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Scientific computing

MyriMatch proteomics
Our benchmarks sometimes come from unexpected places, and such is the case with this one. David Tabb is a friend of mine from high school and a long-time TR reader. He has provided us with an intriguing new benchmark based on an application he's developed for use in his research work. The application is called MyriMatch, and it's intended for use in proteomics, or the large-scale study of protein. I'll stop right here and let him explain what MyriMatch does:

In shotgun proteomics, researchers digest complex mixtures of proteins into peptides, separate them by liquid chromatography, and analyze them by tandem mass spectrometers. This creates data sets containing tens of thousands of spectra that can be identified to peptide sequences drawn from the known genomes for most lab organisms. The first software for this purpose was Sequest, created by John Yates and Jimmy Eng at the University of Washington. Recently, David Tabb and Matthew Chambers at Vanderbilt University developed MyriMatch, an algorithm that can exploit multiple cores and multiple computers for this matching. Source code and binaries of MyriMatch are publicly available.

In this test, 5555 tandem mass spectra from a Thermo LTQ mass spectrometer are identified to peptides generated from the 6714 proteins of S. cerevisiae (baker's yeast). The data set was provided by Andy Link at Vanderbilt University. The FASTA protein sequence database was provided by the Saccharomyces Genome Database.

MyriMatch uses threading to accelerate the handling of protein sequences. The database (read into memory) is separated into a number of jobs, typically the number of threads multiplied by 10. If four threads are used in the above database, for example, each job consists of 168 protein sequences (1/40th of the database). When a thread finishes handling all proteins in the current job, it accepts another job from the queue. This technique is intended to minimize synchronization overhead between threads and minimize CPU idle time.

The most important news for us is that MyriMatch is a widely multithreaded real-world application that we can use with a relevant data set. I should mention that performance scaling in MyriMatch tends to be limited by several factors, including memory bandwidth, as David explains:

Inefficiencies in scaling occur from a variety of sources. First, each thread is comparing to a common collection of tandem mass spectra in memory. Although most peptides will be compared to different spectra within the collection, sometimes multiple threads attempt to compare to the same spectra simultaneously, necessitating a mutex mechanism for each spectrum. Second, the number of spectra in memory far exceeds the capacity of processor caches, and so the memory controller gets a fair workout during execution.

Here's how the processors performed.

Interestingly, AMD's six-core Phenom IIs snatch a victory over the two non-Hyper-Threaded Sandy Bridge quads here. The Core i7-2600K is a little bit faster than the i7-875K, but not by much more than the clock speed differences between the chips might dictate, given similar per-clock performance.

STARS Euler3d computational fluid dynamics
Charles O'Neill works in the Computational Aeroservoelasticity Laboratory at Oklahoma State University, and he contacted us to suggest we try the computational fluid dynamics (CFD) benchmark based on the STARS Euler3D structural analysis routines developed at CASELab. This benchmark has been available to the public for some time in single-threaded form, but Charles was kind enough to put together a multithreaded version of the benchmark for us with a larger data set. He has also put a web page online with a downloadable version of the multithreaded benchmark, a description, and some results here.

In this test, the application is basically doing analysis of airflow over an aircraft wing. I will step out of the way and let Charles explain the rest:

The benchmark testcase is the AGARD 445.6 aeroelastic test wing. The wing uses a NACA 65A004 airfoil section and has a panel aspect ratio of 1.65, taper ratio of 0.66, and a quarter-chord sweep angle of 45º. This AGARD wing was tested at the NASA Langley Research Center in the 16-foot Transonic Dynamics Tunnel and is a standard aeroelastic test case used for validation of unsteady, compressible CFD codes.

The CFD grid contains 1.23 million tetrahedral elements and 223 thousand nodes . . . . The benchmark executable advances the Mach 0.50 AGARD flow solution. A benchmark score is reported as a CFD cycle frequency in Hertz.

So the higher the score, the faster the computer. Charles tells me these CFD solvers are very floating-point intensive, but they're oftentimes limited primarily by memory bandwidth. He has modified the benchmark for us in order to enable control over the number of threads used. Here's how our contenders handled the test with optimal thread counts for each processor.

The improvements to Sandy Bridge's memory subsystem are likely the source of its solid gains over the prior generation in this application. Just look at how far we've come on this front from the days of the Pentium EE 840. Amazing.