cudaRegistration

PACC: pipelined accelerator

PACC is an extention of OpenACC directives.

Please see the README file for more information about this program.

Download Source Code (20170112)

For any comments or questions, please contact me (ino(at)ist.osaka-u.ac.jp).
* Please replace (at) with @.

References:
[1] Nobuhiro Miki, Fumihiko Ino, and Kenichi Hagihara, ``An Extension of OpenACC Directives for Out-of-Core Stencil Computation with Temporal Blocking,'' In Proceedings of the 3rd Workshop on Accelerator Programming Using Directives (WACCPD 2016), pp. 36--45, Salt Lake City, UT, USA, (2016-11). [DOI]


cuShiftOr: exact and approximate string matching

cuShift is an implementation of string matching algorithms accelerated on a CUDA-compatible GPU.

Please see the README file for more information about this program.

Download Source Code (20160623)

For any comments or questions, please contact me (ino(at)ist.osaka-u.ac.jp).
* Please replace (at) with @.


All-pairs comparison based on SW#

This tar ball includes a sample program and a patch file to SW#, a CUDA-accelerated Smith-Waterman implementation distributed at http://sourceforge.net/projects/swsharp/

Please see the README file for more information about this program.

Download Source Code (20150801)

For any comments or questions, please contact me (ino(at)ist.osaka-u.ac.jp).
* Please replace (at) with @.

References:
[1] Daiki Okada, Fumihiko Ino, and Kenichi Hagihara, ``Accelerating the Smith-Waterman Algorithm with an Interpair Pruning Method for All-Pairs Comparison of Base Sequences,'' BMC Bioinformatics, Vol.16, No.321, 15 pages, Oct. 2015. [DOI]


cudaRegistration

cudaRegistration contains a program for accelerating nonrigid registrations of medical images [1,2].

The following code includes a GPU implementation of nonrigid registrations based on Rueckert's registration algorithm. The implementation of the rigid registration program is NOT included.

Please see the README file for more information about this program.

Download Source Code (20140320)

For any comments or questions, please contact me (i-kei(at)ist.osaka-u.ac.jp).
* Please replace (at) with @.

References:
[1] Kei Ikeda, Fumihiko Ino, and Kenichi Hagihara, ``Efficient Acceleration of Mutual Information Computation for Nonrigid Registration Using CUDA,'' IEEE Journal of Biomedical and Health Informatics, Vol.18, No.3, pp.956--968, May 2014. [DOI]
[2] Kei Ikeda, Fumihiko Ino, and Kenichi Hagihara, ``Accelerating Mutual Information Computation for Nonrigid Registration the GPU,'' In Poster in the 3rd GPU Technology Conference (GTC 2012), San Jose, CA, USA, (2012-05). [PDF]