Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking
Creators
- 1. KTH Royal Institute of Technology, Stockholm, Sweden
- 2. Politecnico di Milano, Milano, Italy
Description
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.
Files
2.Understanding_the_I_O_Impact_on_the_Performance_of_High_Throughput_Molecular_Docking.pdf
Files
(1.2 MB)
Name | Size | Download all |
---|---|---|
md5:e954738db265bde50876d23fabb93256
|
1.2 MB | Preview Download |