Performance Impact of Containerized METADOCK 2 on Heterogeneous Platforms

TL;DR

This paper evaluates the performance of containerized METADOCK 2 on heterogeneous HPC platforms, showing negligible overhead and highlighting its scalability and efficiency for virtual screening in drug discovery.

Contribution

It provides the first comprehensive assessment of containerization impact on METADOCK 2's performance across diverse HPC configurations.

Findings

Containerization introduces less than 1% performance overhead.

METADOCK 2 efficiently processes large molecular complexes.

Containerized deployment enhances portability and reproducibility.

Abstract

Virtual screening (VS) is a computationally intensive process crucial for drug discovery, often requiring significant resources to analyze large chemical libraries and predict ligand-protein interactions. This study evaluates the performance impact of containerization on METADOCK 2, a high-throughput docking software when deployed on heterogeneous high-performance computing (HPC) platforms. By testing three containerization technologies - Docker, Singularity, and Apptainer - across varying CPU and GPU configurations, the experiments reveal that containerization introduces negligible performance overhead, with deviations below 1%. Moreover, METADOCK 2 demonstrated the capability to efficiently process large molecular complexes, surpassing the limitations of commercial tools such as AutoDock Vina. The results underscore the advantages of container-based deployment for ensuring portability, reproducibility, and scalability in scientific computing. This study concludes that containerized METADOCK 2 is a robust and efficient solution for VS tasks on heterogeneous HPC platforms.