ABSTRACTMolecular Dynamics (MD) is one of processes that requires High Performance Computing
environments to complete its jobs. In the preparation of virtual screening experiments, MD is one of
the important processes particularly for tropical countries in searching for anti-Malaria drugs. The
search for anti-Malaria has previously conducted, for example by WISDOM project utilizing 1,700
CPUS. This computing infrastructure will be one of the limitation for country like Indonesia that also
needs in silico anti malaria compounds searching from the country medical plants. Thus finding
suitable and affordable computing environment is very important. Our previous works showed that our
dedicated Cluster computing power with 16 cores performance better than those using fewer cores,
however the GPU GTX family computing power is much better.
In this study, we investigate further our previous experiment in finding more suitable computing
environment on much better hardware specification of non dedicated Cluster computing and GPU
Tesla. We used two computing environments, the first one is Barrine HPC Cluster of The University of
Queensland which has 384 compute nodes with 3144 computing cores. The second one is Delta Future
Grid GPU Cluster which has 16 computing nodes with 192 computing cores, each nodes equipped
with 2 NVIDIA Tesla C2070 GPU (448 cores). The results show that running the experiment on a
dedicated computing power is much better than that on non dedicated ones, and the GPU performance
is still much better than that of Cluster.
