Dear all,
Just passing by and saw this thread. It seems lots of people would rather have BWA running on multi-core. Given INDEX is a one-off task for a certain batch of files, and ALN is supporting -t, thus only left SAMPE, SAMSE single-threaded.
I have a version of SAMPE able to run multithreaded. Although it's done on Windows under CRT (C Runtime), the basic idea can be easily transfered back to the Linux code base, only needed knowledge of MemoryMappedFiles, and some threading concepts, it's just some plumbing wrapped around some core function calls. SAMSE can be done in the same way ( I didn't do that because I only have PE data in my hand).
My project site is here http://bow.codeplex.com/, you can find some performance data on the release page. Source code is on GitHub: https://github.com/xied75, (oh, should be this branch https://github.com/xied75/bwa/tree/mt-sampe)
I recently tested this MT-SAMPE on Windows Azure (Cloud) large instance with 4 cores 8GB memory, it runs without any problem on -t 4.
Best,
dong
Just passing by and saw this thread. It seems lots of people would rather have BWA running on multi-core. Given INDEX is a one-off task for a certain batch of files, and ALN is supporting -t, thus only left SAMPE, SAMSE single-threaded.
I have a version of SAMPE able to run multithreaded. Although it's done on Windows under CRT (C Runtime), the basic idea can be easily transfered back to the Linux code base, only needed knowledge of MemoryMappedFiles, and some threading concepts, it's just some plumbing wrapped around some core function calls. SAMSE can be done in the same way ( I didn't do that because I only have PE data in my hand).
My project site is here http://bow.codeplex.com/, you can find some performance data on the release page. Source code is on GitHub: https://github.com/xied75, (oh, should be this branch https://github.com/xied75/bwa/tree/mt-sampe)
I recently tested this MT-SAMPE on Windows Azure (Cloud) large instance with 4 cores 8GB memory, it runs without any problem on -t 4.
Best,
dong
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