The K computer Operations: Experiences and Statistics

AbstractThe K computer, released on September 29, 2012, is a large-scale parallel supercomputer system consisting of 82,944 compute nodes. We have been able to resolve a significant number of operation issues since its release. Some system software components have been fixed and improved to obtain higher stability and utilization. We achieved 94% service availability because of a low hardware failure rate and approximately 80% node utilization by careful adjustment of operation parameters. We found that the K computer is an extremely stable and high utilization system

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Software of the Earth Simulator

Abstract The Earth Simulator (ES) is a distributed-memory parallel system with a peak performance of 40 TFLOPS. The system consists of 640 nodes connected via a fast 640 × 640 single-stage crossbar network. In this paper, an overview of software of the Earth Simulator (the operating system, Operation Management Software and a programming environment) is presented. The operating system of ES (ES OS) is based on SUPER-UX, which is the operating system for NEC’s commercial Supercomputer SX series, and ES OS is enhanced to meet a scalability of the ES system, and Operation Management Software is developed to man-age this large system efficiently. They provide Single System Image (SSI) system operation, system manage-ment and batch job control for the ES system. As a programming environment, ES provides a three-level hier-archy of parallel processing. Useful languages and libraries are prepared for users to develop well-parallelized programs and to achieve the highest performance. FORTRAN90/ES and C++/ES have advanced capabilities of automatic vectorization and microtasking, and HPF/ES enables users to develop parallel programs easily. MPI/ES provides high-speed communication optimized for the ES architecture