INTRODUCTION
CUDA-MEME is a motif discovery software based on MEME (version 3.5.4) algorithm for a single GPU device using CUDA programming model. At present, CUDA-MEME only supports the OOPS and ZOOPS models. This algorithm has been fully tested on a Tesla C1060 and a GeForce GTX 280 graphics card, and has been incorporated to NVIDIA Tesla Bio Workbench.
mCUDA-MEME
is an ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0)
algorithm for mutliple GPUs using a hybrid combination of CUDA, MPI and
OpenMP parallel programming models. This algorithm is a further extension of CUDA-MEME with respect to accuracy and speed and has been tested on a
GPU cluster with eight compute nodes and two Fermi-based Tesla S2050
(and Tesla-based Tesla S1070) quad-GPU computing systems, running the Linux OS with the MPICH2
library. The experimental results showed that our algorithm scales well
with respect to both dataset sizes and the number of GPUs. At present,
OOPS and ZOOPS models are supported, which are sufficient for most motif
discovery applications. The source code is available for download.
DOWNLOADS
USAGE
Refer to the usage in the MCUDA-MEME page.
CITATION
CONTACT
- When modifying, copying or distributing CUDA-MEME, please read carefully about the copyright in the file tarball. If having any questions or improvement sabout this software, please contact Liu Yongchao (School of Computer Engineering, Nanyang Technological University, Singapore) without hesitation (liuy0039@ntu.edu.sg; yongchao.liu@live.com; nkcslyc@hotmail.com). Enjoy it.
- Before compiling the program, please check the compute capability of your GPU device.
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