Automated Systematic Review - Simulation [DEPRECATED]

This project contains the code of the simulation study for the Automated Systematic Review project. It contains code to run batches of simulation runs in parallel using MPI.

We make use of the SURFSara HPC infrastructure. But with some modifications, the code can be run on other HPC facilities as well.

Some of the code in the repository is old an no longer maintained. Batch functionality has been (or will soon be) integrated into the core ASReview project. Other scripts will be copied to more suitable repositories.

Installation

The Automated Systematic Review project requires Python 3.6+. To run the code you also need an implementation of the MPI standard. The most well known standard is OpenMPI. This is not a python package and should be installed separately.

The simulation project itself can be directly installed with:

pip install --user git+https://github.com/asreview/automated-systematic-review-simulations

Dependencies are automatically installed.

Running a batch

To run a batch of simulations on 4 cores and 12 runs, use the following command:

mpirun -n 4 asreview batch ${DATA_SET} --state_file ${DIR}/results.json --n_runs 12

It will create 12 files in the ${DIR} directory, while running on 4 cores in parallel.

Related packages

• asreview-visualization Package for visualization of log files.

• asreview-hyperopt Package for optimizing ASReview hyperparameters.