Reproducing IA^3 2021 paper: Mapping Irregular Computations for Molecular Docking to the SX-Aurora TSUBASA Vector Engine

This repository contains the scripts and configuration files used in the Artifact Appendix of the article accepted at:

The 11th Workshop on Irregular Applications: Architectures and Algorithms (IA^3), 2021

and published on IEEExplore:

https://doi.org/10.1109/IA354616.2021.00008.

Contents

These scripts automate the evaluation of two molecular docking programs on different platforms:

• AutoDock-Aurora (developed in this work) on the SX-Aurora TSUBASA Vector Engine
• AutoDock-GPU (state-of the art) on GPUs & CPUs

Instructions are provided for each program:

1. AutoDock-Aurora (instructions)
2. AutoDock-GPU (instructions)

Optional step: automates the collecting of runtimes used in the article's discussion:

• Collecting results

Further information

Additional material include the paper preprint and presentation slides.