Basics

• Home
  • Getting Started
  • How-To: Contribute to this Document
• Quick Start
  • Prelude Instructions
• 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:
• Mathematical modeling in Physics Engineering, Biological and Social Science with QwQ LLM from China
  • Prompt:
  • Response:
  • Interpretation:
  • References:
• Mathematics and Statistics Tools
  • MATLAB singularity with License server enabled
  • RStudio on Jupyter with The Rocker Project
    • How to
  • RStudio Server(outdate)
• Excel Macro Runner Docker
• Apptainer/Singularity
  • Basic Usage
  • Build Apptainer Image without root privilage
• Workshop
  • HPC Basic
• 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:
• Electrical Energy Saving
  • What are peak hours?
  • What are off-peak hours?
  • Recommend to submit job to schedule running during OFF PEAK
• Quantum Machine Learning
  • Quantum-classical hybrid paradigm and variational quantum algorithms
  • Covalent
  • Quantum computing with Dask Parallel:
• Pytorch DISTRIBUTED DATA PARALLEL
  • Multi-node Multi-GPU Training
  • Toy model with PyTorch
• NVIDIA Parabricks
  • Test on a compute node
  • EXAMPLE RUN
• Cryogenic electron microscopy
• Relion 4.0 for cryo-EM structure determination
  • Relion 3 or 4 on Exascale Cluster with Singularity
  • Download Data
  • Signle particle tutorial
• Computational Imaging System for Transmission Electron Microscopy(cisTEM)
  • Run cisTEM on a DGX-A100
  • Download Data
• LLaMA
• LoRA: AI at the edge is comming.
• Goolge’s LLM: Gemma
• Responsible AI
  • Inference Gemma on DGX A100:
  • Get up and running with large language models on private cloud
• Get Source repository and make them work on K8S for Ollama
• RestAPI test on host that port forwarded
  • New LLaMa 3.1 NOW suport Thai
• Multi-lingual capabilities in Llama3.1 405B
• API inferencing check available model :
  • Build LLM Apps with Low-code
• Extreme-scale Scientific Software Stack (E4S)
  • Run with Container
  • Parallel Electronic Simulation
• 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