Postnuc speed #30
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Postnuc speed #30
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Previously each `Node` in the alignment graph was wasting huge amounts of memory. Each `Score` structure had seven bytes of padding at the end. Thus, roughly a third of the memory occupied by a `Node` is unused. With the new format, values are tightly packed making a `Node` smaller. For an unrepresentative sample of two E. coli genomes, the new postnuc is 10% faster and uses 50% less memory. The former might be due to better caching.
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I came across this via https://blog.kloetzl.info/mummer-the/ via Twitter. As an occasional user of mummer for genome assembly alignment as part of QA, I'd welcome the reported typical 1/3 less memory usage and 20% speed increase. |
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Ouf this is quite old |
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Is there any reason why this hasn’t been merged? Is this code base being maintained any more? |
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Hi,
I am happy to see that there is still work done on MUMmer. Here is a patch, that I had lying around for a while. It greatly increases the performance of postnuc. This pull request also includes the patch to issue #29.
Best,
Fabian