Title :
Comparative NAMD benchmarking on BlueGene/P
Author :
Poghosyan, A.H. ; Arsenyan, L.H. ; Astsatryan, H.V.
Author_Institution :
Int. Sci.-Educ. Center, Yerevan, Armenia
Abstract :
Series of benchmarking of 210K atoms of inverse micelle/oil/water system have been carried out on Bulgarian BlueGene/P at Bulgarian Supercomputing Centre and on computational resources of Armenian National Grid Initiative (ArmGrid). The experiments show that the linear increase of speed of calculation with the increase of number of processors has been obtained. It should be noted that no saturation is observed and finally we received 0.121day/ns using 4096 processors of BlueGene/P, meanwhile the data within the ArmGrid infrastructures shows the breakdown in scaling, which is depends on communication time between processors.
Keywords :
benchmark testing; molecular dynamics method; parallel machines; parallel processing; ArmGrid infrastructures; Armenian national grid initiative; Bulgarian BlueGene/P; Bulgarian supercomputing centre; NAMD benchmarking; computational resources; parallel molecular dynamics code; Benchmark testing; Biological system modeling; Computational modeling; Electric breakdown; Physics; Program processors; Supercomputers;
Conference_Titel :
MIPRO, 2012 Proceedings of the 35th International Convention
Conference_Location :
Opatija
Print_ISBN :
978-1-4673-2577-6
