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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.

Title Description Category Tags Skill Level Affinity Group
Introduction to Python for Digital Humanities and Computational Research This documentation contains introductory material on Python Programming for Digital Humanities and… more

Documentation        

ai big-data data-analysis more Beginner
PyTorch for Deep Learning and Natural Language Processing PyTorch is a Python library that supports accelerated GPU processing for Machine Learning and Deep… more

Documentation        

ai big-data data-analysis more Beginner
Paraview UArizona HPC links (advanced) These links take you to visualization resources supported by the University of Arizona's HPC… 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… more

Documentation        

ai data-analysis deep-learning more Intermediate, Advanced, Expert
ACCESS KB Guide - Anvil

Documentation        

Anvil
ACCESS KB Guide - DELTA

Documentation        

Delta
ACCESS KB Guide - DELTA

Documentation        

AI Institutes Cyberinfrastructure
ACCESS KB Guide - Expanse

Documentation        

composable-systems gpu Expanse
ACCESS Pegasus Documentation

Documentation        

pegasus Beginner, Intermediate, Advanced, Expert Pegasus
AHPCC documentary This link is a documentary website to use AHPCC.

Documentation        

login batch-jobs slurm more Beginner, Intermediate
Building the ArduPilot environment for Linux This article provides instructions for building AirSim, an open-source simulator for autonomous… more

Documentation        

setup profiling data-transfer more Beginner
CUDA Toolkit Documentation NVIDIA CUDA Toolkit Documentation: If you are working with GPUs in HPC, the NVIDIA CUDA Toolkit is… more

Documentation        

documentation c c++ more Intermediate, Advanced
DARWIN Documentation Pages

Documentation        

big-data DARWIN
Fairness and Machine Learning The "Fairness and Machine Learning" book offers a rigorous exploration of fairness in ML… more

Documentation        

ai data-analysis deep-learning more Intermediate, Advanced, Expert
GIS: Geocoding Services Geocoding is the process of taking a street address and converting it into coordinates that can be… more

Documentation        

geographic-information-system Beginner, Intermediate
Guide to building AirSim on Linux machines This article provides step-by-step instructions on how to build AirSim, a simulator for autonomous… more

Documentation        

documentation setup github more Beginner, Intermediate
Info about retiring of R GIS packages rgdal, rgeos, maptools in 2023 R GIS packages "rgdal", "rgeos", and "maptools" are package set to be… more

Documentation        

r Beginner, Intermediate, Advanced, Expert
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… more

Documentation        

ai big-data data-analysis more Beginner
Jetstream2 Docs Site

Documentation        

jetstream Beginner, Intermediate, Advanced, Expert Jetstream-2
Moving-Lid-Driven Flow Simulation by Finite Difference Method The listed repository contains code written in C++ to model the flow inside a cavity with a lid… more

Documentation        

computational-fluid-dynamics Intermediate
Paraview UArizona HPC links (beginner) These links take you to visualization resources supported by the University of Arizona's HPC… 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… more

Documentation        

ai machine-learning Advanced, Expert
QGIS Processing Executor Running QGIS tools from the command line

Documentation        

geographic-information-system Intermediate
Rockfish at Johns Hopkins University Resources and User Guide available at Rockfish

Documentation        

rockfish Intermediate
Vulkan Support Survey across Systems It's not uncommon to see beautiful visualizations in HPC center galleries, but the majority of… more

Documentation        

anvil bridges-2 darwin more Beginner, Intermediate
What is fairness in ML? This article discusses the importance of fairness in machine learning and provides insights into… more

Documentation        

ai visualization data-analysis more Intermediate
Cornell Virtual Workshop Comprehensive training resource for high performance computing topics. Current tags are just a… more

Learning        

performance-tuning python more Beginner, Intermediate, Advanced, Expert
HPC University A comprehensive list of training resources. The tag list does not represent the full extent of… more

Learning        

python r more 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… 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… more

Learning        

version-control github git Beginner
ACCESS Campus Champion Example Allocation ACCESS requests proposals to be written following NSF proposal guidelines. The link provides an… 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… more

Learning        

big-data deep-learning machine-learning more Beginner, Intermediate AI Institutes Cyberinfrastructure
Active inference textbook This textbook is the first comprehensive treatment of active inference, an integrative perspective… more

Learning        

ai machine-learning neural-networks Beginner, Intermediate, Advanced
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… more

Learning        

data-analysis machine-learning python Beginner, Intermediate
Automated Machine Learning Book The authoritative book on automated machine learning, which allows practitioners without ML… more

Learning        

ai data-analysis deep-learning more Intermediate, Advanced, Expert
Bash shell tutorial Training materials for using the bash (and zsh) shell.

Learning        

bash Intermediate
CHARMM Links to Install, Run, and Troubleshoot MD Simulations CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a widely distributed molecular simulation… more

Learning        

charmm molecular-dynamics namd more Beginner, Intermediate
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… 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… more

Learning        

parallelization gpu cuda 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… more

Learning        

faster file-limit SCRATCH more 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… more

Learning        

ai deep-learning machine-learning more Intermediate
FreeSurfer Tutorials The official MGH / Harvard tutorial page for FreeSurfer. The FreeSurfer group has provided and… 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… 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… more

Learning        

r 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… 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… 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… 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… more

Learning        

optimization performance-tuning profiling more 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… 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… more

Learning        

resources c++ Intermediate, Advanced
Hour of Ci Hour of Cyberinfrastructure (Hour of CI) is a nationwide campaign to introduce undergraduate and… more

Learning        

arcgis Beginner ArcGIS Users
How to use Rclone Learn how to use Rclone to transfer data, specifically from your local drive to the Open Storage… more

Learning        

data-transfer Beginner
Introduction to Parallel Computing Tutorial The tutorial is intended to provide a brief overview of the extensive and broad topic of Parallel… more

Learning        

Beginner
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… 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… more

Learning        

data-analysis machine-learning r 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 more Beginner
MPI Resources Workshop for beginners and intermediate students in MPI which includes helpful exercises. Open MPI… more

Learning        

parallelization mpi Beginner, Intermediate
NCSA HPC Training Moodle Self-paced tutorials on high-end computing topics such as parallel computing, multi-core… more

Learning        

performance-tuning profiling parallelization more Beginner, Intermediate
NCSA HPC-Moodle Self-paced tutorials on high-end computing topics such as parallel computing, multi-core… more

Learning        

technical-training-for-hpc training workforce-development Beginner, Intermediate, Advanced, Expert
NERSC Training and Tutorials A comprehensive collection of NERSC developed training and tutorial events, offered on regular… more

Learning        

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

Learning        

PROFESSIONAL and WORKFORCE DEVELOPMENT technical-training-for-hpc training Beginner, Intermediate, Advanced, Expert
Python Python course offered by Texas A&M HPRC

Learning        

python Beginner
Setting up PyFR flow solver on clusters These instructions were executed on the FASTER and Grace cluster computing facilities at Texas A… more

Learning        

faster computational-fluid-dynamics c++ more Advanced
Slurm Tutorials Introduction to the Slurm Workload Manager for users and system administrators, plus some material… more

Learning        

administering-hpc cluster-management hpc-cluster-architecture more 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… more

Learning        

resources more 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… more

Learning        

PROFESSIONAL and WORKFORCE DEVELOPMENT technical-training-for-hpc jupyterhub more Beginner, Intermediate
Why 'N How: Martinos Center for Biomedical Imaging: The Why & How seminar series is designed to introduce research assistants, graduate students,… 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… more

Learning        

Beginner
Slurm User Group Mailing List

Mailing List        

schedulers slurm
UCLA Extended Reality (XR) collaboration resources and Workshop Comprehensive Extended Reality (XR) collaboration resources for building a high performance… more

Presentation        

documentation setup neural-networks Beginner, Intermediate, Advanced, Expert
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… more

Tool        

finite-element-analysis benchmarking parallelization more Intermediate
DAGMan for orchestrating complex workflows on HTC resources (High Throughput Computing) DAGMan (Directed Acyclic Graph Manager) is a meta-scheduler for HTCondor. It manages dependencies… more

Tool        

open-science-grid Intermediate, Advanced, Expert
Higher Ed Controlled Unclassified Information Slack (HigherEdCUI) Slack channel for the Higher Ed CUI community

Tool        

cybersecurity Cybersecurity for Research Computing
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.… more

Tool        

computational-chemistry materials-science python 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
Quick and Robust Data Augmentation with Albumentations Library Data augmentation is a crucial step in the pipeline for image classification with deep learning.… more

Tool        

deep-learning python Advanced, Expert
Use Windows Subsystem for Linux for HPC Command Line Access from Windows Windows Subsystem for Linux (WSL) provides a Linux environment for Windows users to access HPC… more

Tool        

workflow ssh Beginner
DELTA Introductory Video Introductory video about DELTA. Speaker Tim Boerner, Senior Assistant Director, NCSA

video        

gpu training Delta
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… more

Video Link        

data-analysis data-science psychology more Beginner
Displaying Scientific Data with Tableau Tableau is a popular and capable software product for creating charts that present data and… more

Video Link        

big-data data-analysis technical-training-for-hpc more Intermediate
Python Tools for Data Science Python has become a very popular programming language and software ecosystem for work in Data… more

Video Link        

ai big-data data-analysis more Intermediate
Reinforcement Learning For Beginners with Python This course takes through the fundamentals required to get started with reinforcement learning with… more

Video Link        

deep-learning machine-learning tensorflow more Beginner
WRF in the Public Cloud CAC summer student employee Jeff Lantz describes his experiences in running the WRF weather… more

Video Link        

aws azure cloud-commercial more Advanced
HPC Carpentry An HPC focused Carpentry community. Trainings include: HPC fundamentals, python, chapel, LAMMPS,… more

Website        

software-carpentry training Beginner, Intermediate, Advanced, Expert
Open OnDemand Open OnDemand home page. https://openondemand.org

Website        

more Beginner, Intermediate, Advanced, Expert Open Ondemand
Open OnDemand Open OnDemand home page. https://openondemand.org

Website        

more Beginner, Intermediate, Advanced, Expert AI Institutes Cyberinfrastructure
The Carpentries We teach foundational coding and data science skills to researchers worldwide.

Website        

training Beginner, Intermediate, Advanced, Expert
Neurostars A question and answer forum for neuroscience researchers, infrastructure providers and software… more

Website        

documentation image-processing data-sharing more Beginner, Intermediate, Advanced, Expert
ACCESS Support Portal

Website        

ACCESS Support
ACCESS Support Portal

Website        

AI Institutes Cyberinfrastructure
Anvil Home Page

Website        

Anvil
Ask.CI Q&A Platform for Research Computing

Website        

Beginner, Intermediate, Advanced, Expert Ask.CI Moderators
Better Scientific Software (BSSw) The Better Scientific Software (BSSw) project provides a community to collaborate and learn about… more

Website        

PROFESSIONAL and WORKFORCE DEVELOPMENT community-outreach project-management more Beginner, Intermediate, Advanced, Expert
Bridges-2 Home Page Landing Page for Bridges-2 information

Website        

Bridges-2
Campus Champions Home Page

Website        

community-outreach professional-development Beginner, Intermediate, Advanced, Expert Campus Champions
CaRCC Data Facing Track The Data-Facing Track of the People Network brings together people from research computing groups,… more

Website        

data-access-protocols data-analysis data-compliance Beginner, Intermediate, Advanced, Expert Large Data Sets
ConnectCI Connect.Cybinfrastructure is a family of portals, each representing a program that is serving a… more

Website        

Beginner, Intermediate, Advanced, Expert Connect CI Alliance
Educause HEISC-800-171 Community Group The purpose of this group is to provide a forum to discuss NIST 800-171 compliance. Participants… more

Website        

cybersecurity Cybersecurity for Research Computing
Expanse Home Page

Website        

big-data Expanse
HPCwire HPCwire is a prominent news and information source for the HPC community. Their website offers… more

Website        

documentation bioinformatics pytorch more Beginner, Intermediate, Advanced, Expert
Jetstream Home

Website        

Jetstream-2
Jetstream Home

Website        

AI Institutes Cyberinfrastructure
Jetstream2 Status

Website        

jetstream Beginner, Intermediate, Advanced, Expert Jetstream-2
Mechanism and Implementation of Various MPI Libraries There is a detailed explanation about communication routines and managing methods of different MPI… more

Website        

mpi Beginner
Neurodesk Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of… more

Website        

psychology containers software-installation more Beginner, Intermediate, Advanced
NITRC The Neuroimaging Tools and Resources Collaboratory (NITRC) is a neuroimaging informatics knowledge… more

Website        

data-analysis image-processing data-sharing Beginner, Intermediate, Advanced, Expert
Open Storage Network The Open Storage Network, a national resource available through the XSEDE resource allocation… more

Website        

data-management data-retention more Beginner, Intermediate, Advanced, Expert Large Data Sets
Open Storage Network The Open Storage Network, a national resource available through the XSEDE resource allocation… more

Website        

data-management data-retention more Beginner, Intermediate, Advanced, Expert Open Storage Network
Recommended Libraries for Cyberinfrastructure Users Developing Jupyter Notebooks This repository contains information about Jupyter Widgets and how they can be used to develop… more

Website        

ANALYSES and ALGORITHMS ai big-data more 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… more

Website        

community-outreach cybersecurity Beginner, Intermediate, Advanced, Expert Cybersecurity for Research Computing
Research Security Operations Center at IU The NSF-funded ResearchSOC helps make scientific computing resilient to cyberattacks and capable of… more

Website        

cybersecurity Cybersecurity for Research Computing
Resource to active inference Active inference is an emerging study field in machine learning and computational neuroscience.… more

Website        

ai Beginner, Intermediate, Advanced
RMACC Website Rocky Mountain Advanced Computing Consortium Website

Website        

community-outreach RMACC/Campus Champions Region 8
RRCoP Resources Page Very helpful list of Regulated Research Community of Practice's collaborating communities.

Website        

community-outreach cybersecurity Beginner, Intermediate, Advanced, Expert Cybersecurity for Research Computing
Slurm Scheduling Software Documentation Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling… more

Website        

slurm cluster-support Intermediate, Advanced
Trusted CI The mission of Trusted CI is to lead in the development of an NSF Cybersecurity Ecosystem with the… more

Website        

cybersecurity training Beginner, Intermediate, Advanced, Expert Cybersecurity for Research Computing
Trusted CI Resources Page Very helpful list of external resources from Trusted CI

Website        

cybersecurity Cybersecurity for Research Computing
Tutorial for OpenMP Building up and Utilization The following link elaborates the usage of OpenMP API and its related syntax. There are also… more

Website        

openmp Beginner
Warewulf documentation Warewulf is an operating system provisioning platform for Linux that is designed to produce secure… more

Website        

documentation administering-hpc distributed-computing more Beginner, Intermediate
Women in HPC

Website        

community-outreach Beginner