User Guides#
To provide comprehensive guide for HPC users and native cloud users.
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- Home
- Quick Start
- Software Guide
- Macromolecular Modeling and Visualization:
- GROMACS: High Performance Molecular Dynamics
- Pilot Test: Cluster Access and Performance Awareness:
- SLURM Job Submit Guide
- SLURM Array Jobs Guide
- Watchdog & Checkpoint Survival Guide
- Core Principle
- Golden Rules
- 1. Numbered Checkpoints Are Mandatory
- 2. Atomic Writes Prevent Corruption
- 3. Smart Resume Logic
- 4. Checkpoint Interval vs. Risk
- 5. SLURM-Specific: Handle Job Preemption
- 6. SLURM Checkpoint Directory on Persistent Storage
- 7. Progress Metadata Is Unreliable
- 8. Limit Checkpoint Count to Save Disk Space
- SLURM Job Template (Crash-Proof)
- Watchdog / Monitoring Script
- Implementation Checklist
- Anti-Patterns (Don’t Do These)
- Recovery Procedure
- Cost of Getting It Wrong
Math\/Physics tools
Bioinformatics tools
Chemistry and materials science
- ⚗️ NVIDIA ALCHEMI: AI-Powered Chemistry & Materials Simulation at Mahidol
- GPU-Accelerated Atomistic Simulation via NVIDIA NIM Microservices
- 📊 Service Specifications
- 🔬 What Is ALCHEMI?
- 🧪 Use Case 1: BGR — Batched Geometry Relaxation
- 🧪 Use Case 2: BMD — Batched Molecular Dynamics
- 🧪 Use Case 3: Combined BGR + BMD Workflow
- 🔌 Integration with AI Agents (Qwen / Hermes)
- 🧪 Verification & Testing
- 🛠 Troubleshooting
- 📝 Usage Notes
- 📚 References
Large Model tools
- LLaMA
- LoRA: AI at the edge is comming.
- Goolge’s LLM: Gemma
- Responsible AI
- Get Source repository and make them work on K8S for Ollama
- RestAPI test on host that port forwarded
- Multi-lingual capabilities in Llama3.1 405B
- API inferencing check available model :
- 🚀 Using Qwen on the Mahidol Cluster
- Metasearch for AI-Powered Organizations
- OpenClaw — Local Agentic AI Framework
- Hermes Remote HPC + Slack — Research Acceleration Guide
- Table of Contents
- 1. Executive Summary
- 2. Prerequisites
- 3. Step 1: SSH Setup
- 4. Step 2: Install Hermes Locally
- 5. Step 3: Configure Hermes SSH Backend
- 6. Step 4: Slack Gateway Setup
- 7. Step 5: SLURM Job Templates + Singularity
- 8. Step 6: Simple CNN Demo
- 9. Step 7: Automated Research Loop via Hermes Cron
- 10. Step 8: Security Hardening
- 11. Troubleshooting
- 12. Citations
Engineering
- Ansys HFSS
- Gowin FPGA AI Workflow — User Guide
- Mahidol University AI Center · Design House R&D Laboratory
- Executive Summary
- System Architecture
- Technical Perspective
- Quick Start
- FPGA Hardware Setup
- MCP Tools Reference
- Workflow Examples
- Obsidian Integration
- Slack Integration
- Gowin Toolchain Reference
- Security & Operations
- Troubleshooting
- Quick Reference Card
DevOps - AI
- 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
- HPC-AI User Guide: NCCL DDP Multi-Node Training