Dinh:COMPUTATIONAL/GPU Project
<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.