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Hazama, Osamu; Guo, Z.
Proceedings of International Conference on Supercomputing in Nuclear Applications (SNA 2003) (CD-ROM), p.119 - 120, 2003/09
In order for the numerical simulations to reflect textquotedblleft real-worldtextquotedblright phenomena and occurrences, incorporation of multidisciplinary and multi-physics simulations considering various physical models and factors are becoming essential. However, there still exist many obstacles which inhibit such numerical simulations. For example, it is still difficult in many instances to develop satisfactory software packages which allow for such coupled simulations and such simulations will require more computational resources. A precise multi-physics simulation today will require parallel processing which again makes it a complicated process. Under the international cooperative efforts between CCSE/JAERI and Fraunhofer SCAI, a German institute, a library called the MpCCI, or Mesh-based Parallel Code Coupling Interface, has been implemented together with a library called STAMPI to couple two existing codes to develop an textquotedblleft integrated numerical simulation systemtextquotedblright intended for meta-computing environments.
Pinak, M.; Nemoto, Toshiyuki*
Proceedings of International Conference on Supercomputing in Nuclear Applications (SNA 2003) (CD-ROM), 15 Pages, 2003/00
The molecular dynamics (MD) studies of oxidative lesions on DNA molecules are presented with respect to the proper recognition of lesions by their respective repair enzymes. The recognition of lesion and the formation of stable DNA-enzyme complex are necessary conditions for the onset of the enzymatic repair process. Two DNA lesions, thymine glycol and 8-oxoguanine were subjected to the MD simulations for several hundreds picoseconds using MD simulation codes AMBER 5.0 and AMBER 7.0. Amber was changed and partly vectorized to be able to handle this large systems. Simulations were performed on FUJITSU VPP5000/64 vector/parallel type, the HITACHI SR8000 and FUJITSU PRIMEPOWER parallel types supercomputers.
Higuchi, Kenji; Otani, Takayuki; Hasegawa, Yukihiro*; Suzuki, Yoshio; Yamagishi, Nobuhiro*; Kimura, Kazuyuki*; Aoyagi, Tetsuo; Nakajima, Norihiro; Fukuda, Masahiro; Imamura, Toshiyuki*; et al.
Proceedings of International Conference on Supercomputing in Nuclear Applications (SNA 2003) (CD-ROM), 11 Pages, 2003/00
An experimental application of Grid computing was executed in ITBL project promoted by six member institutes of MEXT. Key technologies that are indispensable for construction of virtual organization were implemented onto ITBL Middleware and examined in the experiment from a view point of availability. It seems that successful result in the implementation and examination of those technologies such as security infrastructure, component programming and collaborative visualization in practical computer/network systems means significant progress in Science Grid in Japan.
Takase, Kazuyuki; Yoshida, Hiroyuki; Ose, Yasuo*; Tamai, Hidesada; Akimoto, Hajime
Proceedings of International Conference on Supercomputing in Nuclear Applications (SNA 2003) (CD-ROM), 15 Pages, 2003/00
no abstracts in English