Dinh:COMPUTATIONAL/GPU Project

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<calendar> name=Dinh format=%name/NOTES/%year-%month-%day date=2009/07/01 view=oneyear </calendar>

Note for Future Directions (July 2009):

1. Write development strategy for CUDA implementation w.r.t. to distinct developmental milestones

2. Design testing procedure for each developmental milestones

3. Begin coding ASAP

4. Map out all tasks/data structures involved in ./bwa aln function.


Update: June 27, 2009

Dinh: reconfigured NVIDIA driver so that CUDA can recognize device. Confirmed device recognition by running SDK programs: deviceQuery and bandWidthTest.


Dinh: Used findCuda.cmake to create makefile for bwtalnGPU project linked to a test cuda program. (Note that nvcc can be used to compile .c source code as well. Cuda syntax can be used within a .c file. However, the file extension should be changed to .cu when it contain Cuda syntax and needs to be compiled with nvcc.)


Update: June 26, 2009

Dinh: completed analysis of current BWT aligners with emphasis on Bowtie and BWA and w.r.t. to ease of implementation to CUDA. See "bwt aligners" for details.


Update: June 22, 2009

Dinh: completed case study/analysis of MUMmerGPU-1.1 with descriptions of important aspects which could be implemented in future GPU aligners. See "MUMmerGPU study" for more details


Update: June 2, 2009

Matt: completed installation of CUDA 2.2 for development.