The UCL Pandemic modelling tool used for modelling COVID-19. This is available from https://github.com/mrc-ide/covid-sim/

Installation: you will need a compiler module, the cmake module and python3.

So, e.g. module load gnu_comp/9.3.0 python/3.6.5 cmake

This is a cmake build process:

mkdir build
cd build
cmake ../src
make

If using the Intel compiler, the following options can be used:

cmake -DCMAKE_CXX_COMPILER:FILEPATH=icpc DCMAKE_CXX_FLAGS:STRING="-O3 -no-prec-sqrt -no-prec-div -fp-model fast=2 -xAVX" -DOpenMP_CXX_FLAGS:STRING="-qopenmp" -DCMAKE_C_COMPILER:FILEPATH=icc -DCMAKE_C_FLAGS:STRING="-O3 -no-prec-sqrt -no-prec-div -fp-model fast=2 -xAVX" -DOpenMP_C_FLAGS:STRING="-qopenmp" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCOUNTRY:STRING=UK -DUSE_OPENMP:BOOL=ON ../src/

The regression test in tests/ will attempt to compile its own version of the code, e.g. when you run:

python3 regressiontest_UK_100th.py

To avoid this, edit the file and replace the subprocess.check_call lines that call cmake with something appropriate (e.g. nothing, or a cp if copying your CovidSim from elsewhere)

Running

Once you have compiled the code, you can run it using the data/run_sample.py script.

python3 run_sample.py --covidsim=../build/CovidSim --datadir=./ --paramdir=param_files/ --outputdir=outputdir United_Kingdom

Batch script:

#!/bin/bash -l
#SBATCH --ntasks 16
#SBATCH -J covidsim
#SBATCH -o slurmout%J.txt
#SBATCH -e slurmerr%J.txt
#SBATCH -p cosma
#SBATCH -A durham
#SBATCH --exclusive
#SBATCH -t 1:00:00
#SBATCH --mail-type=END
#SBATCH --mail-user=your.email@here
module purge#load the modules used to build your program.
module load intel_comp
module load python/3.6.5
module load cmake
cd data
python3 run_sample.py --covidsim=../build/CovidSim --datadir=./ --paramdir=param_files/ --outputdir=outputdir United_Kingdom