Optimizing Research Workflows - A Documentation of Snakemake
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Snakemake is a powerful and versatile workflow management system that simplifies the creation, execution, and management of data analysis pipelines. It uses a user-friendly, Python-based language to define workflows, making it particularly valuable for automating and reproducibly managing complex computational tasks in research and data analysis.
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.
Expanse Home Page
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Expanse at SDSC is a cluster designed by Dell and SDSC delivering 5.16 peak petaflops, and offers Composable Systems and Cloud Bursting.
Better Scientific Software (BSSw)
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The Better Scientific Software (BSSw) project provides a community to collaborate and learn about best practices in scientific software development. Software—the foundation of discovery in computational science & engineering—faces increasing complexity in computational models and computer architectures. BSSw provides a central hub for the community to address pressing challenges in software productivity, quality, and sustainability.
Horovod: Distributed deep learning training framework
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Horovod is a distributed deep learning training framework. Using horovod, a single-GPU training script can be scaled to train across many GPUs in parallel. The library supports popular deep learning framework such as TensorFlow, Keras, PyTorch, and Apache MXNet.
Numpy - a Python Library
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Numpy is a python package that leverages types and compiled C code to make many math operations in Python efficient. It is especially useful for matrix manipulation and operations.
Git Branching Workflow and Maneuvers
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A couple of resources that:
1.) Presents and defends a git branching workflow for stable collaborative git based projects. ("A Successful Git Branching Model")
2.) Maps "What do you want to do?" to the commands necessary to accomplish it. ("Git Flight Rules")
Open-Source Server Virtualization Platform
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Proxmox Virtual Environment is a hyper-converged infrastructure open-source software. It is a hosted hypervisor that can run operating systems including Linux and Windows on x64 hardware.
Rockfish at Johns Hopkins University
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Resources and User Guide available at Rockfish
Texas A&M HPRC Training Site
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Training Resources and Courses offered by Texas A&M's Research Computing Group
Molecular Dynamics Tutorials for Beginner's
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Links to MD tutorials for beginner's across various simulation platforms.
R for Data Science
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R for Data Science is a comprehensive resource for individuals looking to harness the power of the R programming language for data analysis, visualization, and statistical modeling. Whether you're a beginner or an experienced data scientist, this guide will help you unlock the full potential of R in the realm of data science.
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.
Intro to GenAI Chatbot
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Data Analysis with R for Educators
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This webinar series is an orientation to R. We start with an overview of R’s history and place in the larger data science ecosystem. Next, we introduce the R Studio user interface and how to access R’s excellent documentation. Finally, we present the fundamental concepts you need to use the R environment and language for data analysis. Along the way, we compare R script files (.R) to R Notebook (.Rmd) files and show how the features of R Notebook support better communication and encourage more dynamic engagement with statistical analysis and code. It is helpful to be familiar with tabular data analysis using statistical software, database tools, or spreadsheet programs.
Workshop materials, including setup directions and slides are available at https://github.com/CornellCAC/r_for_edu/ The Rstudio Cloud project used in the workshop is https://rstudio.cloud/project/4044219.
Performance Engineering Of Software Systems
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A class from MITOpenCourseware that gives a hands on approach to building scalable and high-performance software systems. Topics include performance analysis, algorithmic techniques for high performance, instruction-level optimizations, caching optimizations, parallel programming, and building scalable 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.
Introduction to Parallel Computing Tutorial
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The tutorial is intended to provide a brief overview of the extensive and broad topic of Parallel Computing. It covers the basics of parallel computing, and is intended for someone who is just becoming acquainted with the subject .
Data visualization with Matplotlib
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Data visualization is a critical aspect of data analysis. It allows for a clear and concise representation of data, making it easier for users to understand and interpret complex datasets. One of the most popular libraries for data visualization in Python is Matplotlib. The included website aims to provide a brief overview of Matplotlib, its features, and examples/exercises to dive deeper into its functionalities.
An Introduction to the Julia Programming Language
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The Julia Programming Language is one of the fastest growing software languages for AI/ML development. It writes in manner that's similar to Python while being nearly as fast as C++, while being open source, and reproducible across platforms and environments. The following link provide an introduction to using Julia including the basic syntax, data structures, key functions, and a few key packages.
GIS: Projections and their distortions
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In GIS, projections are helpful to take something plotted on a globe and convert it to a flat map that we can print or show on a screen. Unfortunately it also introduces distortions to the objects and features on the map. This not only distorts the objects visually, but the results for any spatial attribute calculations will also reflect this distortion (such as distance and area ). Below is a link to a quick primer on projections, types of distortions that can occur, and suggestions on how to choose a correct projection for your work.
Campus Research Computing Consortium (CaRCC)
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CaRCC – the Campus Research Computing Consortium – is an organization of dedicated professionals developing, advocating for, and advancing campus research computing and data and associated professions.
Vision: CaRCC advances the frontiers of research by improving the effectiveness of research computing and data (RCD) professionals, including their career development and visibility, and their ability to deliver services and resources for researchers. CaRCC connects RCD professionals and organizations around common objectives to increase knowledge sharing and enable continuous innovation in research computing and data capabilities.
Linux Tutorial from Ryan's Tutorials
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The following pages are intended to give you a solid foundation in how to use the terminal, to get the computer to do useful work for you. You won't be a Unix guru at the end but you will be well on your way and armed with the right knowledge and skills to get you there if that's what you want (which you should because that will make you even more awesome). Here you will learn the Linux command line (Bash) with our 13 part beginners tutorial. It contains clear descriptions, command outlines, examples, shortcuts and best practice. At first, the Linux command line may seem daunting, complex and scary. It is actually quite simple and intuitive (once you understand what is going on that is), and once you work through the following sections you will understand what is going on. Unix likes to take the approach of giving you a set of building blocks and then letting you put them together. This allows us to build things to suit our needs. With a bit of creativity and logical thinking, mixed in with an appreciation of how the blocks work, we can assemble tools to do virtually anything we want. The aim is to be lazy. Why should we do anything we can get the computer to do for us? The only reason I can think of is that you don't know how (but after working through these pages you will know how, so then there won't be a good reason). A question that may have crossed your mind is "Why should I bother learning the command line? The Graphical User Interface is much easier and I can already do most of what I need there." To a certain extent you would be right, and by no means am I suggesting you should ditch the GUI. Some tasks are best suited to a GUI, word processing and video editing are great examples. At the same time, some tasks are more suited to the command line, data manipulation (reporting) and file management are some good examples. Some tasks will be just as easy in either environment. Think of the command line as another tool you can add to your belt. As always, pick the best tool for the job.
Singularity/Apptainer User Manuals
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Singularity/Apptainer is a free and open-source container platform that allows users to build and run containers on high performance computing resources.
SingularityCE is the community edition of Singularity maintained by Sylabs, a company that also offers commercial Singularity products and services.
Apptainer is a fork of Singularity, maintained by the Linux foundation, a community of developers and users who are passionate about open source software.