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https://github.com/Amii-Open-Source/awesome-amii-hpc

A curated list of high-performance computing resources tailored to Amii.
https://github.com/Amii-Open-Source/awesome-amii-hpc

List: awesome-amii-hpc

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A curated list of high-performance computing resources tailored to Amii.

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# Awesome Amii HPC [![Awesome](https://awesome.re/badge-flat.svg)](https://awesome.re)



[![Contributions](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](./CONTRIBUTING.md)



---



## Table of Contents



1. [What is a cluster?](#what-is-a-cluster)

2. [How do I connect to the cluster?](#how-do-i-connect-to-the-cluster)

3. [When should I use a cluster?](#when-should-i-use-a-cluster)

4. [Synchronous parallelism](#synchronous-parallelism)

5. [Slurm](#slurm)

6. [Managing research data](#managing-research-data)



## What is a cluster?



* [Amii: What is a cluster?](content/Intro%20to%20HPC/Module%201%20-%20What%20is%20a%20cluster.md) - A brief description of the components of an HPC cluster.

* [Wikipedia](https://en.wikipedia.org/wiki/High-performance_computing) - An introduction of HPC.

* [Nvidia: MIG user guide documentation](https://docs.nvidia.com/datacenter/tesla/mig-user-guide/index.html#abstract) - A user guide documentation of multi-instance GPU from Nvidia.

* [Current State of Advanced Research Computing in Canada, May 2021](https://alliancecan.ca/sites/default/files/2022-03/arc_current_state_report_0.pdf) - Compute, storage, communication data of Compute Canada HPCs.

* [Ubuntu HPC](https://www.youtube.com/watch?v=tGIobcyKViI&t=2s) - A Youtube video introducing cluster components.

* [Top 500 list](https://www.top500.org/) - The data of top 500 listed supercomputers, which gives a scope of how fast and how much compute nodes are, and also introduction and comparison among these computers.

* [Iowa State University HPC Guides](https://www.hpc.iastate.edu/guides/introduction-to-hpc-clusters) - A collection of introductory guides for HPC including SLURM, globus, unix, python, julia, and much more.

* [An HPC User Guide](https://servicedesk.aub.edu.lb/TDClient/1398/Portal/KB/ArticleDet?ID=66391) - A collection of introductory guides for HPC including connection nodes, SLURM, job examples and applications.



### Compute Canada



* [Compute Canada: an introduction to HPC](https://training.incf.org/lesson/high-performance-computing-compute-canada) - A Youtube video introducing high-performance computing with the Compute Canada network, first providing an overview of use cases for HPC and then a hands-on tutorial.

* [Compute Canada: Cedar](https://docs.alliancecan.ca/wiki/Cedar) - An introduction of Cedar, a heterogeneous cluster located at Simon Fraser University.

* [Compute Canada: Graham](https://docs.alliancecan.ca/wiki/Graham) - An introduction of Graham, a heterogeneous cluster located at the University of Waterloo.

* [Compute Canada: Narval](https://docs.alliancecan.ca/wiki/Narval/en) - An introduction of Narval, a general purpose cluster located at the École de technologie supérieure in Montreal.

* [Compute Canada: Béluga](https://docs.alliancecan.ca/wiki/B%C3%A9luga/en) - An introduction of Béluga, a general purpose cluster situated at the École de technologie supérieure in Montreal.

* [Compute Canada: Niagara](https://docs.alliancecan.ca/wiki/Niagara) - An introduction of Niagara, a homogeneous cluster owned by the University of Toronto and operated by SciNet.

* [Compute Canada: Systems available](https://docs.alliancecan.ca/wiki/Getting_started#What_systems_are_available?) - A brief introduction for the five systems of Compute Canada and the clusters' types.

* [Compute Canada: Allocations and compute scheduling](https://docs.alliancecan.ca/wiki/Allocations_and_compute_scheduling#Choosing_GPU_models_for_your_project) - A brief tutorial of choosing GPU models for your project.



## How do I connect to the cluster?



* [SSH quickstart](https://linuxhandbook.com/ssh-basics/) - Step-by-step ssh and scp guide.

* [Compute Canada: SSH](https://docs.alliancecan.ca/wiki/SSH) - An introduction of Secure Shell used to connect to remote machines securely.

* [Compute Canada: Transferring data](https://docs.alliancecan.ca/wiki/Transferring_data) - Overview of options for transferring data to and between clusters (Globus, rsync, scp, etc.).

* [Compute Canada: Globus](https://docs.alliancecan.ca/wiki/Globus) - Setup and tutorial for Globus with Compute Canada.

* [Globus docs](https://docs.globus.org) - Globus tutorials and documentations.

* [Globus video tutorial](https://www.youtube.com/watch?v=-j7Mp3FN1zo) - Youtube video introduction to Globus for researchers and new users.

* [VS Code remote development](https://code.visualstudio.com/docs/remote/remote-overview) - Visual studio code remote development guide.

* [Rsync quickstart](https://linuxize.com/post/how-to-use-rsync-for-local-and-remote-data-transfer-and-synchronization/) - Step-by-step rsync guide.

* [Compute Canada: Interactive jobs](https://docs.alliancecan.ca/wiki/Running_jobs#Interactive_jobs) - Compute Canada documentation for running interactive jobs.

* [Github SSH authentication](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) - Connecting Github account to your computer and the cluster.

* [git - the simple guide](https://rogerdudler.github.io/git-guide/) - A short introduction and Step-by-step git guide.

* [Compute Canada: Storage and file management](https://docs.alliancecan.ca/wiki/Storage_and_file_management) - An introduction of a wide range of storage options to cover the needs of very diverse users of Compute Canada.



## When should I use a cluster?



* [Job scheduling policies](https://docs.alliancecan.ca/wiki/Job_scheduling_policies) - Time limits of each cluster and number of jobs, helping identify recognize what type of job may use a cluster.

* [The necessity of checkpointing](https://docs.alliancecan.ca/wiki/AI_and_Machine_Learning#Long_running_computations) - When should we use checkpointing.

* [Dealing with heavy computing](https://scil-documentation.readthedocs.io/en/latest/heavy/computing.html) - An example of when and how to use compute canada.

* [When to use HPC cluster](https://www.hpc.iastate.edu/guides/introduction-to-hpc-clusters/when-to-use-hpc-cluster) - Typical cases of when it may be beneficial to request access to an HPC cluster.



## Synchronous Parallelism



* [Tensorflow: Distributed training](https://www.tensorflow.org/guide/keras/distributed_training) - Introduction and tutorial of Multi-GPU and distributed training.

* [Wikipedia: GNU parallel](https://en.wikipedia.org/wiki/GNU_parallel) - Introduction and user's guide of GNU parallel.

* [Compute Canada: GNU parallel](https://docs.alliancecan.ca/wiki/GNU_Parallel) - An introductory tutorial of using GNU parallel.

* [GNU parallel tutorial documentation](https://www.gnu.org/software/parallel/parallel_tutorial.html) - A tutorial of GNU parallel, including its functionality, options and syntax.



### OpenMPI



* [Open-MPI documentation](https://www.open-mpi.org/doc/) - A series of versions for Open MPI documentations.

* [Open MPI v5.0.x](https://docs.open-mpi.org/en/v5.0.x/) - The documentation of current release Open MPI.

* [SLURM: MPI users guide](https://slurm.schedmd.com/mpi_guide.html) - An introductory tutorial of various MPI implementations.

* [Github: Open-MPI tutorial](https://usc-rc.github.io/tutorials/open-mpi) - A tutorial of using Open MPI.

* [Compute Canada: MPI-IO](https://docs.alliancecan.ca/wiki/MPI-IO) - Description and using tutorial of MPI-IO.



### Jax



* [jax.pmap](https://jax.readthedocs.io/en/latest/_autosummary/jax.pmap.html) - Step-by-step jax.pmap guide.

* [Compute Canada: Flax](https://docs.alliancecan.ca/wiki/Flax) - Introduction and tutorial of Flax, a neural network library and ecosystem for JAX that is designed for flexibility, including the guidance of using jax.pmap.



## Slurm

### Preemption and checkpointing



* [Compute Canada: Checkpoints](https://docs.alliancecan.ca/wiki/Points_de_contr%C3%B4le/en) - A tutorial of creating and loading a checkpoint.

* [Compute Canada: Machine Learning tutorial](https://docs.alliancecan.ca/wiki/Tutoriel_Apprentissage_machine/en#Checkpointing_a_long-running_job) - A tutorial of checkpointing a long-running job.

* [Tensorflow: Checkpoint guide](https://www.tensorflow.org/guide/checkpoint) - Guidance for training checkpoints while using Tensorflow.



## Managing Research Data

### HPC Storage Systems

* [Compute Canada: Lustre](https://docs.alliancecan.ca/wiki/Tuning_Lustre) - An introduction and tutorial of Lustre Filesystem.