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Background Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchronous parallel processing service of Grid Engine is not provided on them. To encourage the use of massively parallel supercomputers in bioinformatics, we developed middleware called Virtual Grid Engine, which enables software pipelines to automatically perform their tasks as MPI programs. Result We conducted basic tests to check the time required to assign jobs to workers by VGE. The results showed that the overhead of the employed algorithm was 246 microseconds and our software can manage thousands of jobs smoothly on the K computer. We also tried a practical test in the bioinformatics field. This test included two tasks, the split and BWA alignment of input FASTQ data. 25,055 nodes (2,000,440 cores) were used for this calculation and accomplished it in three hours. Conclusion We considered that there were four important requirements for this kind of software, non-privilege server program, multiple job handling, dependency control, and usability. We carefully designed and checked all requirements. And this software fulfilled all the requirements and achieved good performance in a large scale analysis.

In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space non-bonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space non-bonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.

There are many places where they have no efficient transportation, though they are being worried by traffic jam. To solve this problem we studied qualities and quantities of urban transport, and located some kinds of transportation to the adequate positions in the spectral field of traffic demand. Consequently we noticed that the construction cost is too expensive when the density of traffic is under some degree. In order to reduce the construction cost and business expenditure, we propose a light vehicle and high frequency system. To lower axle load, width of the car is contracted. This means reduction of axle load, at the same time, of carrying capacity. So high frequency system of trains is adopted. It will also present good service to the passengers.

As Director of the Railway Technical Research Institute, JNR, I deem it a great honour to contribute an article to your esteemed Bulletin, about the present status of this Institute and about the latest developments in seismic research and designing in JNR.

Rapidly increasing traffic loads on the 130-mph New Tokaido Line of the Japanese National Railways was considered to affect life endurance of the closely designed structures supporting the line and endanger train operation in the future. In 4.5 yr since its opening to traffic on October 1, 1964, the average daily number of passengers has more than tripled from the initial figure of 60,539 while the average daily number of trains increased by about 2.7 times. Passengers much in excess of seating capacity had to be loaded while the original design load had been determined taking the weight of seated passengers only. The future trend of increases in weight and frequency of loadings and its effect were studied elaborately using statistical data and probability theories. It showed that 5% to 6% shortening of life expectancy is probable in certain short-span beams where the frequency and intensity of stresses are relatively high. Design load for future extension of the NTL was revised taking the aforementioned matter into account.