Taisuke Ozaki

Truong Vinh Truong Duy, Taisuke Ozaki

The fast Fourier transform (FFT) is undoubtedly an essential primitive that has been applied in various fields of science and engineering. In this paper, we present a decomposition method for parallelization of multi-dimensional FFTs with smallest communication amount for all ranges of the number of processes compared to previously proposed methods. This is achieved by two distinguishing features: adaptive decomposition and transpose order awareness. In the proposed method, the FFT data are decomposed based on a row-wise basis that maps the multi-dimensional data into one-dimensional data, and translates the corresponding coordinates from multi-dimensions into one-dimension so that the resultant one-dimensional data can be divided and allocated equally to the processes. As a result, differently from previous works that have the dimensions of decomposition pre-defined, our method can adaptively decompose the FFT data on the lowest possible dimensions depending on the number of processes. In addition, this row-wise decomposition provides plenty of alternatives in data transpose, and different transpose order results in different amount of communication. We identify the best transpose orders with smallest communication amounts for the 3-D, 4-D, and 5-D FFTs by analyzing all possible cases. Given both communication efficiency and scalability, our method is promising in development of highly efficient parallel packages for the FFT.

Yung-Ting Lee, Taisuke Ozaki

The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format such as electron density and molecular orbitals. The web-based GUI program enables us to quickly visualize crystalline and molecular structures by dragging and dropping XYZ, CIF, or OpenMX input/output files, and analyze static/dynamic structural properties conveniently in a web browser. Several basic functionalities such as analysis of Mulliken charges, molecular dynamics, geometry optimization and band structure are included. In addition, based on marching cubes, marching tetrahedra and surface nets algorithms with Affine transformation, 3D isosurface techniques are supported to visualize electron density and molecular/crystalline orbitals in the cube format with superposition of a crystalline or molecular structure. Furthermore, the Band Structure Viewer is implemented for showing a band structure in a web browser. By accessing the website of the OpenMX Viewer, the latest OpenMX Viewer is always available for users to visualize various structures and analyze their properties without installations, upgrades, updates, registration, sign-in and terminal commands.