Fast matrix multiplies using graphics hardware
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
An Investigation of Phylogenetic Likelihood Methods
BIBE '03 Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering
Cg: a system for programming graphics hardware in a C-like language
ACM SIGGRAPH 2003 Papers
Linear algebra operators for GPU implementation of numerical algorithms
ACM SIGGRAPH 2003 Papers
Sparse matrix solvers on the GPU: conjugate gradients and multigrid
ACM SIGGRAPH 2003 Papers
Fast computation of database operations using graphics processors
SIGMOD '04 Proceedings of the 2004 ACM SIGMOD international conference on Management of data
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
An Efficient Program for Phylogenetic Inference Using Simulated Annealing
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Exploring Graphics Processor Performance for General Purpose Applications
DSD '05 Proceedings of the 8th Euromicro Conference on Digital System Design
RAxML-OMP: an efficient program for phylogenetic inference on SMPs
PaCT'05 Proceedings of the 8th international conference on Parallel Computing Technologies
Dynamic multigrain parallelization on the cell broadband engine
Proceedings of the 12th ACM SIGPLAN symposium on Principles and practice of parallel programming
Journal of VLSI Signal Processing Systems
Adapting a message-driven parallel application to GPU-accelerated clusters
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Optimizing the parallel computation of linear recurrences using compact matrix representations
Journal of Parallel and Distributed Computing
Data parallel acceleration of decision support queries using Cell/BE and GPUs
Proceedings of the 6th ACM conference on Computing frontiers
Scheduling dynamic parallelism on accelerators
Proceedings of the 6th ACM conference on Computing frontiers
A translation system for enabling data mining applications on GPUs
Proceedings of the 23rd international conference on Supercomputing
GPU parallelization of algebraic dynamic programming
PPAM'09 Proceedings of the 8th international conference on Parallel processing and applied mathematics: Part II
Bio-sequence database scanning on a GPU
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Parallel Position Weight Matrices algorithms
Parallel Computing
Bit-parallel multiple pattern matching
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part II
Direct approaches to exploit many-core architecture in bioinformatics
Future Generation Computer Systems
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Bioinformatics applications are one of the most relevant and compute-demanding applications today. While normally these applications are executed on clusters or dedicated parallel systems, in this work we explore the use of an alternative architecture. We focus on exploiting the compute-intensive characteristics offered by the graphics processors (GPU) in order to accelerate a bioinformatics application. The GPU is a good match for these applications as it is an inexpensive, high-performance SIMD architecture. In our initial experiments we evaluate the use of a regular graphics card to improve the performance of RAxML, a bioinformatics program for phylogenetic tree inference. In this paper we focus on porting to the GPU the most time-consuming loop, which accounts for nearly 50% of the total execution time. The preliminary results show that the loop code achieves a speedup of 3x while the whole application with a single loop optimization, achieves a speedup of 1.2x.