Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS
One of application that needs high performance computing
resources is molecular dynamic. There is some software
available that perform molecular dynamic, one of these is a well
known GROMACS. Our previous experiment simulating
molecular dynamics of Indonesian grown herbal compounds
show sufficient speed up on 32 nodes Cluster computing
environment. In order to obtain a reliable simulation, one usually
needs to run the experiment on the scale of hundred nodes. But
this is expensive to develop and maintain. Since the invention of
Graphical Processing Units that is also useful for general
programming, many applications have been developed to run on
this. This paper reports our experiments that evaluate the
performance of GROMACS that runs on two different
environment, Cluster computing resources and GPU based PCs. We run the experiment on BRV-1 and REM2 compounds. Four
different GPUs are installed on the same type of PCs of quad
cores; they are Gefore GTS 250, GTX 465, GTX 470 and Quadro
4000. We build a cluster of 16 nodes based on these four quad
cores PCs. The preliminary experiment shows that those run on
GTX 470 is the best among the other type of GPUs and as well
as the cluster computing resource. A speed up around 11 and 12
is gained, while the cost of computer with GPU is only about 25
percent that of Cluster we built.
Keywords: Dynamic, GROMACS, GPU, Cluster Computing, Performance Analysis
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