Le mardi 23 novembre 2010 Ã 17:28 -0500, George Bosilca a Ã©crit :
> 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 !
> On Nov 23, 2010, at 17:17 , SÃ©bastien Boisvert wrote:
> > I now use MPI_Isend, so the problem is no more.
> devel mailing list
M. SÃ©bastien Boisvert
Ãtudiant au doctorat en physiologie-endocrinologie Ã l'UniversitÃ© Laval
Boursier des Instituts de recherche en santÃ© du Canada
Ãquipe du Professeur Jacques Corbeil
Centre de recherche en infectiologie de l'UniversitÃ© Laval
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Canada G1V 4G2
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