Yuichi Inadomi

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A key challenge in next-generation supercomputing is to effectively schedule limited power resources. Modern processors suffer from increasingly large power variations due to the chip manufacturing process. These variations lead to <i>power inhomogeneity</i> in current systems and manifest into <i>performance inhomogeneity</i> in power constrained(More)
All electron calculations were performed on the photosynthetic reaction center of Blastochloris viridis, using the fragment molecular orbital (FMO) method. The protein complex of 20,581 atoms and 77,754 electrons was divided into 1398 fragments, and the two-body expansion of FMO/6-31G* was applied to calculate the ground state. The excited electronic states(More)
A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the(More)
Recently to achieve the Exa-flops next generation computer system, the power consumption becomes the important issue. On the other hand, the power consumption character of application program is not so considered now. In this study we examine the power character of our Magneto hydrodynamic (MHD) simulation code for the global magnetosphere to evaluate the(More)
A program package for molecular simulations of biological molecules was developed. The package, "PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem.Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations(More)
We consider a parallel method for solving generalized eigenvalue problems that arise from molecular orbital computations. We use a moment-based method that finds several eigenvalues and their corresponding eigenvectors in a given domain, which is suitable for masterworker type parallel programming models. The computation of eigenvalues using explicit(More)
A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark(More)
We present our perspective and goals on highperformance computing for nanoscience in accordance with the global trend toward “peta-scale computing.” After reviewing our results obtained through the grid-enabled version of the fragment molecular orbital method (FMO) on the grid testbed by the Japanese Grid Project, National Research Grid Initiative (NAREGI),(More)