Abstract
NAMD is a molecular dynamics program designed for high-performance simulation of large biomolecular systems. TH-1A, installed in National Supercomputer Center in Tianjin, is the first petaflops supercomputer of China. We test performance of two biomolecular systems of NAMD respectively on TH-1A in this study: one is STMV simulation with 1,066,628 atoms and the other is ApoA1 with 92,222 atoms. With the high-speed interconnected communication and powerful computing capabilities of TH-1A supercomputer, NAMD program can scale up to 10,240 cores and achieve a very good parallel efficiency and scalability.
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© 2012 Springer-Verlag Berlin Heidelberg
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Zhu, X., Liu, X., Jian, X., Meng, X., Feng, J. (2012). The Performance Analysis of Massively Parallel Program NAMD on TH-1A. In: Zeng, D. (eds) Advances in Information Technology and Industry Applications. Lecture Notes in Electrical Engineering, vol 136. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-26001-8_35
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DOI: https://doi.org/10.1007/978-3-642-26001-8_35
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