An exa-scale high-performance molecular dynamics simulation program: MODYLAS.

A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.

Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations.

In the era of exascale supercomputers, large-scale, and long-time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)-communication in the MPI-parallelized fast multipole method (FMM) combined with MD calculations under three-dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM. In communications of multipole coefficients, the reduction rate of communication data in the new algorithm relative to the amount of data in the conventional one increases as both the number of FMM levels and the number of MPI processes increase. The aforementioned rate increase could exceed 50% as the number of MPI processes becomes larger for very large systems. The proposed algorithm, named the minimum-transferred data (MTD) method, should enable large-scale and long-time MD calculations to be calculated efficiently, under the condition of massive MPI-parallelization on exascale supercomputers.

A case of a teenage boy with eosinophilic gastroenteritis with esophageal involvement developing a hemorrhagic duodenal ulcer.

A boy in his early teens visited our hospital with chief complaints of hematemesis and tarry stools. Upper gastrointestinal endoscopy identified a hemorrhagic duodenal ulcer, for which hemostasis was performed using a clip. Proton pump inhibitor (PPI) administration diminished the ulcer but relapse occurred after PPI discontinuation. The esophagus showed concentric rings and longitudinal linear furrows considered to be characteristic of eosinophilic esophagitis. Biopsies of the duodenal ulcer and the esophagus revealed marked infiltration of eosinophils, leading to a diagnosis of eosinophilic gastroenteritis with esophageal involvement. Steroid treatment was initiated, and the duodenal ulcer and esophagitis resolved. Endoscopic findings characteristic of eosinophilic esophagitis were key to the diagnosis of eosinophilic gastroenteritis.