Knowledge Base Resources

• Carpentries.org

We teach foundational coding and data science skills to researchers worldwide.

• HPC University Resources

A comprehensive list of training resources from the HPC University. HPCU is a virtual organization whose primary goal is to provide a cohesive, persistent, and sustainable on-line environment to share educational and training materials for a continuum of high performance computing environments that span desktop computing capabilities to the highest-end of computing facilities offered by HPC centers.

• Open Ondemand Home Page

Open OnDemand is an easy-to-use web portal that lets students, researchers, and industry professionals use supercomputers from anywhere. It is installed on supercomputing resources at hundreds of sites. By eliminating the need for client software or command-line interface, Open OnDemand empowers users of all skill levels and significantly speeds up the time to their first computing.

• Relion Website

RELION (REgularised LIkelihood OptimisatioN, pronounced rely-on) is a stand-alone software package developed by Sjors Scheres' group at the MRC Laboratory of Molecular Biology. It employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination, specifically for refining multiple 3D reconstructions or 2D class averages.

• ACCESS Pegasus Documentation

The documentation provides an overview of using Pegasus, a workflow management system, on ACCESS resources for high throughput computing (HTC) workloads, covering logging in, workflow creation, resource configuration, and monitoring options.

• PyTorch Documantation

PyTorch is an optimized tensor computation library that supports automatic differentiation and is designed to accelerate deep learning research and production on both GPUs and CPUs. Built with flexibility and performance in mind, PyTorch provides a dynamic computational graph and a rich ecosystem of tools for building and deploying deep learning models.

• HPC Carpentry

An HPC focused Carpentry community. Trainings include: HPC fundamentals, python, chapel, LAMMPS, parallelization with python, scaling studies, etc.

• DARWIN Documentation

DARWIN (Delaware Advanced Research Workforce and Innovation Network) is a big data and high performance computing system designed to catalyze Delaware research and education

• Roadmaps in Cornell Virtual Workshop
• Search for topics

Cornell Virtual Workshop is a comprehensive training resource for high performance computing topics. The Cornell University Center for Advanced Computing (CAC) is a leader in the development and deployment of Web-based training programs. Our Cornell Virtual Workshop learning platform is designed to enhance the computational science skills of researchers, accelerate the adoption of new and emerging technologies, and broaden the participation of underrepresented groups in science and engineering. Over 350,000 unique visitors have accessed Cornell Virtual Workshop training on programming languages, parallel computing, code improvement, and data analysis. The platform supports learning communities around the world, with code examples from national systems such as Frontera, Stampede2, and Jetstream2.

• Open OnDemand Documentation repo

This is the main documentation repo for the Open OnDemand Portal which enables researchers to access HPC resources from a familiar web interface.

• https://www.udacity.com/blog/2021/01/best-r-packages-for-data-science.html

This Udacity article listed the most frequently used R packages for data science and statistics. For each package, the article provided the link to its official documentation. It will be a great start point if you want to start your data science journey in R.

• https://r4ds.had.co.nz/index.html

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.

• MDAnalysis

MDAnalysis is a python based library of tools for the analysis of molecular dynamics simulations. It is able to read and write many popular simulation formats including CHARMM, LAMMPS, GROMACS, and AMBER and more. This link contains the documentation pages of all MDAnalysis functions and has links to tutorials using Jupyter Notebooks.

• DELTA Youtube Video

Introductory video about DELTA. Speaker Tim Boerner, Senior Assistant Director, NCSA

• Anvil Home Page

Purdue University is the home of Anvil, a powerful supercomputer that provides advanced computing capabilities to support a wide range of computational and data-intensive research spanning from traditional high-performance computing to modern artificial intelligence applications.

• Docker Tutorial for Beginners

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.

• Extended Reality (XR) Resource workshop/Guide for Building collaboration

Comprehensive Extended Reality (XR) collaboration resources for building a high performance extended reality (XR), augmented reality (AR), virtual reality (VR) and mixed reality campus teams. The tags set are a small subset of the the topics covered.

• Horovod

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.

• Trusted CI Resources Page

Very helpful list of external resources from Trusted CI

• SSL Configuration Generator

The webpage SSL Configuration Generator by Mozilla provides recommended SSL/TLS configurations for various server platforms, helping administrators enhance security. Users can select their server type, OpenSSL version, and desired security level (Modern, Intermediate, or Old) to generate optimized configurations. The site also includes explanations of best practices and compatibility considerations for different client environments.

• Examples of I/O Files for Mopac

MOPAC (Molecular Orbital PACkage) is a semi-empirical quantum chemistry package used to compute molecular properties and structures by using approximations of the Schrödinger equation. This tutorial explains the process of using MOPAC for different forms of calculations.

• https://www.openmp.org/resources/tutorials-articles/

OpenMP (Open Multi-Processing) is an API that supports multi-platform shared-memory multiprocessing programming in C, C++, and Fortran on many platforms, instruction-set architectures and operating systems, including Solaris, AIX, FreeBSD, HP-UX, Linux, macOS, and Windows. It consists of a set of compiler directives, library routines, and environment variables that influence run-time behavior.

• Probabilistic Semantic Data Association for Collaborative Human-Robot Sensing

Humans cannot always be treated as oracles for collaborative sensing. Robots thus need to maintain beliefs over unknown world states when receiving semantic data from humans, as well as account for possible discrepancies between human-provided data and these beliefs. To this end, this paper introduces the problem of semantic data association (SDA) in relation to conventional data association problems for sensor fusion. It then, develops a novel probabilistic semantic data association (PSDA) algorithm to rigorously address SDA in general settings. Simulations of a multi-object search task show that PSDA enables robust collaborative state estimation under a wide range of conditions.

• Recording of CI ACCESS Talk
• Flyer about ACCESS
• Slides from CI ACCESS Talk

Materials from the SAIL meeting (https://aiinstitutes.org/2023/06/21/sail-2023-summit-for-ai-leadership/). A space where AI researchers can learn about using ACCESS resources for AI applications and research.

• "A Successful Git Branching Model"
• "Git Flight Rules"

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")