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The Emory RSPH HPC

Below are general instructions to accessing and using the Emory RSPH high-performance computing (HPC) cluster. This cluster contains a computational platform for running our lab group's modeling simulations and analyses. Follow these steps to get started.

1. Registering for and logging in to HPC
2. Setting up your HPC environment
3. Working with files on the HPC
4. Using git on the command line to access Github repositories
5. Using R via Spack on the HPC
6. Running R interactively with srun
7. Running R with a batch job with sbatch
8. Running complex workflows with slurmworkflow

Coding Tips

These are general coding tips and suggestions for work across our software packages and applied modeling projects.

1. Interactively writing and debugging EpiModel code
2. Diagnostic of an EpiModel module
3. Running network models with checkpoints
4. Assorted tips and tricks for Windows Users
5. Access to the ARTnet Dataset
6. Copying a private branch to a public repository on Github

Applied Modeling Workflow

If you are starting a new applied modeling project (either with EpiModelHIV or EpiModelCOVID), we recommend you follow the general steps listed in the following two tutorials.

• Getting Started with EpiModelHIV

• Getting Started with EpiModelCOVID - coming soon

• EpiModelHIV ‐ New Parameters and Attributes

• Programatically Defining Scenarios

• Processing Scenarios Tibbles

• Making Formatted Tables

• Applied Modeling Project Structure

• Applied Modeling Project Components and Interactions

• Automated Calibration with swfcalib

• Code Conventions

Admin Infos

• Misc
• Spack Environments