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CI Links

These CI links have been crowd-sourced from the ConnectCI community and represent a “vetted” list of useful websites, training modules and tutorials. CI links show up in a tag search if they have the relevant tag attached. Affinity groups can include relevant CI links on their respective affinity group pages. Additional CI links are always welcome, click the “Add New CI Link” button to suggest one.

Cornell Virtual Workshop

Comprehensive training resource for high performance computing topics. Current tags are just a small subset of topics covered.

Learning

performance-tuning python

Beginner, Intermediate, Advanced, Expert

HPC University

A comprehensive list of training resources. The tag list does not represent the full extent of topics covered.

Learning

python r

Beginner, Intermediate, Advanced, Expert

HPC Carpentry

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

Website

software-carpentry training

Beginner, Intermediate, Advanced, Expert

Introduction to Python for Digital Humanities and Computational Research

This documentation contains introductory material on Python Programming for Digital Humanities and Computational Research. This can be a go-to… more

Documentation

ai big-data data-analysis

Beginner

Open OnDemand

Open OnDemand home page. https://openondemand.org

Website

Beginner, Intermediate, Advanced, Expert

PyTorch for Deep Learning and Natural Language Processing

PyTorch is a Python library that supports accelerated GPU processing for Machine Learning and Deep Learning. In this tutorial, I will teach the… more

Documentation

ai big-data data-analysis

Beginner

The Carpentries

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

Website

training

Beginner, Intermediate, Advanced, Expert

Using Linux commands in a python script (and the difference between the subprocess and os python modules)

Learn how to use Linux commands in a python script. Specifically, learn how to use the subprocess and os modules in python to run shell commands (… more

Learning

programming python

Beginner, Intermediate

Version control with Git

Understand the benefits of an automated version control system and the basics of how automated version control systems work. Configure git the first… more

Learning

version-control github git

Beginner

Neurostars

A question and answer forum for neuroscience researchers, infrastructure providers and software developers.

Website

documentation image-processing data-sharing

Beginner, Intermediate, Advanced, Expert

Paraview UArizona HPC links (advanced)

These links take you to visualization resources supported by the University of Arizona's HPC visualization consultant ([rtdatavis.github.io](… more

Documentation

Intermediate, Advanced

A survey on datasets for fairness-aware machine learning

The research paper provides an overview of various datasets that have been used to study fairness in machine learning. It discusses the… more

Documentation

ai data-analysis deep-learning

Intermediate, Advanced, Expert

ACCESS Campus Champion Example Allocation

ACCESS requests proposals to be written following NSF proposal guidelines. The link provides an example of an ACCESS proposal using an NSF LaTeX… more

Learning

allocations-proposal proposal-request research-facilitation

Beginner

ACCESS HPC Workshop Series

Monthly workshops sponsored by ACCESS on a variety of HPC topics organized by Pittsburgh Supercomputing Center (PSC). Each workshop will be telecast… more

Learning

big-data deep-learning machine-learning

Beginner, Intermediate

ACCESS KB Guide - Anvil

Documentation

ACCESS KB Guide - DELTA

Documentation

ACCESS Pegasus Documentation

Documentation

pegasus

Beginner, Intermediate, Advanced, Expert

Active inference textbook

This textbook is the first comprehensive treatment of active inference, an integrative perspective on brain, cognition, and behavior used across… more

Learning

ai machine-learning neural-networks

Beginner, Intermediate, Advanced

AHPCC documentary

This link is a documentary website to use AHPCC.

Documentation

login batch-jobs slurm

Beginner, Intermediate

Anvil Home Page

Website

Applications of Machine Learning in Engineering and Parameter Tuning Tutorial

Slides for a tutorial on Machine Learning applications in Engineering and parameter tuning given at the RMACC conference 2019.

Learning

data-analysis machine-learning python

Beginner, Intermediate

Ask.CI Q&A Platform for Research Computing

Website

Beginner, Intermediate, Advanced, Expert

Automated Machine Learning Book

The authoritative book on automated machine learning, which allows practitioners without ML expertise to develop and deploy state-of-the-art machine… more

Learning

ai data-analysis deep-learning

Intermediate, Advanced, Expert

Bash shell tutorial

Training materials for using the bash (and zsh) shell.

Learning

bash

Intermediate

Benchmarking with a cross-platform open-source flow solver, PyFR

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… more

Tool

finite-element-analysis benchmarking parallelization

Intermediate

Better Scientific Software (BSSw)

The Better Scientific Software (BSSw) project provides a community to collaborate and learn about best practices in scientific software development.… more

Website

PROFESSIONAL and WORKFORCE DEVELOPMENT community-outreach project-management

Beginner, Intermediate, Advanced, Expert

Bridges-2 Home Page

Landing Page for Bridges-2 information

Website

Campus Champions Home Page

Website

community-outreach professional-development

Beginner, Intermediate, Advanced, Expert

CaRCC Data Facing Track

The Data-Facing Track of the People Network brings together people from research computing groups, libraries, research institutes, and other… more

Website

data-access-protocols data-analysis data-compliance

Beginner, Intermediate, Advanced, Expert

CHARMM Links to Install, Run, and Troubleshoot MD Simulations

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a widely distributed molecular simulation program with a broad array of applications.… more

Learning

charmm molecular-dynamics namd

Beginner, Intermediate

ConnectCI

Connect.Cybinfrastructure is a family of portals, each representing a program that is serving a segment of the research computing and data community… more

Website

Beginner, Intermediate, Advanced, Expert

CUDA Toolkit Documentation

NVIDIA CUDA Toolkit Documentation: If you are working with GPUs in HPC, the NVIDIA CUDA Toolkit is essential. You can access the CUDA Toolkit… more

Documentation

documentation c c++

Intermediate, Advanced

Data Analysis with R for Educators

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… more

Video Link

data-analysis data-science psychology

Beginner

DELTA Introductory Video

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

video

gpu training

Displaying Scientific Data with Tableau

Tableau is a popular and capable software product for creating charts that present data and dashboards that allow you to explore data. It is… more

Video Link

big-data data-analysis technical-training-for-hpc

Intermediate

Educause HEISC-800-171 Community Group

The purpose of this group is to provide a forum to discuss NIST 800-171 compliance. Participants are encouraged to collaborate and share effective… more

Website

cybersecurity

Examples of code using JSON nlohmann header only Library for C++

This code showcases how to work with the header-only nlohmann JSON library for C++. In order to compile, change the extensions from json_test.txt to… more

Learning

c++

Advanced

Examples of Thrust code for GPU Parallelization

Some examples for writing Thrust code. To compile, download the CUDA compiler from NVIDIA. This code was tested with CUDA 9.2 but is likely… more

Learning

parallelization gpu cuda

Intermediate, Advanced, Expert

Fairness and Machine Learning

The "Fairness and Machine Learning" book offers a rigorous exploration of fairness in ML and is suitable for researchers, practitioners,… more

Documentation

ai data-analysis deep-learning

Intermediate, Advanced, Expert

File management of Visual Studio Code on clusters

Visual Studio Code, commonly known as VSCode, is a popular tool used by programmers worldwide. It serves as a text editor and an Integrated… more

Learning

faster file-limit SCRATCH

Intermediate

Framework to help in scaling Machine Learning/Deep Learning/AI/NLP Models to Web Application level

This framework will help in scaling Machine Learning/Deep Learning/Artificial Intelligence/Natural Language Processing Models to Web Application… more

Learning

ai deep-learning machine-learning

Intermediate

FreeSurfer Tutorials

The official MGH / Harvard tutorial page for FreeSurfer. The FreeSurfer group has provided and designed a series of tutorials for using FreeSurfer… more

Learning

data-analysis image-processing psychology

Beginner, Intermediate

FSL Lectures

This is the official University of Oxford FSL group lecture page. This includes information on upcoming and past courses (online and in-person), as… more

Learning

data-analysis image-processing psychology

Beginner, Intermediate, Advanced

GDAL Multi-threading

Multi-threading guidance when using GDAL.

Learning

parallelization geographic-information-system

Intermediate

Geocomputation with R (Free Reference Book)

Below is a link for a book that focuses on how to use "sf" and "terra" packages for GIS computations. As of 5/1/2023, this book… more

Learning

r

Beginner, Intermediate

GIS: Geocoding Services

Geocoding is the process of taking a street address and converting it into coordinates that can be plotted on a map. This conversion typically… more

Documentation

geographic-information-system

Beginner, Intermediate

GIS: Projections and their distortions

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.… more

Learning

geographic-information-system

Beginner, Intermediate

GIS: What is a Geodetic Datums?

Often when working with GIS, or spatial data, one encounters the word "datum" and it may require that you choose a "datum" when… more

Learning

FIELD of SCIENCE

Beginner

Git Branching Workflow and Maneuvers

A couple of resources that:

1.) Presents and defends a git branching workflow for stable collaborative git based projects. ("A… more

Learning

github git

Beginner, Intermediate, Advanced

GPU Computing Workshop Series for the Earth Science Community

GPU training series for scientists, software engineers, and students, with emphasis on Earth science applications.

The content of this… more

Learning

optimization performance-tuning profiling

Beginner

Harnessing the Power of Cloud and Machine Learning for Climate and Ocean Advances

Documentation and presentation on how to use machine learning and deep learning framework using TensorFlow, Keras and sci-kit learn for Climate and… more

Learning

CLOUD machine-learning

Intermediate

Header-only C++ JSON library

JSON is a lightweight format for storing and transporting data, for example in a config file. This library is header-only, and has easy-to-read… more

Learning

resources c++

Intermediate, Advanced

Higher Ed Controlled Unclassified Information Slack (HigherEdCUI)

Slack channel for the Higher Ed CUI community

Tool

cybersecurity

Hour of Ci

Hour of Cyberinfrastructure (Hour of CI) is a nationwide campaign to introduce undergraduate and graduate students to cyberinfrastructure and… more

Learning

arcgis

Beginner

How to use Rclone

Learn how to use Rclone to transfer data, specifically from your local drive to the Open Storage Network, vice versa.

Learning

data-transfer

Beginner

HPCwire

HPCwire is a prominent news and information source for the HPC community. Their website offers articles, analysis, and reports on HPC technologies,… more

Website

documentation bioinformatics pytorch

Beginner, Intermediate, Advanced, Expert

Info about retiring of R GIS packages rgdal, rgeos, maptools in 2023

R GIS packages "rgdal", "rgeos", and "maptools" are package set to be archived and no longer supported by end of 2023… more

Documentation

r

Beginner, Intermediate, Advanced, Expert

Introduction to Parallel Computing Tutorial

The tutorial is intended to provide a brief overview of the extensive and broad topic of Parallel Computing. It covers the basics of parallel… more

Learning

Beginner

Introductory Tutorial to Numpy and Pandas for Data Analysis

In this tutorial, I present an overview with many examples of the use of Numpy and Pandas for data analysis. Beginners in the field of data analysis… more

Documentation

ai big-data data-analysis

Beginner

Jetstream Home

Website

Jetstream2 Docs Site

Documentation

jetstream

Beginner, Intermediate, Advanced, Expert

Jetstream2 Status

Website

jetstream

Beginner, Intermediate, Advanced, Expert

Language models and using HPC resources

Documentation and research based on the latest NLP text generation detection methods for 2023.

Learning

ACCESS RPs

Intermediate

Linux Tutorial from Ryan's Tutorials

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… more

Learning

file-systems bash unix-environment

Beginner

Machine Learning in R online book

The free online book for the mlr3 machine learning framework for R. Gives a comprehensive overview of the package and ecosystem, suitable from… more

Learning

data-analysis machine-learning r

Beginner, Intermediate, Advanced, Expert

MDAnalysis - Python library for the analysis of molecular dynamics simulations

MDAnalysis is a python based library of tools for the analysis of molecular dynamics simulations. It is able to read and write many popular… more

Tool

computational-chemistry materials-science python

Beginner, Intermediate, Advanced, Expert

Molecular Dynamics Tutorials for Beginner's

Links to MD tutorials for beginner's across various simulation platforms.

Learning

cloud-computing amber charmm

Beginner

MPI Resources

Workshop for beginners and intermediate students in MPI which includes helpful exercises. Open MPI documentation.

Learning

parallelization mpi

Beginner, Intermediate

NCSA HPC Training Moodle

Self-paced tutorials on high-end computing topics such as parallel computing, multi-core performance, and performance tools. Other related topics… more

Learning

performance-tuning profiling parallelization

Beginner, Intermediate

NERSC Training and Tutorials

A comprehensive collection of NERSC developed training and tutorial events, offered on regular schedules. All sessions are archived, including slide… more

Learning

PROFESSIONAL and WORKFORCE DEVELOPMENT technical-training-for-hpc training

Beginner, Intermediate, Advanced, Expert

Neurodesk

Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for… more

Website

psychology containers software-installation

Beginner, Intermediate, Advanced

NITRC

The Neuroimaging Tools and Resources Collaboratory (NITRC) is a neuroimaging informatics knowledge environment for MR, PET/SPECT, CT, EEG/MEG,… more

Website

data-analysis image-processing data-sharing

Beginner, Intermediate, Advanced, Expert

Oakridge Leadership Computing Facility (OLCF) Training Events and Archive

Upcoming training events and archives of training materials detailing general HPC best practices as well as how to use OLCF resources and services.

Learning

PROFESSIONAL and WORKFORCE DEVELOPMENT technical-training-for-hpc training

Beginner, Intermediate, Advanced, Expert

Open Storage Network

The Open Storage Network, a national resource available through the XSEDE resource allocation system, is high quality, sustainable, distributed… more

Website

data-management data-retention

Beginner, Intermediate, Advanced, Expert

OpenMP and Multithreaded Jobs in GRASS

Techniques and support for multithreaded geospatial data processing in GRASS.

Tool

parallelization geographic-information-system openmp

Intermediate

Paraview UArizona HPC links (beginner)

These links take you to visualization resources supported by the University of Arizona's HPC visualization consultant (rtdatavis.github.io). The… more

Documentation

Beginner

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… more

Documentation

ai machine-learning

Advanced, Expert

Python

Python course offered by Texas A&M HPRC

Learning

python

Beginner

Python Tools for Data Science

Python has become a very popular programming language and software ecosystem for work in Data Science, integrating support for data access, data… more

Video Link

ai big-data data-analysis

Intermediate

QGIS Processing Executor

Running QGIS tools from the command line

Documentation

geographic-information-system

Intermediate

Quick and Robust Data Augmentation with Albumentations Library

Data augmentation is a crucial step in the pipeline for image classification with deep learning. Albumentations is an extremely versatile Python… more

Tool

deep-learning python

Advanced, Expert

Recommended Libraries for Cyberinfrastructure Users Developing Jupyter Notebooks

This repository contains information about Jupyter Widgets and how they can be used to develop interactive workflows, data dashboards, and web… more

Website

ANALYSES and ALGORITHMS ai big-data

Beginner, Intermediate, Advanced, Expert

Regulated Research Community of Practice

The daily news clearly shows the increasing threat to safety and privacy of data, personal as well as intellectual property. While the requirements… more

Website

community-outreach cybersecurity

Beginner, Intermediate, Advanced, Expert

Research Security Operations Center at IU

The NSF-funded ResearchSOC helps make scientific computing resilient to cyberattacks and capable of supporting trustworthy, productive research… more

Website

cybersecurity

Resource to active inference

Active inference is an emerging study field in machine learning and computational neuroscience. This website in particular introduces "active… more

Website

ai

Beginner, Intermediate, Advanced

RMACC Website

Rocky Mountain Advanced Computing Consortium Website

Website

community-outreach

Rockfish at Johns Hopkins University

Resources and User Guide available at Rockfish

Documentation

rockfish

Intermediate

RRCoP Resources Page

Very helpful list of Regulated Research Community of Practice's collaborating communities.

Website

community-outreach cybersecurity

Beginner, Intermediate, Advanced, Expert

Setting up PyFR flow solver on clusters

These instructions were executed on the FASTER and Grace cluster computing facilities at Texas A&M University. However, the process can be… more

Learning

faster computational-fluid-dynamics c++

Advanced

Slurm Scheduling Software Documentation

Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Slurm… more

Website

slurm cluster-support

Intermediate, Advanced

Slurm Tutorials

Introduction to the Slurm Workload Manager for users and system administrators, plus some material for Slurm programmers.

Learning

administering-hpc cluster-management hpc-cluster-architecture

Beginner

Texas A&M HPRC Training Site

Training Resources and Courses offered by Texas A&M's Research Computing Group

Learning

Beginner, Intermediate, Advanced, Expert

Thrust resources

Thrust is a CUDA library that optimizes parallelization on the GPU for you. The Thrust tutorial is great for beginners. The documentation is helpful… more

Learning

resources

Intermediate, Advanced, Expert

Trusted CI

The mission of Trusted CI is to lead in the development of an NSF Cybersecurity Ecosystem with the workforce, knowledge, processes, and… more

Website

cybersecurity training

Beginner, Intermediate, Advanced, Expert

Trusted CI Resources Page

Very helpful list of external resources from Trusted CI

Website

cybersecurity

UCLA Extended Reality (XR) collaboration resources and Workshop

Comprehensive Extended Reality (XR) collaboration resources for building a high performance extended reality (XR), augmented reality (AR), virtual… more

Presentation

documentation setup neural-networks

Beginner, Intermediate, Advanced, Expert

UNIX/command line basics tutorial

Introductory training materials for working on the UNIX command line.

Learning

bash

Beginner

Using Dask on HPC Systems

A tutorial on the effective use of Dask on HPC resources. The four-hour tutorial will be split into two sections, with early topics focused on novice… more

Learning

PROFESSIONAL and WORKFORCE DEVELOPMENT technical-training-for-hpc jupyterhub

Beginner, Intermediate

Vulkan Support Survey across Systems

It's not uncommon to see beautiful visualizations in HPC center galleries, but the majority of these are either rendered off the HPC or created… more

Documentation

anvil bridges-2 darwin

Beginner, Intermediate

What is fairness in ML?

This article discusses the importance of fairness in machine learning and provides insights into how Google approaches fairness in their ML models.… more

Documentation

ai visualization data-analysis

Intermediate

Why 'N How: Martinos Center for Biomedical Imaging:

The Why & How seminar series is designed to introduce research assistants, graduate students, and postdoctoral and clinical fellows – really,… more

Learning

image-processing

Beginner, Intermediate, Advanced

Wiki for Onboarding onto the C3DDB Cluster at MGHPCC

This is a resource for researchers and students looking to on-board onto the c3ddb cluster at MGHPCC. In the code section, there are example job… more

Learning

Beginner

Women in HPC

Website

community-outreach

Beginner

WRF in the Public Cloud

CAC summer student employee Jeff Lantz describes his experiences in running the WRF weather forecasting application in the public cloud. He compares… more

Video Link

aws azure cloud-commercial

Advanced