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Subject: Re: [OMPI devel] Simple program (103 lines) makes Open-1.4.3 hang
From: Sébastien Boisvert (Sebastien.Boisvert.3_at_[hidden])
Date: 2010-11-23 17:36:25


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
Téléphone: 418 525 4444 46342
Courriel: SEB_at_[hidden]
Web: http://boisvert.info
"Innovation comes only from an assault on the unknown" -Sydney Brenner