databases on Rahti from CSC supercomputers
- Configuration, ConfigMaps and Secrets
- Core objects
- Custom domain names and secure transport
- Deploying a static web server using the command line
- Deploying a static web server using the web interface
- How to add docker hub credentials to a project
- How to manually cache images in Rahti's registry
- How to package a Kubernetes application with Helm?
- How to transfer data to Rahti?
- Reverse proxy authentication using a sidecar container
- Short introduction to YAML
- Webhooks
Sensitive Data
Visualisation
CSC Resources for Courses
- A Puhti webinterface demo for course organizers
- CSC Notebooks environment for creating custom notebooks
Last update:
February 26, 2024