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diff --git a/benchmarks/CUDA/MUM/README b/benchmarks/CUDA/MUM/README deleted file mode 100644 index b48d9ff..0000000 --- a/benchmarks/CUDA/MUM/README +++ /dev/null @@ -1,99 +0,0 @@ -MUMmerGPU 1.0 -August 7, 2007 -Michael Schatz, Cole Trapnel, Art Delcher, & Amitabh Varshney -------------------------------------------------------------- -MUMmerGPU is a high-throughput DNA exact sequence alignment program that -runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video -card to achieve a more than 3-fold speedup over the widely used serial CPU -program MUMmer. It is supports many of the same options as MUMmer, and in -many cases, can be used as a drop in replacement. - -MUMmerGPU uses the "Compute Unified Device Architecture" (CUDA) Software -development kit to program the graphics cards. If you do not have a nVidia -G80, you can still use MUMmerGPU using the G80 emulator available in CUDA. -The emulated version with run much slower than the native version, and -potentially slower than the CPU version of MUMmer. - -Table of Contents ------------------ -. Build & Usage Instructions -. FAQ -. Acknowledgements - - - - -Build & Usage Instructions ------------------- -1) Download and install the CUDA Toolkit 1.0 for your OS from: - http://developer.nvidia.com/object/cuda.html - -2) Download and install the Linux display driver (100.14) from: - http://developer.nvidia.com/object/cuda.html - -3) Edit the CUDA_INSTALL_PATH in the src/Makefile to point to the top level - directory where you installed the CUDA Toolkit. - -4) Run 'make' in the src directory, which will compile the program to run on - the GPU as: - bin/linux32/release/mummergpu - - If you do not have a G80, you can also run 'make emu=1' which will compile - the program to run on the CPU with an emulator as: - bin/linux32/emurelease/mummergpu - -5) Usage: mummergpu [options] reference.fa query.fa - reference.fa must be a single sequence in fasta format - query.fa is a multi-fasta file containing your sequences the more - sequences you provide, the faster MUMmerGPU will execute. - See mummergpu -h for an explanation of the options, many of the options are - the same as those available in MUMmer. - See: http://mummer.sourceforge.net/manual/#mummer for more information - - -FAQs ----- -Q: I have a G70 or other older nVidia graphics card. Can I run MUMmerGPU on it? - -A: No, MUMmerGPU requires a G80 or later video card. You can run MUMmerGPU -with the G80 emulator, but the alignments will be computed much slower than -if you had a G80. - - - -Q: How does MUMmerGPU handle the MUMmer uniqueness options: -mum, -mumcand, --mumreference, and -maxmatch? - -A: MUMmerGPU does not filter matches by uniques and always computes all -maximal matches regardless of their uniqueness (-maxmatch). The filtering -options provided by MUMmer (-mum, -mumcand, & -mumreference) are heuristics to -speed up the alignment process. This is not necessary with the very efficient -MUMmerGPU. If you want to filter your alignments to report only the most -biologically significant, you should use 'delta-filter' instead, which uses a -more sophisticated algorithm for finding the best set of alignments. - -See the MUMmer manual for more information: -http://mummer.sourceforge.net/manual/#filter - - -Q: How does MUMmerGPU handle ambiguous bases? - -A: MUMmerGPU only supports DNA characters (ACGT). Non DNA characters in the -reference are converted arbitrarily to a DNA character (A). Non-DNA characters -in the query set are converted to 'x' to guarantee a mis-match. - - -Q: How can I get help with MUMmerGPU? - -A: Subscribe and post to the mailing list at: - http://sourceforge.net/mail/?group_id=201280 - - - - -Acknowledgements ----------------- -This work was supported in part by National Institutes of Health grants -R01-LM006845 and R01-LM007938, and National Science Foundation CISE RI grant -CNS 04-03313. - |