Scripts to run SimPaths and process the results in parallel

Usage

Run in your terminal to copy the code to your machine

git clone [email protected]:MRC-CSO-SPHSU/simpaths_parallel.git

Copy simpaths.jar to simpaths_parallel and run the following:

cd simpaths_parallel
chmod +x ./do_full_run.sh

Typical use would be

./do_full_run.sh -b 20 -p 150000 -s 2017 -e 2023 -g false

or

./do_full_run.sh --batch_size=20 --population_size=150000 --start_year=2017 --end_year=2023 --gui=false

Trailing commas

There is an additional step to clean the ouput data and prepare it to the next stage. Currently, SimPaths leaves trailing commas at the end of all lines in *.csv files which leads to an extra empty column during file reading. To avoid this we run an extra script right after the simulation to remove aforementioned commas from the files. This takes some extra time and relatively expensive in terms of computational resources but leads to correcly formatted data.