Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking

被引：10

作者：

Markidis, Stefano ^{[1
,2
]}

Gadioli, Davide ^{[2
]}

Vitali, Emanuele ^{[2
]}

Palermo, Gianluca ^{[2
]}

机构：

[1] KTH Royal Inst Technol, Stockholm, Sweden

[2] Politecn Milan, Milan, Italy

来源：

PROCEEDINGS OF IEEE/ACM SIXTH INTERNATIONAL PARALLEL DATA SYSTEMS WORKSHOP (PDSW 2021) | 2021年

基金：

瑞典研究理事会; 欧盟地平线“2020”;

关键词：

High-Throughput Molecular Docking; Parallel I/O; Darshan; I/O Profiling; LIGEN;

D O I：

10.1109/PDSW54622.2021.00007

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

High-throughput molecular docking is a data-driven simulation methodology to estimate millions of molecules' position and interaction strength (ligands) when interacting with a given protein site. Because of its data-driven nature, the high-throughput molecular docking performance depends on how fast we can ingest data into the processing pipeline and how efficiently we can write molecular docking results to a shared file. This work characterizes the I/O performance of a high-performance, high-throughput molecular docking application, called Docker-HT, running on a supercomputer up to 512 computing nodes with two different parallel I/O configurations. We show that a tuned I/O configuration can improve the overall parallel efficiency from 71% to 90% on 512 nodes and identify and solve a performance degradation observed when running on 16 and 32 nodes.

引用

页码：9 / 14

页数：6

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