Array files for computational chemistry: MP2 energies

Abstract

A simple message-passing implementation for distributed disk storage, called array files (AF), is described. It is designed primarily for parallelizing computational chemistry applications but it should be useful for any application that handles large amounts of data stored on disk. AF allows transparent distributed storage and access of large data files. An AF consists of a set of logically related records, i.e., blocks of data. It is assumed that the records have the typical dimension of matrices in quantum chemical calculations, i.e., they range from 0.1 to approximately 32 MB in size. The individual records are not striped over nodes; each record is stored on a single node. As a simple application, second-order Møller-Plesset (MP2) energies have been implemented using AF. The AF implementation approaches the efficiency of the hand-coded program. MP2 is relatively simple to parallelize but for more complex applications, such as Coupled Cluster energies, the AF system greatly simplifies the programming effort.