Application of Pfortran and Co-Array Fortran in the parallelization of the GROMOS96 molecular dynamics module

Article type: Research Article

Authors: Bała, Piotr | Clark, Terry | Scott, L. Ridgway

Affiliations: Faculty of Mathematics and Computer Science, N. Copernicus University, Chopina 12/18, 87-100 Toruń, Poland. Tel.: +48 56 611 3468; Fax: +48 56 622 8979; E-mail: bala@mat.uni.torun.pl | Department of Computer Science, University of Chicago and Computation Institute, 1100 E. 58th Street, Chicago, IL 60637, USA. E-mail: {ridg,twclark}@cs.uchicago.edu

Abstract: After at least a decade of parallel tool development, parallelization of scientific applications remains a significant undertaking. Typically parallelization is a specialized activity supported only partially by the programming tool set, with the programmer involved with parallel issues in addition to sequential ones. The details of concern range from algorithm design down to low-level data movement details. The aim of parallel programming tools is to automate the latter without sacrificing performance and portability, allowing the programmer to focus on algorithm specification and development. We present our use of two similar parallelization tools, Pfortran and Cray's Co-Array Fortran, in the parallelization of the GROMOS96 molecular dynamics module. Our parallelization started from the GROMOS96 distribution's shared-memory implementation of the replicated algorithm, but used little of that existing parallel structure. Consequently, our parallelization was close to starting with the sequential version. We found the intuitive extensions to Pfortran and Co-Array Fortran helpful in the rapid parallelization of the project. We present performance figures for both the Pfortran and Co-Array Fortran parallelizations showing linear speedup within the range expected by these parallelization methods.

Journal: Scientific Programming, vol. 9, no. 1, pp. 61-68, 2001