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. > > > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel -- 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: s...@boisvert.info Web: http://boisvert.info "Innovation comes only from an assault on the unknown" -Sydney Brenner