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NAMD Package Benchmarking on the Base of Armenian Grid Infrastructure

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Author(s): Mikayel Gyurjyan | Hovsep Keropyan | Aram Shahinyan | Armen Poghosyan | Levon Arsenyan | Hrachya Astsatryan

Journal: Journal of Biophysical Chemistry
ISSN 2153-036X

Volume: 04;
Issue: 01;
Start page: 34;
Date: 2012;
Original page

Keywords: Parallel Molecular Dynamics | NAMD Benchmarking | Grid

ABSTRACT
The parallel scaling (parallel performance up to 48 cores) of NAMD package has been investigated by estimation of the sensitivity of interconnection on speedup and benchmark results—testing the parallel performance of Myrinet, Infiniband and Gigabit Ethernet networks. The system of ApoA1 of 92 K atoms, as well as 1000 K, 330 K, 210 K, 110 K, 54 K, 27 K and 16 K has been used as testing systems. The Armenian grid infrastructure (ArmGrid) has been used as a main platform for series of benchmarks. According to the results, due to the high performance of Myrinet and Infiniband networks, the ArmCluster system and the cluster located in the Yerevan State University show reasonable values, meanwhile the scaling of clusters with various types of Gigabit Ethernet interconnections breaks down when interconnection is activated. However, the clusters equipped by Gigabit Ethernet network are sensitive to change of system, particularly for 1000 K systems no breakdown in scaling is observed. The infiniband supports in comparison with Myrinet, make it possible to receive almost ideally results regardless of system size. In addition, a benchmarking formula is suggested, which provides the computational throughput depending on the number of processors. These results should be important, for instance, to choose most appropriate amount of processors for studied system.
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