TY - GEN
T1 - For three easy payments
T2 - 2012 Symposium on Application Accelerators in High Performance Computing, SAAHPC 2012
AU - Weber, Rick
AU - Peterson, Gregory D.
AU - Hettich, Robert
PY - 2012
Y1 - 2012
N2 - In shotgun proteomics, matching peptides to tandem mass spectrometry data is a computationally expensive process that in some cases can take days using conventional software packages. Even though many existing search engines such as Sequest, Myrimatch, and X!Tandem now exploit multiple processors via threading libraries, they leave much on the table in terms of performance and don't exploit computational accelerators. In this paper, we present Specmaster, a Myrimatch implementation written in OpenCL with performance portability in mind. We demonstrate the same Specmaster codebase outperforming Myrimatch by several fold on 32- core AMD and Intel x86 machines and by nearly an order of magnitude on both an AMD Radeon 7970 and Nvidia GTX 480. We describe the rationale behind Specmaster's design, and how to gain portable performance on a plethora of architectures using OpenCL.
AB - In shotgun proteomics, matching peptides to tandem mass spectrometry data is a computationally expensive process that in some cases can take days using conventional software packages. Even though many existing search engines such as Sequest, Myrimatch, and X!Tandem now exploit multiple processors via threading libraries, they leave much on the table in terms of performance and don't exploit computational accelerators. In this paper, we present Specmaster, a Myrimatch implementation written in OpenCL with performance portability in mind. We demonstrate the same Specmaster codebase outperforming Myrimatch by several fold on 32- core AMD and Intel x86 machines and by nearly an order of magnitude on both an AMD Radeon 7970 and Nvidia GTX 480. We describe the rationale behind Specmaster's design, and how to gain portable performance on a plethora of architectures using OpenCL.
KW - Mass spectrometry
KW - Myrimatch
KW - OpenCL
KW - Shotgun proteomics
KW - Specmaster
UR - https://www.scopus.com/pages/publications/84870679771
U2 - 10.1109/SAAHPC.2012.20
DO - 10.1109/SAAHPC.2012.20
M3 - Conference contribution
AN - SCOPUS:84870679771
SN - 9780769548388
T3 - Symposium on Application Accelerators in High-Performance Computing
SP - 102
EP - 110
BT - Proceedings - 2012 Symposium on Application Accelerators in High Performance Computing, SAAHPC 2012
Y2 - 10 July 2012 through 11 July 2012
ER -