Converting best manual practice into generic automatable strategies for unstructured mesh parallelisation

The manual effort required to convert sequential computational mechanics programs into a useful, scalable parallel form is considerable. Tools that can assist in the conversion process are clearly required. Computer aided parallelisation tools (CAPTools) have been developed to generate efficient parallel code for real world structured grid application codes such as Computational Fluid Dynamics. Automatable single-program multi-data (SPMD) overlapping domain decomposition (DD) techniques established for structured grid codes have been adapted by the authors to manually parallelise unstructured mesh applications. Inspector loops have been used to provide generic techniques for the run-time support necessary to extend the capabilities of CAPTools to automatic implementation of SPMD DD techniques in the parallelisation of unstructured mesh codes. Copyright © 1999 John Wiley & Sons, Ltd.

Three parallel programming paradigms: Comparisons on an archetypal PDE computation

Three paradigms for distributed-memory parallel computation that free the application programmer from the details of message passing are compared for an archetypal structured scientific computation -- a nonlinear, structured-grid partial differential equation boundary value problem -- using the same algorithm on the same hardware. All of the paradigms -- parallel languages represented by the Portland Group's HPF, (semi-)automated serial-to-parallel source-to-source translation represented by CAP-Tools from the University of Greenwich, and parallel libraries represented by Argonne's PETSc -- are found to be easy to use for this problem class, and all are reasonably effective in exploiting concurrency after a short learning curve. The level of involvement required by the application programmer under any paradigm includes specification of the data partitioning, corresponding to a geometrically simple decomposition of the domain of the PDE. Programming in SPMD style for the PETSc library requires writing only the routines that discretize the PDE and its Jacobian, managing subdomain-to-processor mappings (affine global-to-local index mappings), and interfacing to library solver routines. Programming for HPF requires a complete sequential implementation of the same algorithm as a starting point, introduction of concurrency through subdomain blocking (a task similar to the index mapping), and modest experimentation with rewriting loops to elucidate to the compiler the latent concurrency. Programming with CAPTools involves feeding the same sequential implementation to the CAPTools interactive parallelization system, and guiding the source-to-source code transformation by responding to various queries about quantities knowable only at runtime. Results representative of "the state of the practice" for a scaled sequence of structured grid problems are given on three of the most important contemporary high-performance platforms: the IBM SP, the SGI Origin 2000, and the CRAYY T3E.

Portability, predictability and performance for parallel computing: BSP in practice

We report on practical experience using the Oxford BSP Library to parallelize a large electromagnetic code, the British Aerospace finite-difference time-domain code EMMA T:FD3D. The Oxford BS Library is one of the first realizations of the Bulk Synchronous Parallel computational model to be targeted at numerically intensive scientific (typically Fortran) computing. The BAe EMMA code is one of the first large-scale applications to be parallelized using this library, and it is an important demonstration of the cost effectiveness of the BSP approach. We illustrate how BSP cost-modelling techniques can be used to predict and optimize performance for single-source programs across different parallel platforms. We provide predicted and observed performance figures for an industrial-strength, single-source parallel code for a variety of real parallel architectures: shared memory multiprocessors, workstation clusters and massively parallel platforms.

Parallel bandwidth characteristics calculations for thin avalanche photodiodes on a SGI Origin 2000 supercomputer

An important factor for high-speed optical communication is the availability of ultrafast and low-noise photodetectors. Among the semiconductor photodetectors that are commonly used in today’s long-haul and metro-area fiber-optic systems, avalanche photodiodes (APDs) are often preferred over p-i-n photodiodes due to their internal gain, which significantly improves the receiver sensitivity and alleviates the need for optical pre-amplification. Unfortunately, the random nature of the very process of carrier impact ionization, which generates the gain, is inherently noisy and results in fluctuations not only in the gain but also in the time response. Recently, a theory characterizing the autocorrelation function of APDs has been developed by us which incorporates the dead-space effect, an effect that is very significant in thin, high-performance APDs. The research extends the time-domain analysis of the dead-space multiplication model to compute the autocorrelation function of the APD impulse response. However, the computation requires a large amount of memory space and is very time consuming. In this research, we describe our experiences in parallelizing the code in MPI and OpenMP using CAPTools. Several array partitioning schemes and scheduling policies are implemented and tested. Our results show that the code is scalable up to 64 processors on a SGI Origin 2000 machine and has small average errors.