300x Faster Matlab using MatlabMPI

TL;DR

MatlabMPI enables Matlab programs to efficiently utilize multiple processors by implementing MPI standards through simple file I/O, achieving high speedups and excellent software efficiency on various high-performance computing systems.

Contribution

This paper introduces MatlabMPI, a compact and portable implementation of MPI in Matlab that achieves near-C performance and high productivity for parallel computing in Matlab.

Findings

Achieves ~300x speedup with 304 CPUs on an IBM SP2.

Matches C MPI bandwidth at large message sizes.

High software efficiency with 0.85 Gflop/SLOC.

Abstract

The true costs of high performance computing are currently dominated by software. Addressing these costs requires shifting to high productivity languages such as Matlab. MatlabMPI is a Matlab implementation of the Message Passing Interface (MPI) standard and allows any Matlab program to exploit multiple processors. MatlabMPI currently implements the basic six functions that are the core of the MPI point-to-point communications standard. The key technical innovation of MatlabMPI is that it implements the widely used MPI ``look and feel'' on top of standard Matlab file I/O, resulting in an extremely compact (~250 lines of code) and ``pure'' implementation which runs anywhere Matlab runs, and on any heterogeneous combination of computers. The performance has been tested on both shared and distributed memory parallel computers (e.g. Sun, SGI, HP, IBM and Linux). MatlabMPI can match the bandwidth of C based MPI at large message sizes. A test image filtering application using MatlabMPI achieved a speedup of ~300 using 304 CPUs and ~15% of the theoretical peak (450 Gigaflops) on an IBM SP2 at the Maui High Performance Computing Center. In addition, this entire parallel benchmark application was implemented in 70 software-lines-of-code (SLOC) yielding 0.85 Gigaflop/SLOC or 4.4 CPUs/SLOC, which are the highest values of these software price performance metrics ever achieved for any application. The MatlabMPI software will be available for download.