SpatialRust is an individual based model that simulates Coffee Leaf Rust epidemics within a coffee farm.
Move to this project's directory and run:
$ julia install.jl
There are two script files available. You can run a single simulation using a fixed parameter set using scripts/OneRun.jl
as follows:
$ julia scripts/OneRun.jl
Results from this single run will be saved in a results
folder as singlerun.csv
.
The second option, scripts/ParameterRuns.jl
, lets you run a parameter exploration experiment. The default setup of this experiment will run 880 simulations. To modify the parameter values to be evaluated or the replicates for each combination, open scripts/ParameterRuns.jl
and edit lines 7 to 11. Like the first option, you can run the script from bash:
$ julia scripts/ParameterRuns.jl
Results from this experiment will be saved in a results
folder as parameterexp.csv
. Both scripts take care of creating the results
folder if it has not been created yet.
- Establish an account on Open Science Grid https://osg-htc.org/research-facilitation/accounts-and-projects/general/index.html
- Create a host alias for your OSG account (https://github.com/comses-education/fair-osg-template#set-up-your-user-account-on-the-open-science-grid)
- Build a singularity image and deploy it to your OSG
/public/<username>
directory via$ make OSG_USERNAME=<your-osg-username> deploy
- ssh into the OSG login node, cd into the
spatialrust
directory and submit the generatedspatialrust.submit
via$ condor_submit spatialrust.submit
- this runs the ParameterRuns.jl on OSG and should drop off a
results.zip
file with the data in the same directory you submitted the job script.