Parallel k-mer counting: 1 thread per sample#102
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This was referenced Aug 4, 2017
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Closed in favor of #107. |
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The most time intensive steps of kevlar,
kevlar countandkevlar novel, are in need of some significant speedup. This PR is investigating a simple change so that the 3-4 samples in a simplex are loaded in parallel in dedicated threads. Testing on small sample files gives the approximate speedup expected. But after having gone through this trouble, it's probably worth taking a closer look at how khmer handles multithreaded loading for a single sample, which would give much more flexibility and (hopefully performance increase) when more threads are available.