User Guides

To provide comhensive guide for HPC users and native cloud users.

Danger

This guide is still under active development, and we make no promises about the reliability of content. Your feedback and contribution help improving document.

Get started

• Home
  • Getting Started
  • How-To: Contribute to this Document
• Quick Start
  • Prelude Instructions
• Software Guide
  • RNA and ChIP-sequencing analysis
  • Single Particle Analysis:
  • Software Define Radio and Cloud Radio Access Network:
• Macromolecular Modeling and Visualization:
  • Amber:
  • VMD:
• GROMACS: High Performance Molecular Dynamics
  • Example GROMACS on 4 GPUs 128CPU MPIs
  • Download Benchmark Dataset
  • Run on Singularity:
  • Performance x 2 with Direct GPUs NVLINK
• Pilot Test: Cluster Access and Performance Awareness:
  • Given Test at:
  • Features:
  • Principal investigators (PIs) or Project Owners:
  • HPC system administrators:
  • Center directors:

Math\/Physics tools

• Mathematical modeling in Physics Engineering, Biological and Social Science with QwQ LLM from China
  • Prompt:
  • Response:
  • Interpretation:
  • References:
• Quantum Machine Learning
  • Quantum-classical hybrid paradigm and variational quantum algorithms
  • Covalent
  • Quantum computing with Dask Parallel:
• Mathematics and Statistics Tools
  • MATLAB singularity with License server enabled
  • RStudio on Jupyter with The Rocker Project
    • How to
  • RStudio Server(outdate)

Bioinformatics tools

• Biomedical Application
  • BLAST
  • Allocate resource for testing
  • Making example file
  • Blasting
• Reproducting research results with Python and Conda Package management
  • How to
• Nextflow:Reproducible scientific workflows
  • Run Nextflow core or nf-core AlphaFold2 workflow
• AlphaFold 3 : The inference pipeline
  • Dataset
  • ALPHAFOLD 3 MODEL PARAMETERS TERMS OF USE
  • Step 0: Clone Alphafold 3 source code
  • Step 1: Create Alphafold 3 input
  • Step 2: Run Alphafold 3 in container, Singularity
  • Step 3: View oupput
  • Reference:
• NVIDIA Parabricks
  • Test on a compute node
  • EXAMPLE RUN

ollama llm

Engineering

• Ansys HFSS
  • Create tmp and design folders.
  • Activate singularity and run hfss image
  • Stop singularity instance