https://github.com/l30nardosv/reproduce-ia3-2021-moldocking-vector

Reproducing IA^3 2021 paper: "Mapping Irregular Computations for Molecular Docking to the SX-Aurora TSUBASA Vector Engine"
https://github.com/l30nardosv/reproduce-ia3-2021-moldocking-vector

autodock-gpu cpu gpu molecular-docking molecular-docking-scripts opencl paper reproducible-research sx-aurora-tsubasa

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

• Host: GitHub
• URL: https://github.com/l30nardosv/reproduce-ia3-2021-moldocking-vector
• Owner: L30nardoSV
• License: cc0-1.0
• Created: 2021-10-03T21:41:15.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-01-07T17:06:55.000Z (about 3 years ago)
• Last Synced: 2023-06-05T15:35:28.501Z (over 1 year ago)
• Topics: autodock-gpu, cpu, gpu, molecular-docking, molecular-docking-scripts, opencl, paper, reproducible-research, sx-aurora-tsubasa
• Language: Python
• Homepage:
• Size: 40 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://hpc.pnl.gov/IA3)

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](https://github.com/esa-tu-darmstadt/AutoDock-Aurora) **(developed in this work)** on the SX-Aurora TSUBASA Vector Engine

* [AutoDock-GPU](https://github.com/ccsb-scripps/AutoDock-GPU) (state-of the art) on GPUs & CPUs

Instructions are provided for each program:

1. [AutoDock-Aurora (instructions)](./USAGE_AURORA.md)

2. [AutoDock-GPU (instructions)](./USAGE_GPU.md)

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

* [Collecting results](./USAGE_COLLECT-RESULT-SCRIPT.md)

## Further information

Additional material include the [paper preprint](https://www.esa.informatik.tu-darmstadt.de/assets/publications/materials/2021/IA3_2021_LVS_merged_09102021.pdf) and [presentation slides](https://www.esa.informatik.tu-darmstadt.de/assets/publications/materials/2021/IA3_2021_LVS_slides_15-11-2021.pdf).