HPC Deployment

SMINT is designed to run efficiently on High-Performance Computing (HPC) clusters, taking advantage of multiple CPUs and GPUs for processing large spatial omics datasets. This page explains how to deploy SMINT on SLURM-based HPC systems.

Overview

Running SMINT on an HPC cluster involves the following steps:

1. Install SMINT on the HPC system
2. Prepare your configuration file
3. Submit jobs using SLURM submission scripts
4. Monitor job progress
5. Collect and analyze results

Installation on HPC

Using Environment Modules

Most HPC systems use environment modules. Load the required modules and install SMINT:

```bash

Load required modules

module load python/3.8 module load cuda/11.3 module load miniconda3

Create a conda environment

conda create -n smint python=3.8 conda activate smint

Install SMINT

pip install smint