Parallelizing the Protein Threading Problem in a Hybrid Peer-to-Peer Based High Performance Computing Platform

2009 ◽  
Author(s):  
Fei Luo ◽  
Lin Chen
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Peer To Peer ◽  
Computing Platform ◽  
Protein Threading ◽  
Performance Computing

scholarly journals Scalability of DL_POLY on High Performance Computing Platform

2017 ◽  
Vol 29 (3) ◽  
Author(s):  
Mabule Samuel Mabakane ◽  
Daniel Mojalefa Moeketsi ◽  
Anton Lopis
Keyword(s):  
Molecular Dynamics ◽  
High Performance Computing ◽  
High Performance ◽  
Computing Platform ◽  
Speed Up ◽  
Linux Cluster ◽  
Large Systems ◽  
Performance Computing ◽  
Better Than

This paper presents a case study on the scalability of several versions of the molecular dynamics code (DL_POLY) performed on South Africa‘s Centre for High Performance Computing e1350 IBM Linux cluster, Sun system and Lengau supercomputers. Within this study different problem sizes were designed and the same chosen systems were employed in order to test the performance of DL_POLY using weak and strong scalability. It was found that the speed-up results for the small systems were better than large systems on both Ethernet and Infiniband network. However, simulations of large systems in DL_POLY performed well using Infiniband network on Lengau cluster as compared to e1350 and Sun supercomputer.

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