IDSC ACS User Guide

These pages cover common workflows for using IDSC cluster resources. Start here for connection, projects, job scheduling, software environments, containers, and other workflows that apply across supported clusters.

Getting Started

• Quickstart
  • Before You Begin
  • 1. Connect to a Cluster
  • 2. Create a Scratch Working Directory
  • 3. Prepare the Example Files Locally
  • 4. Transfer the Files to the Cluster
  • 5. Verify the Uploaded Files
  • 6. Submit the LSF Job
  • 7. Monitor the Job
  • 8. Inspect the Output
  • 9. Download the Result
  • 10. Disconnect
  • Next Steps
• Important Guidelines
  • Accounts, Projects, and Policies
  • Network Access
  • Use Login Nodes Responsibly
  • Use Scratch Storage for Active Jobs
  • Request Appropriate Job Resources
  • Manage Software with Modules and Environments
  • Use the Data Transfer Node for I/O-Intensive Work
  • Getting Help

Resources and Scheduling

• Projects & Resources
• Job Scheduling
  • LSF Overview
  • Queues
  • Commands
  • Submitting Jobs
  • Monitoring Jobs
  • Examining Jobs
  • Interactive Jobs
  • Serial/Parallel Job Scripts
  • How to Request GPUs
  • Memory Management

Software and Environments

• Software and Modules
  • Software Modules
  • Python
  • Conda and Miniforge
  • R
  • JupyterHub
  • MATLAB
  • Machine Learning Frameworks
  • Workflow Tools
  • Debugging and Profiling Tools
  • Specialized Scientific Software
• Apptainer Containers
  • Quick Start
  • Container Images and Builds
  • Inspecting and Verifying Images
  • Working with Files and Bind Mounts
  • Running Jobs with LSF
  • GPU Containers
  • Troubleshooting Common Issues
  • Practical Examples
  • Advanced Topics

Advanced Workflows

• Parallel Computing
  • Loading the Appropriate MPI Module
  • Sample parallel programs:
  • The LSF script to run parallel jobs

Sylvester HPC

• Sylvester HPC QuickStart
  • How do I get started?
  • Sylvester Utilization
  • Sylvester Dedicated HPC Queues
  • What are specs of available HPC Nodes?
  • How do I reset my IDSC password?
  • How do I access the Secure Network remotely?
  • How do I run Nextflow on Sylvester HPC resources?