[mira_talk] Re: building 4.9.5 with gcc 4.4.7?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 28 Oct 2015 21:39:39 -0400
On 10 Oct 2015, at 7:18 , Langhorst, Brad <Langhorst@xxxxxxx> wrote:
Just for mirabait?
Yep, just for mirabait.
Interesting what a single post can do. In short, the next release of MIRA will
have a revamped mirabait, with a 2^31bp limit in sequence lengths, but which
also will be quite a deal faster.
30kb limit in sequences? Oooops, I was using old routines. Changing to new ones
drops the limit and gives instant 25% boost in baiting speed.
Hmmm, loading takes quite long? A few tweaks here and there doubles the loading
speed.
These two steps alone reduce runtime by 40%.
But then … why is the baiting step not multithreaded? Oh wait, a simple version
is trivial to implement.
Result: with 4 cores, the new version is now 3x faster than the old one. Yay.
B.
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