Knowledge Base Resources
These resources have been contributed and “vetted” by the community of cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators) that are participating in programs such as this one, that are supported by the ConnectCI community management platform. Additional Knowledge Base Resources are always welcome!
Rockfish at Johns Hopkins University
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Resources and User Guide available at Rockfish
Globus Documentation
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Globus is a data transfer, sharing, automation, and discovery service used by hundreds of thousands of researchers to manage "big data" at universities, research labs, and national systems such as ACCESS. The Globus documentation website provides how-to guides, reference documentation, and examples for Globus's web application, command-line interface, Python software development kit (SDK), and APIs.
Bridges-2 Home Page
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Landing Page for Bridges-2 information
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.
CMake Tutorials
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CMake is an open-source tool used to manage the build process in operating systems. This tutorial takes you through how to use CMake from the very basics with example projects.
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.
Raftlib: Open Source library for concurrent data processing pipelines
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Raftlib is an open-source C++ Library that provides a framework for implementing parallel and concurrent data processing pipelines. It is designed to simplify the development of high-performance data processing applications by abstracting away the complexities of parallelism, concurrency, and data flow management.
It enables stream/data-flow parallel computation by linking parallel compute kernels together using simple right shift operators, similar to C++ streams for string manipulation. RaftLib eliminates the need for explicit usage of traditional threading libraries such as pthreads, std::thread, or OpenMP, which can lead to non-deterministic behavior when misused.
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.
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.
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.
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
Termius - Modern ssh platform
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**Termius: The Modern SSH Client for 2023**
Termius is the future-facing SSH client that's redefining remote server access in 2023. Designed for ease and efficiency, Termius offers a seamless connection experience across all devices, be it mobile or desktop. Gone are the days of re-inputting IP addresses, ports, and passwords; with Termius, one-click connectivity is the new norm.
**How Termius Elevates Remote Server Access:**
1. **One-Click Connectivity:** Save the hassle of remembering and re-entering connection details. Termius provides an immediate connection to your infrastructure with a single click.
2. **Synchronized Across Devices:** Termius ensures that your data, connection settings, and preferences are consistent across all your devices, from mobile to desktop.
3. **Unparalleled Security:** With the Cloud Vault feature, users can securely store their data in an encrypted environment, accessible only from their specific devices. Shared vaults allow for safe connection sharing within teams.
4. **AI-Powered Terminal Experience:** Advanced AI-driven autocomplete means users can input command descriptions, and Termius will swiftly convert them into accurate bash commands, simplifying and enhancing the terminal interaction.
5. **Collaborative Troubleshooting:** Share terminal sessions with teammates, facilitating cooperative problem-solving or knowledge sharing. No additional server-side installations needed.
6. **Automation and Snippets:** Streamline routine processes with the ability to save and run frequently used shell scripts. Sharing these Snippets with your team can lead to increased productivity and fewer manual errors.
7. **All-Device Compatibility:** Whether on iPad, iPhone, Android, macOS, Windows, or Linux, Termius ensures a consistent and fluid experience. The platform's synchronization capability means you're always ready to respond swiftly, irrespective of the device in use.
For professionals and businesses aiming for top-notch server access efficiency, Termius is the gold standard in 2023. Experience the revolution in SSH connectivity and optimize your workflow with Termius.
Oakridge Leadership Computing Facility (OLCF) Training Events and Archive
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Upcoming training events and archives of training materials detailing general HPC best practices as well as how to use OLCF resources and services.
Python Tools for Data Science
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Python has become a very popular programming language and software ecosystem for work in Data Science, integrating support for data access, data processing, modeling, machine learning, and visualization. In this webinar, we will describe some of the key Python packages that have been developed to support that work, and highlight some of their capabilities. This webinar will also serve as an introduction and overview of topics addressed in two Cornell Virtual Workshop tutorials, available at https://cvw.cac.cornell.edu/pydatasci1 and https://cvw.cac.cornell.edu/pydatasci2
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.
Docker - Containerized, reproducible workflows
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Docker allows for containerization of any task - basically a smaller, scalable version of a virtual machine. This is very useful when transferring work across computing environments, as it ensures reproducibility.
RMACC Website
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Rocky Mountain Advanced Computing Consortium Website
A survey on datasets for fairness-aware machine learning
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The research paper provides an overview of various datasets that have been used to study fairness in machine learning. It discusses the characteristics of these datasets, such as their size, diversity, and the fairness-related challenges they address. The paper also examines the different domains and applications covered by these datasets.
AI/ML TechLab - Accelerating AI/ML Workflows on a Composable Cyberinfrastructure
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This technology lab contains a set of sessions to help a new user start an AI project on the ACES cluster, a composable accelerator testbed at Texas A&M University. You will learn how to create and activate a virtual environment, manipulate and visualize data with Pandas and Matplotlib, use Scikit-learn for linear regression and classification applications, and use Pytorch to create and train a simple image classification model with deep neural networks (DNN).
AI Institutes Cyberinfrastructure Documents: SAIL Meeting
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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.
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.
InsideHPC
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InsideHPC is an informational site offers videos, research papers, articles, and other resources focused on machine learning and quantum computing among other topics within high performance computing.
Representation Learning in Deep Learning
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Representation learning is a fundamental concept in machine learning and artificial intelligence, particularly in the field of deep learning. At its core, representation learning involves the process of transforming raw data into a form that is more suitable for a specific task or learning objective. This transformation aims to extract meaningful and informative features or representations from the data, which can then be used for various tasks like classification, clustering, regression, and more.
ACCESS KB Guide - Expanse
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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.
UCLA Extended Reality (XR) collaboration resources and Workshop
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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.