---
title: "SimCov epidemiological simulation"
description: "Run the SimCov agent-based model of SARS-CoV-2 infection dynamics in lung tissue."
type: Tutorial
tags:
  - Simulation
  - Epidemiology
generated:
  by: "claude/fable-5"
  at: "2026-08-29T00:00:00Z"
sources:
  - id: quickbytes
    resource: "https://github.com/UNM-CARC/QuickBytes/blob/master/SimCov.md"
    title: "UNM-CARC QuickBytes: SimCov.md"
    author: "team:unm-carc"
    last_modified: "2022-09-21T16:03:25-06:00"
---

# SimCov epidemiological simulation

This tutorial contains instructions for compiling and running the SimCov immunology model on CARC systems.

## 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 the required modules and set UPCXX variables (NOTE: modules subject to change use 'module spider' to find availability):
```
export UPCXX_THREADMODE=seq
export UPCXX_CODEMODE=opt
module load gcc/11.2.0-otgt
module load cmake/3.22.2-c2dw
module load upcxx/2021.9.0-r4of
```
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 
A sample batch script is provided by the developers. We have submitted the script below to the simcov developers - so hopefully by the time you pull simcov the code below will already be in the repository's sample submission script. If not update the script to contain the following: 
 
This PBS submission script will run simcov on a compute node using covid_default.config:
```
#!/bin/bash

#PBS -q normal
#PBS -l nodes=2:ppn=8
#PBS -l walltime=01:00:00
#PBS -N simcov_test
#PBS -j oe

module load gcc/11.2.0-otgt
module load upcxx/2021.9.0-r4of
module load cmake/3.22.2-c2dw

cd $PBS_O_WORKDIR

upcxx-run -n $PBS_NP -N $PBS_NUM_NODES -- install/bin/simcov --config=covid_default.config --output=results
``` 
To run simcov on a compute node enter
```
qsub wheeler_simcov_run.pbs
```

Outputs will be in a results folder by default

## Video walkthrough

**CS491/591: Computational Immunology — SimCov Compilation and Submission** — from the [CARC video tutorials](../training/videos.md):

<iframe class="carc-video" src="https://www.youtube-nocookie.com/embed/7x3voqNX0QY" title="CS491/591: Computational Immunology \u2014 SimCov Compilation and Submission" loading="lazy" allow="accelerometer; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

<p class="carc-provenance" markdown>Migrated from [UNM-CARC QuickBytes](https://github.com/UNM-CARC/QuickBytes/blob/master/SimCov.md){target=_blank} (last source update 2022-09-21). Spotted a problem? [Open an issue or pull request](https://github.com/UNM-CARC/QuickBytes){target=_blank}.</p>