Le mardi 23 novembre 2010 à 17:28 -0500, George Bosilca a écrit :
> Sebastien,
>
> Using MPI_Isend doesn't guarantee asynchronous progress. As you might be
> aware, the non-blocking communications are guaranteed to progress only when
> the application is in the MPI library. Currently very few MPI implementations
> progress asynchronously (and unfortunately Open MPI is not one of them).
>
Regardless, I just need the non-blocking behavior.
I call MPI_Request_free just after MPI_Isend, and I use a ring allocator
to allocate message buffers.
Message recipients just reply with another message to the source, using
a NULL buffer.
The sender waits for the reply before sending the next message.
And it works for assembling bacterial genomes on many MPI ranks:
...
Rank 0: 162 contigs/4576725 nucleotides
Rank 0 reports the elapsed time, Tue Nov 23 01:35:48 2010
---> Step: Collection of fusions
Elapsed time: 0 seconds
Since beginning: 17 minutes, 33 seconds
Elapsed time for each step, Tue Nov 23 01:35:48 2010
Beginning of computation: 1 seconds
Distribution of sequence reads: 7 minutes, 49 seconds
Distribution of vertices: 19 seconds
Calculation of coverage distribution: 1 seconds
Distribution of edges: 29 seconds
Indexing of sequence reads: 1 seconds
Computation of seeds: 2 minutes, 33 seconds
Computation of library sizes: 1 minutes, 47 seconds
Extension of seeds: 3 minutes, 34 seconds
Computation of fusions: 59 seconds
Collection of fusions: 0 seconds
Completion of the assembly: 17 minutes, 33 seconds
Rank 0 wrote Ecoli-THEONE.CoverageDistribution.txt
Rank 0 wrote Ecoli-THEONE.fasta
Rank 0 wrote Ecoli-THEONE.ReceivedMessages.txt
Rank 0 wrote Ecoli-THEONE.Library0.txt
Rank 0 wrote Ecoli-THEONE.Library1.txt
Au revoir !
> george.
>
> On Nov 23, 2010, at 17:17 , Sébastien Boisvert wrote:
>
> > I now use MPI_Isend, so the problem is no more.
>
>
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--
M. Sébastien Boisvert
Étudiant au doctorat en physiologie-endocrinologie à l'Université Laval
Boursier des Instituts de recherche en santé du Canada
Équipe du Professeur Jacques Corbeil
Centre de recherche en infectiologie de l'Université Laval
Local R-61B
2705, boulevard Laurier
Québec, Québec
Canada G1V 4G2
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Web: http://boisvert.info
"Innovation comes only from an assault on the unknown" -Sydney Brenner
