Development of Special Purpose Computers for Various Kinds of Chemical Simulations

Umpei NAGASHIMAa*, Tohru SASAKIb, Yasuaki OHTANIc, Masamitsu UEHARAd, Masaru Tsukadae and Kazuaki Murakamif

aGrid Technology Research Center, National Institute for Advanced Industrial Science and Technology
1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
bA-Priori Microsystems, Inc.
236 KBIC 308-10 Ogura, Saiwai-ku, Kwawasaki, Kanagawa 212-0054, Japan
cScience and Technology, Mizuho Information & Research Institute, Inc.
2-3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101-8443, Japan
dSeiko Epson Corporation
3-3-5 Owa, Suwa, Nagano, 392-0001, Japan
eDepartment of Nanoscience and Nanoengineering, Graduate School of Science and Engineering, Waseda University
513 Waseda Tsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
fGraduate school of Information Sciences and Electrical Engineering, Kyushu University
6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan

(Received: July 28, 2005; Accepted for publication: November 7, 2005; Published on Web: December 15, 2005)

Special purpose computers for ab initio molecular orbital calculation and the first principle density functional theory with special hardware, including special purpose LSI, for some heavy load processes (hot spots), have been developed as an attempt to make a cost effective supercomputer for personal use. The system was realized using embedded cell architecture recently adapted to game computers and electrical appliance. The nick name of the project is Embedded High Performance Computing system (EHPC project).
A kind of software/hardware co-design approach was taken to realize the development in a short period during 2000-2004. Three types of hardware (Figure 3) were developed for 5 chemical calculation programs. At first we designed the platform architecture (EHPC platform: Figure 3-a) as the base system which has a large number of general purpose CPUs instead of special purpose LSIfs and can emulate functions of the LSI with the firmware on the CPU. In the next step we developed the system (Figure 3-b) with special purpose LSI for ab initio molecular orbital calculation and the system (Figure 3-c)with FPGAs for three dimensional FFT calculation usung the Car-Parrinello method.
The special purpose LSI for molecular integral evaluation is named Eric (Electron repulsion integral calculator). The size of Eric is 5mm*10mm with 2.1 MGates. The memory size is 704Kbytes and clock speed is 200MHZ. The performance power ratio is almost the same as Intel Pentium 4 (3.2GHz, 1Mb L2, 2GB Memory). The FPGA showed almost four times faster performance than the fastest program: FFTW on the Intel Xeon (2.4GHz).

Keywords: Parallel processing, Special purpose computer, Embedded high performance computing, Molecular orbital calculation, Density functional theory


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