The results from the simulations, which were run on a dedicated HPC
cluster, are stored in the results folder. The figures and
tables in the paper, generated from these results, are stored in
figures/
and tables/
respectively.
The results from our paper were run through a singularity container. Check the releases for pre-built singularity containers that you can download and use.
To reproduce the results, always use the singularity container. To run an experiment from the singularity container, call
singularity run --bind results:/project/results container.sif <script>
where <script>
should be a name of a script in the experiments
folder, such as simulateddata.R
.
If you want to re-build the singularity container from scratch (or simply want to clone the repo to your local drive), you can do so via the following steps.
-
Make sure you have installed and enabled Git-LFS. On ubuntu, for instance, you can install Git-LFS by calling
sudo apt update sudo apt install git-lfs
Then activate git-lfs by calling
git lfs install
-
Clone the repository to your local hard drive. On linux, using SSH authentication, run
git clone git@github.com:jolars/HessianScreening.git
-
Navigate to the root of the repo and build the singularity container by calling
cd HessianScreening sudo singularity build container.sif Singularity
Then proceed as in Reproducing the Results to run the experiments.
Alternatively, you may also reproduce the results by cloning this
repository, then either opening the HessianScreening.Rproj
file in R
Studio or starting R in the root directory of this folder (which will
activate the renv repository) and then run
renv::restore()
to restore the project library. Then build the R package (see below) and run the simulations directly by running the scripts in the experiments folder. This is not recommended, however, since it, unlike the Singularity container approach, does not exactly reproduce the software environment used when these simulations where originally run and may result in discrepancies due to differences in for instance operating systems, compilers, and BLAS/LAPACK implementations.
If you want to build and experiment with the package, you can do so by calling
R CMD INSTALL .
provided you have cd
ed to the root folder of this repository. First
ensure, however, that you have enabled the renv project library by
calling renv::restore()
(see the section above).
The datasets used in these simulations are stored in the data
folder. Scripts to retrieve these datasets from their original
sources can be found in data-raw/
.
Note that pushing large files using Git-LFS against forks of this repo counts against the bandwidth limits of this repo, and so may fail if these limits are exceeded. If you for some reason need to do this and it fails, please file as issue here.