Performance Impact of Containerized METADOCK 2 on Heterogeneous Platforms
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arXiv
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| Hauptverfasser: | , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866918048088195072 |
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| author | Banegas-Luna, Antonio Jesús Tudela, Baldomero Imbernón Martínez-Cortés, Carlos Cecilia, José María Pérez-Sánchez, Horacio |
| author_facet | Banegas-Luna, Antonio Jesús Tudela, Baldomero Imbernón Martínez-Cortés, Carlos Cecilia, José María Pérez-Sánchez, Horacio |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_06450 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Performance Impact of Containerized METADOCK 2 on Heterogeneous Platforms Banegas-Luna, Antonio Jesús Tudela, Baldomero Imbernón Martínez-Cortés, Carlos Cecilia, José María Pérez-Sánchez, Horacio Distributed, Parallel, and Cluster Computing Performance 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. |
| title | Performance Impact of Containerized METADOCK 2 on Heterogeneous Platforms |
| topic | Distributed, Parallel, and Cluster Computing Performance |
| url | https://arxiv.org/abs/2506.06450 |