[mira_talk] Re: Parallel Implementation of MIRA
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 1 Oct 2013 20:39:09 +0200
On Oct 1, 2013, at 11:05 , Habeeb Syed <habeeb.syed@xxxxxxx> wrote:
> I was wondering if anybody tried on large machines, something like few
> hundred cores? How is the scale up?
Someone (maybe Jorge? I don't remember) made a couple of test runs on larger
machines. He found out that on his machine, performance improvements plateaued
out at around 40 cores iirc. I suppose that either the bus or the disk were a
bottleneck, but this was never investigated.
MIRA itself has only one part left which could "easily" be multithreaded and is
not yet: the Smith-Waterman matrix calculation and recursive alignment
generation. Incidentally, I suppose large speed-ups there could be achieved by
using SIMD instructions (SSE2/3/4 family) combined with more intelligent memory
usage and plain old parallelism on multiple cores. Of that, I may attack the
latter sometime this year.
Almost all other parts of MIRA which can be parallelised have been
parallelised. However, one of the key steps in MIRA - the contig building -
cannot be parallelised unless MIRA does like other assemblers and stops at
repeats. Which I don't plan to implement because, well, a repeat is only a true
repeat if it is 100% identical and not, like other assemblers think, just
almost identical.
> GPU acceleration will be nice; have you tried?
> What about GPU implementation of MIRA. Can anybody share some insight on
> this?
As far as I am aware of, GPU implementations of bioinformatics algorithms have
not had a terrible success in the wild. Either because they didn't deliver that
much of a speed-up or, equally important, because it's too much work to
implement several different GPU algorithms for all the different cards out
there. Even more vexing, quite a number of larger servers have no GPU at all.
SSE instructions on the other hand are quite common nowadays, one would be hard
pressed to find machines which have no SSE4 (let alone 3 or 2).
As last point, the paper you cited in your initial posting (if it's the one I
have in mind, I did not check yet) had come as a complete surprise to me when I
initially discovered it, totally by chance, a couple of months ago. Someone had
been working on MIRA code without contacting me to find out whether I could
make use of the changes or integrate it back into MIRA. That had been a quite
strange experience at the time.
B.
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