Parallel Haskell: 2-year project to push real world use
Christian Höner zu Siederdissen
choener at tbi.univie.ac.at
Mon May 3 21:10:31 EDT 2010
* Ben Lippmeier <benl at ouroborus.net> [04.05.2010 02:21]:
> You can certainly create an array with these values, but in the provided code it looks like each successive array element has a serial dependency on the previous two elements. How were you expecting it to parallelise?
actually, in reality it is rather more complex, in a 2d-array, each cell
(i,j) requires a linear number of accesses to previously calculated
cells that all have indices bounded by the current (i,j).
One of the simplest codes is like this:
forall i in [1..n]
forall j in [i..n]
set (i,j) to: minimum of (i,k)+(k,j) (forall k in [i+1..j-1])
So, either I use destructive updates or need a tricky way to extend the
already computed part of the array with the new part (i,j). The above
code shows only why I need destructive updates. RNA folding is one of
those where it is needed.
I will try to distill the code down to an example that shows a
possibility for parallelization. I would want to use this for future
algorithms where it makes much more sense (O(n^4) or more), but that
still first update an array element, and then access it later.
Here http://www.tbi.univie.ac.at/newpapers/Abstracts/98-06-009.ps.gz is
a description of a parallel version of RNAfold.
> Repa arrays don't support visible destructive update. For many algorithms you should't need it, and it causes problems for parallelisation.
> I'm actively writing more Repa examples now. Can you sent me some links explaining the algorithm that you're using, and some example data + output?
> On 04/05/2010, at 9:21 AM, Christian Höner zu Siederdissen wrote:
> > a = array (1,10) [ (i,f i) | i <-[1..10]] where
> > f 1 = 1
> > f 2 = 1
> > f i = a!(i-1) + a!(i-2)
> > (aah, school ;)
> > Right now, I am abusing vector in ST by doing this:
> > a <- new
> > a' <- freeze a
> > forM_ [3..10] $ \i -> do
> > write a (a'!(i-1) + a!(i-2))
> > Let's say I wanted to do something like this in dph (or repa), does that
> > work? We are actually using this for RNA folding algorithms that are at
> > least O(n^3) time. For some of the more advanced stuff, it would be
> > really nice if we could "just" parallelize.
> > To summarise: I need arrays that allow in-place updates.
> > Otherwise, most libraries that do heavy stuff (O(n^3) or worse) are
> > using vector right now. On a single core, it performs really great --
> > even compared to C-code that has been optimized a lot.
> > Thanks and "Viele Gruesse",
> > Christian
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