JINR CICC in computational chemistry and nanotechnology problems: DL_POLY performance for different communication architectures

Abstract

This report compares the performance of the DL POLY general-purpose molecular dynamics simulation package on the LIT JINR computing cluster CICC with various communication systems. The comparison involved two cluster architectures: Gigabit Ethernet and InˇniBand technologies, respectively. The code performance tests include some comparison of the CICC cluster with the special-purpose computer MDGRAPE-3 developed at RIKEN for a high-speed acceleration of the MD (molecular dynamics) without aˇxed cutoff. The DL POLY benchmark covers a set of typical MD system simulations detailed below. ‚ • ¡μÉ¥¸• ¢´¨¢ ¥É¸Ö ¶•μ¨ §¢μ¤¨É¥²Ó´μ¸ÉÓ ¶ ±¥É ³´μ£μÍ¥²¥¢μ£μ¨¸ ¶μ²Ó §μ¢ ´¨Ö ¤²Ö ³μ²¥±Ê-²Ö•´μ-¤¨´ ³¨Î¥¸±μ£μ ³μ¤¥²¨•μ¢ ´¨Ö DL POLY´ ¢ÒΨ¸²¨É¥²Ó´μ³ ±² ¸É¥•¥-ˆ‚Š ‹ˆ' ˆŸˆ• §²¨Î´Ò³¨¸¥É¥¢Ò³¨É¥Ì´μ²μ£¨Ö³¨. '• ¢´¥´¨¥ ±μ¤μ¢ DL POLY ¶•μ¢μ¤¨²μ¸Ó ¤²Ö ¤¢ÊÌ ¢¨¤μ¢ ±²-É¥•´ÒÌ •Ì¨É¥±ÉÊ•´ μ¸´μ¢¥¸¥É¥¢ÒÌ É¥Ì´μ²μ£¨°Gigabit Ethernet¨InˇniBand. '¥¸É¨•μ¢ ´¨¥ ±μ¤ ¢±²ÕÎ ¥É¸• ¢´¥´¨¥ ±² ¸É¥•-ˆ‚Š¸±μ³ ¶ÓÕÉ¥•μ³¸ ¶¥Í¨ ²Ó´μ£μ´ §´ Î¥´¨Ö MDGRAPE-3, • §•-¡μÉ ´´Ò³ ¢ RIKEN ¤²Ö ¢Ò¸μ±μ ¶•μ¨ §¢μ¤¨É¥²Ó´ÒÌ OE" (³μ²¥±Ê²Ö•´μ-¤¨´ ³¨Î¥¸±¨Ì) ¢ÒΨ¸²¥´¨°¡¥ §¸ ¶ μ²Ó §μ¢ ´¨Ö • ¤¨Ê¸ μ¡•¥ § ´¨Ö ¤ ²Ó´μ¤¥°¸É¢ÊÕÐ¨Ì ³¥¦³μ²¥±Ê²Ö•´Ò̸¨². '¥¸É¨•μ¢ ´¨¥ ¶•μ-§¢μ¤¨É¥²Ó´μ¸É¨ ¶ ±¥É DL POLY μÌ¢ ÉÒ¢ ¥É ɨ ¶¨Î´Ò¥ ³μ²¥±Ê²Ö•´μ-¤¨´ ³¨Î¥¸±¨¥ ¢ÒΨ¸²¥´¨Ö, μ ¶¨¸ ´´Ò¥´¨¦¥.

Procedure for constructing of explicit, implicit and symmetric simplectic schemes for numerical solving of Hamiltonian systems of equations

“…• распараллеливание и ускорение межпроцессорных обменов на многопроцессорных системах [Dushanov et al, 2009]; • Разработка спецпроцессоров [Ohmura et al, 2014].…”