Welcome to the UCR Research Computing Knowledge Base! This resource hub provides practical guides, how-to articles, and technical information to help you effectively utilize UCR’s research computing resources. Use the categories below or the search bar above to find the information you need.

Getting Started

• Introduction to Research Computing at UCR - A beginner’s guide covering concepts, HPC, cloud, data management, and AI/ML.
• About Research Computing at UCR - Mission, vision, strategy, projects (Ursa Major, RCSAS), grants, and team information.

Computing Resources

High-Performance Computing (HPC)

• What is HPC? - Definition and uses of High-Performance Computing.
• BLAST Searches on the HPCC Cluster - Guide to running BLAST, covering access, partitions, job submission, and optimization.
• Launching and Managing HPC Clusters - Links to guides for launching Ursa Major (GCP) HPC clusters.
• Launching Custom Ursa Major Cluster - Links to UCR-specific custom blueprints and Slurm job examples for Ursa Major.
• HPC Job Scheduling (Slurm) - Connecting to GCP HPC clusters and using basic Slurm commands.
• Ursa Major HPC Clusters - Overview of UCR’s Google Cloud-based, customizable, and scalable HPC service.
• HPCC - Information on UCR’s on-premise High-Performance Computing Center resources, access, and policies.
• Building an HPC Cluster - Technical guide on building HPC clusters with Warewulf, Slurm, and modern tools.
• Comprehensive Guide to Warewulf HPC Cluster Deployment - In-depth guide to Warewulf 4.x, Slurm, and MUNGE deployment.
• Building R1 AAU Research Cluster - Proposal for an AI HPC cluster, comparing with other R1 university resources.
• Open Science Grid - Overview of OSG, its benefits, technologies, and getting started.
• Submit Job to OSG - Guide to submitting HTCondor jobs to the Open Science Grid.
• How to Log Into SDSC Comet and Run a Test Job - Detailed steps for accessing SDSC Comet and submitting a sample job.

Cloud Computing

• Cloud Computing Overview - Summary of UCR’s computing resources including HPC, cloud, and national platforms.
• GCP and AWS Cloud Credits - Information on obtaining and using GCP/AWS cloud credits for research.
• GCP Subscription Agreements - Details on GCP subscription agreements for UCR.
• Mounting Google Cloud Storage - Guide to mounting GCS buckets on Linux using Rclone.
• GCS and AWS S3 - Overview of GCS and AWS S3 storage solutions and their features under UCR’s EDP.
• Google Drive - Information on UCR Google Drive usage, quotas, and best practices for collaborative files.
• Creating a Budget for a Ursa Major/Cloud Project - Guide to setting up GCP budgets with discounts and alerts.
• Globus Transfer - How to use Globus Personal Connect for data transfers between HPCC and external centers.
• Running Genomics Nextflow Pipelines - Guide to using Nextflow on UCR HPCC for genomics.
• Genomics 101 - Fundamental concepts and tools in genomics research.

AI/ML and Edge Computing

• AI/ML Overview - UCR’s AI/ML Hub, covering LLMs, chatbots, software tools, and models.
• AI-Optimized HPC Clusters - Whitepaper on designing and building AI-HPC clusters in 2025.
• Ursa Major Research Services for AI/ML - Overview of AI/ML services available through UCR’s Ursa Major (GCP).
• LLM Inference Settings - Explanation of common inference parameters (Seed, Temperature, Top P/K, etc.).
• Using Gemini for Genomics Research at UCR - Guide on leveraging Google Gemini in genomics, with examples and ethical considerations.
• The Edge AI Revolution - Whitepaper on Edge Computing, AI at the Edge, hardware, software, and challenges.
• Building AI-Optimized High-Performance Computing - Technical guide to AI-HPC cluster architecture and components for 2025.
• Gemini for Physics Researchers - Guide on using Google Gemini in physics research, with applications and practical tips.

Other Computing Resources

• Ursa Major Research Workstations - Overview of customizable, high-performance virtual workstations on Ursa Major (GCP).
• Connecting to a Ursa Major Research Workstation - How-to guide for SSH, RDP, and gcloud connections.
• Launching a Ursa Major Research Workstation - How-to guide for launching workstations via GCP Console or gcloud.
• Research Workstations
• The Nautilus Cluster (Kubernetes)
• Nautilus - Overview of the NRP Nautilus Kubernetes cluster, access, and documentation.
• Linux Manual
• Local Lab Storage
• On-Prem Facilities - Information on UCR’s data centers and on-premise research computing infrastructure.
• Web-Based Research Tools - Listing of available web-based tools for research.
• Accessing SDSC Comet and Running a Test Job - Guide to connecting to SDSC Comet and running a sample Slurm job.
• Using Gemini for Genomics Research at UCR - Guide on leveraging Google Gemini in genomics, with examples and ethical considerations.
• The Edge AI Revolution - Whitepaper on Edge Computing, AI at the Edge, hardware, software, and challenges.
• Building AI-Optimized High-Performance Computing - Technical guide to AI-HPC cluster architecture and components for 2025.
• Gemini for Physics Researchers - Guide on using Google Gemini in physics research, with applications and practical tips.

Interactive Simulations and Visualizations

• Astrophysics 101 - Introductory concepts in astrophysics with interactive elements.
• Earth Carbon Model - A simulation modeling carbon cycles on Earth.
• Earth Model - An interactive model of Earth’s systems.
• HPC Simulation Visualizer - A tool for visualizing HPC job queue and node status (hypothetical description).
• LoRaWAN IoT Visualization - Visualizing data from LoRaWAN IoT devices.
• Solid-State Battery Charging Simulation - An interactive p5.js animation demonstrating electron flow during battery charging with different material properties.
• Interactive Battery Sketch - A p5.js visualization of battery charging dynamics, allowing material and voltage adjustments.

Other Computing Resources

• Storage Overview - Comprehensive guide to UCR’s data storage solutions, specs, costs, and upcoming Ceph RDS.
• Ursa Major Secure Research Storage
• Ursa Major Research Storage - Benefits of Ursa Major (GCP) cloud storage for research data.
• How to: Create a Ursa Major Research Storage Bucket - Guide to creating GCP GCS buckets.
• How to: Access a Ursa Major Research Storage Bucket - Guide to accessing and managing files in GCS buckets.
• S3 Auto Migrate and Delete - Automating data deletion in AWS S3 with lifecycle policies.
• Ceph Secure Research Storage - Information on UCR’s Ceph-based solution (Ceph RDS) for secure research data.
• Dryad - Using the Dryad repository for publishing and archiving research data.
• Ursa Major Data - Overview of data storage and analysis solutions within UCR’s Ursa Major (GCP) environment.

Software and Tools

• Research Software on Ursa Major Cluster - Comprehensive list of software installable via Spack.
• Installing R JAGS on Ursa Major - Guide to installing and testing r-rjags using Spack.
• Molecular Dynamics Simulation Input Files with ChatGPT - Examples of using ChatGPT to generate MD simulation inputs.
• UCR Research Computing Github Org - Access UCR-RC projects, scripts, and documentation.
• Offline LLMs (Ollama) - How to run open-source LLMs on UCR GPU workstations using Ollama.
• UCR Computational Chemistry Software Optimization Report - An interactive report detailing the assessment of computational chemistry software, HPC performance, licensing, and recommendations for UCR’s software stack.
• Computational Chemistry Software Stack Infographic - An interactive infographic detailing the assessment of computational chemistry software, HPC performance, licensing, and recommendations for UCR’s software stack.
• Software and Application Support - Overview of supported software categories at UCR Research Computing.

Research Facilitation

• Research Facilitation Overview - Introduction to UCR’s research computing consultation, training, and support services.
• Grant Colab - Support for incorporating computing resources into grant proposals and finding opportunities.
• Ursa Major Ask - AI-powered tool to generate and execute research computing code and Slurm scripts.

Support and Training

• Lab Support - Tailored computing support for research labs, including infrastructure, software, and workflows.
• UCR Research Computing System Administration Service (RCSAS)
• RCSAS MOU - Memorandum of Understanding for the Research Computing System Administration Service.
• Resources - Directory of UCR Research Computing resources, guides, and partner information.
• Online Courses - Curated list of online courses, tutorials, and videos for research computing, GCP, and ML.
• Workshops and Webinars - Schedule of UCR Research Computing workshops, webinars, and office hours.
• Emerging Research Computing Trends at R1s - Analysis of trends, challenges, and best practices at R1 universities.

Policies and Security

• Policies - Central UCR Research Computing guidelines on resources, data, support, security, and SLAs.
• Ursa Major Policy - Detailed guidelines for UCR’s Ursa Major (GCP) service.
• UCR Data Security Plans
• Research Security - UCR guidelines on data security plans, classification, and compliance (IS-3, NIST, CMMC).
• Backup - Overview of UCR’s data backup solutions including cloud archival and endpoint protection.
• Cost Models - Explanation of funding and cost models for UCR research computing resources.
• GCP, AWS, EDP - Information on UCR’s Enterprise Discount Programs for Google Cloud, AWS, and Azure.
• HPCC GPFS - Information on the HPCC’s General Parallel File System for high-speed storage.
• NSF Access - Guide to the NSF ACCESS program for national cyberinfrastructure resources.

Best Practices

• Data Security in Research Computing - Guidelines for data security plans, classification, and compliance.
• Ursa Major Policy - Detailed guidelines for UCR’s Ursa Major (GCP) service, covering access, usage, data, and security.
• SSH to Access - Basic information on using SSH for accessing resources.
• Building a Mature Research Computing Service - Strategies for developing comprehensive RC services at R1 universities.
• Research Infrastructure Support - Overview of UCR’s RCSAS for on-premise research systems.
• Containerization for Reproducible Research - A tutorial on using Docker or Singularity to create reproducible computational environments for research projects.
• Infographic: Containerization for Reproducible Research - An infographic visually guiding UCR researchers on best practices for using containerization to achieve reproducible research.
• AI Audio Summary: Containerization for Reproducible Research - An AI-generated audio summary of the containerization and reproducibility report. (MP3)