# Tutorials

## General

* [Getting started with supercomputing at CSC](hpc-quick.md)
* [Getting started with Quantum computers](../../computing/quantum-computing/access.md)
* [Managing data on supercomputer scratch disks](clean-up-data.md)
* [CSC Quick reference (pdf)](../../img/csc-quick-reference/csc-quick-reference.pdf)
* [Linux basics for CSC](env-guide/index.md)
* [Interactive and batch job hands-on in Roihu](cmdline-handson.md)
* [Using csc-env command](using_csc_env.md)
* [Developing scripts remotely](remote-dev.md)
* [Using CSC HPC environment efficiently](https://csc-training.github.io/csc-env-eff/)
* [How to run existing containers in Puhti](../../computing/containers/overview.md#running-containers)
* [Getting disk usage using Lue](lue.md)
* [Running Julia batch jobs on CSC clusters](../../apps/julia.md#running-julia-batch-jobs-on-csc-clusters)
* [Using Python on CSC supercomputers](python-usage-guide.md)
* [Setting up SSH keys at CSC](https://csc-training.github.io/csc-env-eff/hands-on/connecting/ssh-keys.html)

## Roihu

* [Getting started with Roihu](roihu.md)
* [Roihu data migration guide](roihu-data.md)
* [Preparing for Roihu: Data management and temporary storage options](roihu-data-preparation.md)

## Installation of tools on supercomputers

* [Installing software with Spack](user-spack.md)
* [Installing software with Spack on Roihu](roihu-user-spack.md)
* [Conda best practices](conda.md)

## Performance and high-throughput workflows

* [General high-throughput guidelines](../../computing/running/throughput.md)
* [Inspecting and controlling CPU affinity](affinity.md)
* [Optimising parallel I/O](lustre_performance.md)
* [Dask & parallel Python](dask-python.md)
* [HyperQueue meta-scheduler](../../apps/hyperqueue.md)
* [FireWorks workflow manager](../../apps/fireworks.md)
* [How to run many short jobs with GNU Parallel](many.md)
* [Running Nextflow pipelines](../../apps/nextflow.md)
* [Running Snakemake pipelines on Puhti](../../apps/snakemake.md)

## Resources for courses

* [Organizing a course using CSC services](services-for-courses.md)
* [A Puhti web interface demo for course organizers](https://github.com/CSCfi/Jupyter_www_puhti)
* [Noppe environment for creating custom notebooks](../../cloud/noppe/guide_for_teachers.md#creating-custom-images)

## Allas

* [Using Allas interactively in Roihu](../../data/Allas/allas-roihu.md)
* [Using Allas in batch jobs](../../data/Allas/allas_batchjobs.md)
* [Using Allas to host a dataset for a research project](../../data/Allas/allas_project_example.md)
* [Tools for client side encryption for Allas](../../data/Allas/allas_encryption.md)
* [Using Allas from LUMI supercomputer](../../data/Allas/allas_lumi.md)

## Bioinformatics

* [Installing packages from Bioconda using Tykky](bioconda-tutorial.md)
* [Singularity applications on Puhti](bioapplications-puhti.md)
* [Running MaxQuant on Puhti](MaxQuant-tutorial.md)
* [Schrödinger Maestro Puhti advanced tutorial](power-maestro.md)
* [Schrödinger GPU-powered screening of the Molport database](gpu-shape.md)
* [Running your first job on Puhti](biojobs-on-puhti.md)

## Chemistry

* [Farming Gaussian jobs with HyperQueue](https://csc-training.github.io/csc-env-eff/hands-on/throughput/gaussian_hq.html)
* [Using Gabedit for Gaussian jobs on Puhti](gabedit_gaussian.md)
* [High-throughput computing with GROMACS](gromacs-throughput.md)
* [Spring School on Computational Chemistry](https://zenodo.org/records/11172973)

## Data analysis

* [Starting with parallel R](parallel-r.md)
* [Parallel R batch job examples](parallel-r-examples.md)
* [Using RStudio or Jupyter notebooks on Roihu](rstudio-or-jupyter-notebooks.md)

## Geoinformatics

* [Introduction to geocomputing in CSC computing environment](https://research.csc.fi/geocomputing)
* [Earth Observation (EO) guide](gis/eo_guide.md)
* [Using geospatial files directly from cloud, inc Allas](gis/gdal_cloud.md)
* [GDAL tutorial](gis/gdal.md)
* [Virtual rasters](gis/virtual-rasters.md)
* For software specific tutorials and examples, see [the respective software pages](../../apps/by_discipline.md#geosciences)

## Machine learning and AI

* [Machine learning guide, what CSC service to use for machine learning](ml-guide.md)
* [Getting started with machine learning at CSC](ml-starting.md)
* [GPU-accelerated machine learning](gpu-ml.md)
* [Data storage for machine learning](ml-data.md)
* [Multi-GPU and multi-node machine learning](ml-multi.md)
* [Hyperparameter search](hyperparameter_search.md)
* [Managing machine learning workflows on CSC's supercomputers](ml-workflows.md)
* [Working with large language models on supercomputers](ml-llm.md)


## Pouta - cloud

You can find Pouta tutorials in [Cloud Services > Pouta > Tutorials](../../cloud/pouta/tutorials/index.md)

## Pukki - database cloud

* [How to migrate a PostgreSQL database to Pukki](./pukki_data_migration.md)

## Rahti - container cloud

You can find Rahti tutorials in [Cloud Services > Rahti > Tutorials](../../cloud/rahti/tutorials/index.md)

## Sensitive Data

* [Using Allas to transport sensitive data](../../data/sensitive-data/sequencing_center_tutorial.md)
* [Running temporary PostgreSQL database in SD Desktop](../../data/sensitive-data/tutorials/postgresql.md)

## Visualisation

* [Blender tutorial](blender-tutorial.md)
