SimCov epidemiological simulation¶

This tutorial contains instructions for compiling and running the SimCov immunology model on the Hopper cluster.

Download the SimCov Source Code from GitHub¶

Change directory to your home:

cd ~

Clone the simcov Github repository into your home directory:

git clone --recurse-submodules https://github.com/AdaptiveComputationLab/simcov.git

Build SimCov from Source¶

Load Hopper modules and set UPCXX variables (NOTE: modules subject to change use 'module spider' to find availability). UPC++ is currently only available as a module on Hopper, not Easley, so this needs to run on Hopper:

export UPCXX_THREADMODE=seq
export UPCXX_CODEMODE=opt
module load gcc/8.5.0-lpgx
module load cmake/3.31.6-qm2s
module load upcxx/2022.3.0-yrwd
module load openmpi/3.1.6-qpl3
export CXX=$(which mpic++)

Run the build script:

cd simcov
./build.sh Release

Configure SimCov¶

The config files are in ~/simcov and end with ".config". You can edit them with a text editor.

Submit a SimCov Job¶

This Slurm submission script will run simcov on a compute node using covid_default.config:

#!/bin/bash

#SBATCH --job-name simcov_test
#SBATCH --partition general
#SBATCH --nodes 2
#SBATCH --ntasks-per-node 8
#SBATCH --time 01:00:00
#SBATCH --output simcov_test.out
#SBATCH --error simcov_test.err

module load gcc/8.5.0-lpgx
module load upcxx/2022.3.0-yrwd
module load cmake/3.31.6-qm2s

cd $SLURM_SUBMIT_DIR

upcxx-run -n $SLURM_NTASKS -N $SLURM_NNODES -- install/bin/simcov --config=covid_default.config --output=results

To run simcov on a compute node enter

sbatch hopper_simcov_run.sh

Outputs will be in a results folder by default

Video walkthrough¶

CS491/591: Computational Immunology — SimCov Compilation and Submission — from the CARC video tutorials:

Migrated from UNM-CARC QuickBytes (last source update 2022-09-21). Spotted a problem? Open an issue or pull request.

Machine-readable versions of this page: Markdown twin · raw source on GitHub · llms.txt · llms-full.txt (whole site). See For AI agents.