Docker Tutorial for Beginners
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A Docker tutorial for beginners is a course that teaches the basics of Docker, a containerization platform that allows you to package your application and its dependencies into a standardized unit for development, shipment, and deployment.
DELTA Introductory Video
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Introductory video about DELTA. Speaker Tim Boerner, Senior Assistant Director, NCSA
CUDA Toolkit Documentation
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NVIDIA CUDA Toolkit Documentation: If you are working with GPUs in HPC, the NVIDIA CUDA Toolkit is essential. You can access the CUDA Toolkit documentation, including programming guides and API references, at this provided website
Astronomy data analysis with astropy
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Astropy is a community-driven package that offers core functionalities needed for astrophysical computations and data analysis. From coordinate transformations to time and date handling, unit conversions, and cosmological calculations, Astropy ensures that astronomers can focus on their research without getting bogged down by the intricacies of programming. This guide walks you through practical usage of astropy from CCD data reduction to computing galactic orbits of stars.
Active inference textbook
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This textbook is the first comprehensive treatment of active inference, an integrative perspective on brain, cognition, and behavior used across multiple disciplines including computational neurosciences, machine learning, artificial intelligence, and robotics. It was published in 2022 and it's open access at this time. The contents in this textbook should be educational to those who want to understand how the free energy principle is applied to the normative behavior of living organisms and who want to widen their knowledge of sequential decision making under uncertainty.
Research Software Engineering Training Materials
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An ongoing collection of RSE training material, workshops, and resources. We are compiling this list as a starting point for future activities. We are especially seeking material that goes beyond basic research computing competency (e.g. what The Carpentries does so well) and is general enough to span multiple domains. Specific tools and technologies used only in one domain, or applicable to only one subset of computing (i.e. HPC) are typically too narrowly focused. When in doubt, submit it to be included or reach out and we’d be happy to discuss.
Conda
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Conda is a popular package management system. This tutorial introduces you to Conda and walks you through managing Python, your environment, and packages.
Women in HPC
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Through collaboration and networking, WHPC strives to bring together women in HPC and technical computing while encouraging women to engage in outreach activities and improve the visibility of inspirational role models.
Thrust resources
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Thrust is a CUDA library that optimizes parallelization on the GPU for you. The Thrust tutorial is great for beginners. The documentation is helpful for anyone using Thrust.
Neocortex Documentation
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Neocortex is a new supercomputing cluster at the Pittsburgh Supercomputing Center (PSC) that features groundbreaking AI hardware from Cerebras Systems.
Research Security Operations Center at IU
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The NSF-funded ResearchSOC helps make scientific computing resilient to cyberattacks and capable of supporting trustworthy, productive research through operational cybersecurity services, training, and information sharing necessary to a community as unique and variable as research and education (R&E).
ResearchSOC is a service offering from Indiana University's OmniSOC.
Benchmarking with a cross-platform open-source flow solver, PyFR
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What is PyFR and how does it solve fluid flow problems?
PyFR is an open-source Computational Fluid Dynamics (CFD) solver that is based on Python and employs the high-order Flux Reconstruction technique. It effectively solves fluid flow problems by utilizing streaming architectures, making it suitable for complex fluid dynamics simulations.
How does PyFR achieve scalability on clusters with CPUs and GPUs?
PyFR achieves scalability by leveraging distributed memory parallelism through the Message Passing Interface (MPI). It implements persistent, non-blocking MPI requests using point-to-point (P2P) communication and organizes kernel calls to enable local computations while exchanging ghost states. This design approach allows PyFR to efficiently operate on clusters with heterogeneous architectures, combining CPUs and GPUs.
Why is PyFR valuable for benchmarking clusters?
PyFR's exceptional performance has been recognized by its selection as a finalist in the ACM Gordon Bell Prize for High-Performance Computing. It demonstrates strong-scaling capabilities by effectively utilizing low-latency inter-GPU communication and achieving strong-scaling on unstructured grids. PyFR has been successfully benchmarked with up to 18,000 NVIDIA K20X GPUs on Titan, showcasing its efficiency in handling large-scale simulations.
Scikit-Learn: Easy Machine Learning and Modeling
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Scikit-learn is free software machine learning library for Python. It has a variety of features you can use on data, from linear regression classifiers to xg-boost and random forests. It is very useful when you want to analyze small parts of data quickly.
Data Visualization Tools for Julia
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Plots.jl is the most widely used plotting library for the Julia programming language. It's known for being especially powerful in its versatility and intuitiveness. It's limited set of dependencies and wide applicability across different graphics packages make it especially helpful in visualizing the results of your latest Julia implementation.
However, there are still multiple options available for Julia programmers to visualize their datasets. The second link details a comparison against a variety of Julia packages.
Info about retiring of R GIS packages rgdal, rgeos, maptools in 2023
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R GIS packages "rgdal", "rgeos", and "maptools" are package set to be archived and no longer supported by end of 2023. Many other R GIS packages are build on top of these packages, including "sp" and "raster". The packages recommended as replacement for "sp" is "sf" and the replacement for "raster" is "terra". Below are links to published articles regarding this transition. Additionally, I am including links to the documentation for the new packages recommended to be used "sf" and "terra".
Biopython Tutorial
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The Biopython Tutorial and Cookbook website is a dedicated online resource for users in the field of computational biology and bioinformatics. It provides a collection of tutorials and practical examples focused on using the Biopython library.
The website offers a series of tutorials that cover various aspects of Biopython, catering to users with different levels of expertise. It also includes code snippets and examples, and common solutions to common challenges in computational biology.
The Theory Behind Neural Networks (Very Simplified)
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This video by the YouTube channel 3Blue1Brown provides a very simplified introduction to the theory behind neural networks. This tutorial is perfect for those that don't have much linear algebra or machine learning background and are eager to step into the realm of ML!
Creating a Mobile Application
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Goes through in detail on how to build an application that can run on Android and IOS devices, using Qt Creator to develop Qt Quick applications. Goes through the setting up, creation, configuration, optimization, and overall deployment. This provides the fundamental basis, need to click around on the site for more specifics.
Bash shell tutorial
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Training materials for using the bash (and zsh) shell.
Moving-Lid-Driven Flow Simulation by Finite Difference Method
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The listed repository contains code written in C++ to model the flow inside a cavity with a lid moving above from left to right by discretizing incompressible N-S equations with finite difference method. For the governing equations, artificial viscosity has been considered to increase the stability. In terms of solving the resulted algebraic equation system, both the Point Jacobi Method and Symmetric Gauss Seidel methods have been used for the iteration process.
High Performance Computing (HPC) 101 - Cluster
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High Performance Computing (HPC) Cluster
ACCESS Video Learning Center
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A library of short videos about ACCESS allocations, resources and support.
Why 'N How: Martinos Center for Biomedical Imaging:
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The Why & How seminar series is designed to introduce research assistants, graduate students, and postdoctoral and clinical fellows – really, anyone who is interested – to the many tools used in medical imaging. These include software tools and most of the major imaging modalities wielded by investigators (MRI, PET, EEG, MEG, optical, TMS and others). As the name of the series suggests, the talks cover both the reasons researchers might need a particular tool and the nuts and bolts of how to apply it. You can watch videos of the overviews below.
Guide to building AirSim on Linux machines
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This article provides step-by-step instructions on how to build AirSim, a simulator for autonomous vehicles, on Linux. It includes both Docker and host machine setup options, along with details on building Unreal Engine, AirSim, and the Unreal environment. It also provides guidance on how to use AirSim once it is set up.
Running Particle-in-Cell Simulations on HPC
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WarpX is an advanced particle-in-cell code used to model particle accelerators, which needs to be run on HPC. This website contains the tutorial on how to build WarpX on various HPC systems such as NERSC along with examples on how to set up post-processing/visualization tools for different physics cases.