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:

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