Computational chemistry on Fujitsu vector–parallel processors: Development and performance of applications software

Abstract

In this and a preceding paper, we provide an introduction to the Fujitsu VPP range of vector±parallel supercomputers and to some of the computational chemistry software available for the VPP. Here, we consider the implementation and performance of seven popular chemistry application packages. The codes discussed range from classical molecular dynamics to semiempirical and ab initio quantum chemistry. All have evolved from sequential codes, and have typically been parallelised using a replicated data approach. As such they are well suited to the large-memory/fast-processor architecture of the VPP. For one code, CASTEP, a distributed-memory data-driven parallelisation scheme is presented. Ó 2000 Published by Elsevier Science B.V. All rights reserved.

Photoelectrochemical study of lanthanide zirconium oxides, Ln2Zr2O7 (Ln=La, Ce, Nd and Sm)

“…The generalized gradient approximation (GGA) was selected for the theoretical basis of the density function [16]. The code adopted the band-by-band conjugategradient technique to minimize the total energy with respect to the plane-wave expansion coefficient [17]. In setting up the CASTEP run, basic parameters were selected as described in our previous study [14].…”

Photoelectrochemical study of lanthanide titanium oxides, Ln2Ti2O7 (Ln=La, Sm, and Gd)

“…Generalized gradient approximations (GGA) were chosen for the theoretical basis of density function [14]. The code adopted the band-by-band conjugate-gradient technique to minimize the total energy with respect to plane-wave expansion coefficient [15]. In setting up the CASTEP run, basic parameters were chosen as shown in Table 1.…”

Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations

“…Unlike the MM methods, however, the SE QM methods have been challenging to achieve a high degree of parallelization. − One major reason is the iterative nature of the self-consistent field (SCF) procedure of the QM methods, which is necessary to attain the converged electronic energy. Because each routine involved in the SCF iteration has to be executed sequentially, each of them has to be parallelized individually for the entire procedure to be scalable.…”