Performance Modeling and Prediction for the Scalable Solution of Partial Differential Equations on Unstructured Grids

<p>This dissertation studies the sources of poor performance in scientific computing codes based on partial differential equations (PDEs), which typically perform at a computational rate well below other scientific simulations (e.g., those with dense linear algebra or N-body kernels) on modern architectures with deep memory hierarchies. We identify that the primary factors responsible for this relatively poor performance are: insufficient available memory bandwidth, low ratio of work to data size (good algorithmic efficiency), and nonscaling cost of synchronization and gather/scatter operations (for a fixed problem size scaling). This dissertation also illustrates how to reuse the legacy scientific and engineering software within a library framework.</p> <p>Specifically, a three-dimensional unstructured grid incompressible Euler code from NASA has been parallelized with the Portable Extensible Toolkit for Scientific Computing (PETSc) library for distributed memory architectures. Using this newly instrumented code (called PETSc-FUN3D) as an example of a typical PDE solver, we demonstrate some strategies that are effective in tolerating the latencies arising from the hierarchical memory system and the network. Even on a single processor from each of the major contemporary architectural families, the PETSc-FUN3D code runs from 2.5 to 7.5 times faster than the legacy code on a medium-sized data set (with approximately 10⁵ degrees of freedom). The major source of performance improvement is the increased locality in data reference patterns achieved through blocking, interlacing, and edge reordering. To explain these performance gains, we provide simple performance models based on memory bandwidth and instruction issue rates.</p> <p>Experimental evidence, in terms of translation lookaside buffer (TLB) and data cache miss rates, achieved memory bandwidth, and graduated floating point instructions per memory reference, is provided through accurate measurements with hardware counters. The performance models and experimental results motivate algorithmic and software practices that lead to improvements in both parallel scalability and per-node performance. We identify the bottlenecks to scalability (algorithmic as well as implementation) for a fixed-size problem when the number of processors grows to several thousands (the expected level of concurrency on terascale architectures). We also evaluate the hybrid programming model (mixed distributed/shared) from a performance standpoint.</p>

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Computer Science

Year dc:date.available

2002

Author dc:creator

• Kaushik, Dinesh Kumar

Contributors dc:contributor

• David Keyes
• William Gropp
• Alex Pothen
• Chester Grosch
• Mohammad Zubair

• Cache
• Hybrid programming
• Partial differential equations
• Unstructured grids
• Computer Sciences

Statement dc:rights

• <p>In Copyright. URI: <a href="http://rightsstatements.org/vocab/InC/1.0/">http://rightsstatements.org/vocab/InC/1.0/</a> This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).</p>

Identifier

9780493883694

OAI identifier oai:identifier

oai:digitalcommons.odu.edu:computerscience_etds-1109