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)
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)
We consider a parallel method for solving generalized eigen-value 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 master-worker type parallel programming models. The computation of eigen-values using explicit(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)
— We present our perspective and goals on high-performance 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(More)
SUMMARY In the near future, interconnection networks of massively parallel computer systems will connect more than a hundred thousands of computing nodes. The performance evaluation of the interconnection networks can provide real insights to help the development of efficient communication library. Hence, to evaluate the performance of such intercon-nection(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)