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Oikawa, Kenichi; Kiyanagi, Yoshiaki*; Sato, Hirotaka*; Omae, Kazuma*; Pham, A.*; Watanabe, Kenichi*; Matsumoto, Yoshihiro*; Shinohara, Takenao; Kai, Tetsuya; Harjo, S.; et al.
Materials Research Proceedings, Vol.15, p.207 - 213, 2020/02
Matsumoto, Kazuya*; Idomura, Yasuhiro; Ina, Takuya*; Mayumi, Akie; Yamada, Susumu
Journal of Supercomputing, 75(12), p.8115 - 8146, 2019/09
Times Cited Count：0 Percentile：100(Computer Science, Hardware & Architecture)A communication-avoiding generalized minimum residual method (CA-GMRES) is implemented on a hybrid CPU-GPU cluster, targeted for the performance acceleration of iterative linear system solver in the gyrokinetic toroidal five-dimensional Eulerian code GT5D. In addition to the CA-GMRES, we implement and evaluate a modified variant of CA-GMRES (M-CA-GMRES) proposed in our previous study to reduce the amount of floating-point calculations. This study demonstrates that beneficial features of the CA-GMRES are in its minimum number of collective communications and its highly efficient calculations based on dense matrix-matrix operations. The performance evaluation is conducted on the Reedbush-L GPU cluster, which contains four NVIDIA Tesla P100 GPUs per compute node. The evaluation results show that the M-CA-GMRES is 1.09x, 1.22x and 1.50x faster than the CA-GMRES, the generalized conjugate residual method (GCR), and the GMRES, respectively, when 64 GPUs are used.
Nakata, Kotaro*; Hasegawa, Takuma*; Solomon, D. K.*; Miyakawa, Kazuya; Tomioka, Yuichi*; Ota, Tomoko*; Matsumoto, Takuya*; Hama, Katsuhiro; Iwatsuki, Teruki; Ono, Masahiko*; et al.
Applied Geochemistry, 104, p.60 - 70, 2019/05
Times Cited Count：0 Percentile：100(Geochemistry & Geophysics)no abstracts in English
Idomura, Yasuhiro; Ina, Takuya*; Mayumi, Akie; Yamada, Susumu; Matsumoto, Kazuya*; Asahi, Yuichi*; Imamura, Toshiyuki*
Proceedings of 8th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (ScalA 2017), p.7_1 - 7_8, 2017/11
A communication-avoiding generalized minimal residual (CA-GMRES) method is applied to the gyrokinetic toroidal five dimensional Eulerian code GT5D, and its performance is compared against the original code with a generalized conjugate residual (GCR) method on the JAEA ICEX (Haswell), the Plasma Simulator (FX100), and the Oakforest-PACS (KNL). The CA-GMRES method has 
higher arithmetic intensity than the GCR method, and thus, is suitable for future Exa-scale architectures with limited memory and network bandwidths. In the performance evaluation, it is shown that compared with the GCR solver, its computing kernels are accelerated by 
, and the cost of data reduction communication is reduced from 
to 
of the total cost at 1,280 nodes.
Sr)
Rh
Sn
Cheung, Y. W.*; Hu, Y. J.*; Goh, S. K.*; Kaneko, Koji; Tsutsui, Satoshi; Logg, P. W.*; Grosche, F. M.*; Kanagawa, Hibiki*; Tanioku, Yasuaki*; Imai, Masaki*; et al.
Journal of Physics; Conference Series, 807(3), p.032002_1 - 032002_4, 2017/04
Times Cited Count：3 Percentile：14.14Chatake, Toshiyuki*; Sazaki, Gen*; Kikko, Tatsuhiko*; Fujiwara, Satoru; Ishikawa, Takuya*; Matsumoto, Osamu*; Morimoto, Yukio*
Crystal Growth & Design, 10(3), p.1090 - 1095, 2010/03
Times Cited Count：4 Percentile：48.73(Chemistry, Multidisciplinary)We propose a technique for DNA crystallization using the thermal reversible process of DNA: a conversion between a double-stranded DNA (dsDNA) and two single-stranded DNAs (ssDNAs) with temperatures. We investigated the solubility of the crystals of a DNA hexamer d(CGCGCG) and their melting temperature, at which the thermal conversion occurs. The results obtained suggest that the conversion from a dsDNA to ssDNAs results in an increase in solubility. It was shown that using this temperature-controlled technique, high-grade single crystals of the DNA hexamer could be obtained from a small amount of DNA samples. This easy-to-apply technique would be superior to the conventional vapor diffusion technique in that it allows the solubility of DNA crystals to be controlled with no need for expensive setups.
SiMatsuda, Tatsuma; Haga, Yoshinori; Ikeda, Shugo; Galatanu, A.; Yamamoto, Etsuji; Shishido, Hiroaki*; Yamada, Mineko*; Yamaura, Junichi*; Hedo, Masato*; Uwatoko, Yoshiya*; et al.
Journal of the Physical Society of Japan, 74(5), p.1552 - 1556, 2005/05
Times Cited Count：21 Percentile：28.43(Physics, Multidisciplinary)We have succeeded in growing a high-quality single crystal of UCuSi with the tetragonal structure by the Sn-flux method and measured the electrical resistivity, magnetic susceptibility, magnetization and specific heat. UCuSi is found to order antiferromagnetically below 
= 106 K, and follows a successive ferromagnetic ordering at 
= 100 K. The magnetic properties are highly anisotropic, reflecting the crystal structure. An easy-axis of magnetization is found to be the [001] direction (
-axis) both in the antiferromagnetic and ferromagnetic phases, while the [100] direction (
-axis) corresponds to the hard-axis in magnetization. The magnetization curve in the antiferromagnetic phase indicates a clear metamagnetic transition at a low field of about 1 kOe and changes smoothly into a ferromagnetic magnetization curve below = 100 K. The saturation moment is determined as 1.75
/U at 2 K. The electronic specific heat coefficient is also determined as 20 mJ/K
mol.
Ni
Al
Haga, Yoshinori; Matsuda, Tatsuma; Ikeda, Shugo; Galatanu, A.; Matsumoto, Takuya*; Sugimoto, Toyonari*; Tada, Toshiji*; Noguchi, Satoru*; Onuki, Yoshichika
Physica B; Condensed Matter, 359-361, p.1006 - 1008, 2005/04
Times Cited Count：2 Percentile：87.41(Physics, Condensed Matter)A new ternary uranium-based intermetallic compound UNiAl has been symthesized. It crystallizes in the unique flat orthorhombic structure. Uranium atoms occupy two crystallographic 4 and 8
sites where local chemical environments are quite similar. The temperature dependence of the magnetic susceptibility 
demonstrates peculiar magnetic anisotropy; along 
- and -axes obeys the Curie-Weiss law above 23 K, while along -axis is small and temperature independent. At 23 K, only 
shows a sharp cusp corresponding to the antiferromagnetic ordering, while 
remains paramagnetic behavior down to 2 K. These results and crystallographical considerations lead to a conclusion that only uranium atoms at the 8 site order antiferromagnetically at = 23 K, while uranium atoms at the 
site do not order down to 50 mK.
Suzuki, Yoshio; Matsumoto, Nobuko*; Yamagishi, Nobuhiro*; Arakawa, Takuya*; Kuraishi, Hideaki*
JAERI-Data/Code 2004-013, 163 Pages, 2005/02
JAERI-Data-Code-2004-013.pdf:33.81MB
The Center for Promotion of Computational Science and Engineering of the Japan Atomic Energy Research Institute has carried out the ITBL (Information-Technology Based Laboratory) project which is one of e-Japan priority policy programs. AVS/ITBL is the visualization tool which has been developed aiming at realizing the efficient visualization in the ITBL environment. This visualization tool is one of the tools of ITBL infrastructure software and operates in cooperation with AVS/Express. In this paper, utilization of AVS/ITBL to the numerical environmental system, which is one of the applications in ITBL project, is presented. And the outline of the operation in this utilization is indicated.
Suzuki, Yoshio; Matsumoto, Nobuko*; Yamagishi, Nobuhiro*; Higuchi, Kenji; Otani, Takayuki; Nagai, Haruyasu; Terada, Hiroaki; Furuno, Akiko; Chino, Masamichi; Kobayashi, Takuya
Computational Science - ICCS 2003, International Conference Saint Petersburg Russian Federation, Melbourne Australia, June 2-4, 2003 Proceedings, p.120 - 129, 2003/00
Information-Technology Based Laboratory (ITBL) project has been propelled as one of e-Japan priority policy programs. The purposes of the project are to share intellectual resources such as remote computers, programs and data in universities and institutes and to support cooperative studies among researchers, building a virtual research environment, ITBL. Japan Atomic Energy Research Institute (JAERI) has been working on installation and management of hardware and development of infrastructure software and applications. As application software, researches on quantum bioinformatics and environmental sciences are carried out. This paper presents utilization of ITBL system infra-structure software for 'Numerical Environment System' which is developed for environmental studies. More effective job executions and visualization are ex-pected by using Task Mapping Editor (TME) and AVS/ITBL, which are tools developed as infrastructure software.
oxidation of H-terminated Si(110) surfaceNakano, Takuya*; Togashi, Hideaki*; Matsumoto, Mitsutaka*; Yamamoto, Yoshihisa*; Suzuki, Yasushi*; Teraoka, Yuden; Yoshigoe, Akitaka; Suemitsu, Maki*
no journal, ,
Time evolution of oxide layers in the H-terminated Si(110) surface by the UV/O treatment at room temperature was observed by photoemission spectroscopy with synchrotron radiation. Special oxidation mechanisms for the H-terminated Si(110) surface were found. Si(110) surfaces were hydrogenated by HF treatments. The surface was irradiated and oxidized by UV light (253.7, 184.9 nm) of a low pressure Hg lamp in the air. The UV/O irradiation time dependence of oxide thickness showed a step-wise profile. The step width was about 0.2 nm. The value is close to one oxide layer thickness (0.19 nm) for the Si(110) surface. Si atoms at the Si(110) surface are categolized to A bonds which are chain-like dense bonds, and B bonds which connect up and down A bond chains. The step-wise oxidation behaviour is reasonable if oxidation at the B bonds, in which oxidation strain is smaller than that of A bonds, has larger reaction rate than at the A bonds.
Mn
O
, 2Matsumoto, Keisuke*; Hoshiyama, Takuya*; Oishi, Daisuke*; Akahama, Hiroshi*; Yoshii, Kenji; Kano, Jun*; Hanasaki, Noriaki*; Kambe, Takashi*; Ikeda, Naoshi*; Mori, Shigeo*
no journal, ,
We have investigated the physical properties of YbFeMnO, a derivative system of the electronic ferroelectric RFe
O (R: rare earths). Electron diffraction measurements showed taht long-range charge ordering of the Fe-3d charges was observed at room temperature for x=0; this ordering is the origin of ferroelectricity. The x=0.1 oxide showed diffuse scattering patterns at room temperature, instead of the charge-ordered pattern. Thus, 5% Mn substitution can collapse the long-range charge ordering. We will also present the correlation between the magnetic/dielectric properties and the crystal structure.
Nishiuchi, Mamiko; Ogura, Koichi; Tanimoto, Tsuyoshi*; Pirozhkov, A. S.; Sakaki, Hironao; Fukuda, Yuji; Kanasaki, Masato; Kando, Masaki; Esirkepov, T. Z.; Sagisaka, Akito*; et al.
no journal, ,
We present the extension of the maximum energy of protons from the interaction between the short-pulse compact laser system and solid thin-foil target. The laser pulses with parameters of 800 nm in wavelength, 40 fs of pulse width, 7 J of energy, 10
contrast are focused onto the target with the peak intensity of more than 10
Wcm
, which is also well confirmed by the measured electron temperature of 16 MeV. We report about the acceleration mechanism as well as future prospect on the proton acceleration experiment at JAEA.
Nishiuchi, Mamiko; Sakaki, Hironao; Sagisaka, Akito; Maeda, Shota; Pirozhkov, A. S.; Pikuz, T.; Faenov, A. Ya.*; Ogura, Koichi; Fukuda, Yuji; Matsukawa, Kenya*; et al.
no journal, ,
no abstracts in English
Maeda, Shota; Nishiuchi, Mamiko; Sakaki, Hironao; Sagisaka, Akito; Pirozhkov, A. S.; Pikuz, T.; Faenov, A. Ya.*; Ogura, Koichi; Fukuda, Yuji; Matsukawa, Kenya*; et al.
no journal, ,
In JAEA, the high energy ions generated by the interaction between Ultra-intense Ultra-Short pulse laser and thin-foil target is being studied. Irradiating condition must be optimized to generate higher energy ions while suppress the becoming gigantic of laser. It is necessary to know the physical phenomenon in plasma to determine the parameter to optimize from the information on the electron and neutron, X-rays, which are generated simultaneously with ion. In this study, in order to measure electron temperature accurately, an electron spectrometer was developed which have broad range (1-200 MeV). The detector is comprised of permanent magnets and a fluorescent plate, CCD camera. In the presentation, the result of the calibration experiment carried out using 4, 9, 12, 15 MeV quasi-monoenergetic electron beam in HIBMC will be reported. Moreover, response analysis method was inspected using PHITS which is particle transporting Monte Carlo simulation code, and will also report the result.
Handa, Takuya; Enuma, Yasuhiro; Ono, Yukihiko*; Nakamura, Yuki*; Sakata, Nobuyasu*; Kushioka, Kiyonori*; Shimoji, Kuniyuki*; Inoue, Tomoyuki*; Matsumoto, Iwao*
no journal, ,
no abstracts in English
IrSnKaneko, Koji; Matsuda, Masaaki*; Tsutsui, Satoshi*; Goh, S. K.*; Matsumoto, Takuya*; Imai, Masaki*; Yoshimura, Kazuyoshi*
no journal, ,
no abstracts in English
Matsumoto, Kazuya; Asahi, Yuichi*; Ina, Takuya; Idomura, Yasuhiro
no journal, ,
We present the implementation and performance evaluation results of the plasma physics simulation code called GT5D on a GPU cluster. In this study, an iterative matrix solver, which is identified as a performance bottleneck in the code, is tuned on the GPU. The measured performance is compared with attainable performance calculated by the roofline model. Additionally, we show the implementation with direction communications between GPUs for utilizing many GPUs.
Kaneko, Koji; Matsuda, Masaaki*; Tsutsui, Satoshi; Cheung, Y. W.*; Hu, Y. J.*; Goh, S. K.*; Matsumoto, Takuya*; Imai, Masaki; Tanioku, Yasuaki*; Kanagawa, Hibiki*; et al.
no journal, ,
no abstracts in English
Matsumoto, Kazuya*; Idomura, Yasuhiro; Ina, Takuya*; Mayumi, Akie; Yamada, Susumu
no journal, ,
Communication avoiding (CA) Krylov methods are promising solutions for communication bottlenecks on supercomputers based on many core processors or accelerators. In this work, we implemented the CA-GMRES method on a GPU cluster, the HA-PACS, and evaluated its performance on a non-symmetric matrix solver from a nuclear CFD code. The result shows that the CA-GMRES method is significantly faster than the conventional Krylov methods such as the GMRES method and the GCR method.
