Nextflow scripts for the experiments in
Biron-Lattes, M., Surjanovic, N., Syed, S., Campbell, T., & Bouchard-Côté, A. (2023). autoMALA: Locally adaptive Metropolis-adjusted Langevin algorithm. arXiv preprint arXiv:2310.16782.
The nextflow.config file instructs Nextflow to use Apptainer with a custom Docker image, so the user only needs to run e.g.,
./nextflow run AM_scaling.nf -profile [CLUSTER_PROFILE]where [CLUSTER_PROFILE] currently supports
sockeye: UBC ARC sockeye clusterCC: Digital Research Alliance of Canada (formerly Compute Canada)
Important: remember to fill the clusterOptions variable in nextflow.config with your credentials.
If you have Docker installed locally, then the same Docker image can be used locally via
sudo ./nextflow run AM_scaling.nf -with-docker alexandrebouchardcote/default:0.1.4Alternatively, if you have Julia and cmdstan installed locally, you can run
./nextflow run AM_scaling.nfNote: this assumes that there is an environment variable CMDSTAN pointing to the directory where cmdstan lives. You can do this via
export CMDSTAN=/full/path/to/cmdstan-vx.xx