User Guides

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

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• 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:
• SLURM Job Submit Guide
  • Basic SLURM Script
  • คำอธิบาย SBATCH Options
  • การใช้ /scratch
  • Multi-GPU Job
  • Multi-Node Job
  • คำสั่งที่ใช้บ่อย

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
  • RStudio Server(Optin II)
  • Troubleshouting Rstudio::
  • Clean Stal files::
  • Start container ::
  • RStudio Customization Library

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
• CellBender Quick-Start Tutorial
  • Introduction
  • Installation
  • Quick-Start Tutorial: remove-background
  • Downstream Analysis
  • Usage Guide: Running on Real Data
  • Examining Output H5 Files
  • Running on HPC (Example: Biowulf/Slurm)
  • Terra / WDL Workflow
  • Command-Line Reference
  • Restarting from Checkpoints
  • Troubleshooting
  • Additional Resources

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Engineering

• Ansys HFSS
  • Create tmp and design folders.
  • Activate singularity and run hfss image
  • Stop singularity instance
• DevOps Engineering HPC & AI
  • Claude Code on Windows + Remote SSH to HPC
  • Part 1: Local Windows Setup
  • Part 2: How the Remote SSH Connection Works
  • Part 3: Connect VS Code to Your HPC
  • Part 4: Install Node.js Locally on HPC (No Module System)
  • Part 5: Install Claude Code on the HPC
  • Part 6: Install the VS Code Extension (Remote Side)
  • Part 7: Authenticate Claude Code
  • Part 8: The “Teleport” Feature
  • Important HPC Considerations
  • Quick Reference: Full Setup Checklist
  • Architecture Diagram