Computers in Biology and Medicine, 27(4):257-266, 1997


Coarse-grain Parallel Computing for Very Large Scale Neural Simulations in the NEXUS Simulation Environment

Ko Sakai1, Paul Sajda2, Shih-Cheng Yen, and Leif H. Finkel

1Current Address: Institute of Physical and Chemical Research (RIKEN), FRP, Laboratory for Neural Modeling, Wako, Japan
2Current Address: David Sarnoff Research Center, CN5300, Princeton, NJ 08533-5300

Department of Bioengineering and
Institute of Neurological Sciences
University of Pennsylvania
Philadelphia, PA 19104, U. S. A.

ko@yugiri.riken.go.jp
sajda@pnet.sarnoff.com
syen@neuroengineering.upenn.edu
leif@neuroengineering.upenn.edu

Abstract
We describe a neural simulator designed for simulating very large scale models of cortical architectures. This simulator, NEXUS, uses coarse-grain parallel computing by distributing computation and data onto multiple conventional workstations connected via a local area network. Coarse-grain parallel computing offers natural advantages in simulating functionally segregated neural processes. We partition a complete model into modules with locally dense connections--a module may represent a cortical area, column, layer, or functional entity. Asynchronous data communications among workstations are established through the Network File System, which, together with the implicit modularity, decreases communications overhead, and increases overall performance. Coarse-grain parallelism also benefits from the standardization of conventional workstations and LAN, including portability between generations and vendors.

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