On 14/11/13 03:25 AM, Hornung, Bastian wrote: > Hi @all, > > I have a sort of stupid problem (or maybe I'm just stupid, don't know), which > is probably not relevant to anyone else, but still wanted to report it: I'm > not able to run ray with only 2 cores. > The command, and the output: > > mpiexec -n 2 ./Ray -p /home/bastian/data/Raw_data/NG-XXX_1_1.fastq > /home/bastian/data/Raw_data/NG-XXX_1_2.fastq
Hi Bastian, I found the issue. It was caused by the changes made to the -route-messages which is not more intelligent. Fix (one line changed !): https://github.com/sebhtml/ray/commit/9729dbce542fca2cbe45ea9cd5a436d573461b87 Thank you ! > > ************************************************** > This program comes with ABSOLUTELY NO WARRANTY. > This is free software, and you are welcome to redistribute it > under certain conditions; see "LICENSE.txt" for details. > ************************************************** > > Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert > Centre de recherche en infectiologie de l'Université Laval > Project funded by the Canadian Institutes of Health Research (Doctoral award > 200902CGM-204212-172830 to S.B.) > http://denovoassembler.sf.net/ > > References to cite: > > Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette > and Jacques Corbeil. > Ray Meta: scalable de novo metagenome assembly and profiling. > Genome Biology (BioMed Central Ltd). > 13:R122, Published: 22 December 2012 > http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 > > Sébastien Boisvert, François Laviolette & Jacques Corbeil. > Ray: simultaneous assembly of reads from a mix of high-throughput sequencing > technologies. > Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New > York, U.S.A.). > November 2010, Volume 17, Issue 11, Pages 1519-1533. > http://dx.doi.org/doi:10.1089/cmb.2009.0238 > > Ray version 2.3.0 > License for Ray: GNU General Public License version 3 > RayPlatform version: 2.0.0 > License for RayPlatform: GNU Lesser General Public License version 3 > > MAXKMERLENGTH: 201 > Maximum coverage depth stored by CoverageDepth: 4294967295 > MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes > FORCE_PACKING = n > ASSERT = n > HAVE_LIBZ = n > HAVE_LIBBZ2 = n > PROFILER_COLLECT = n > MINIRANKS = y > CLOCK_GETTIME = n > __linux__ = y > _MSC_VER = n > __GNUC__ = y > RAY_32_BITS = n > RAY_64_BITS = y > MPI standard version: MPI 2.1 > MPI library: Open-MPI 1.4.3 > Compiler: GNU gcc/g++ 4.6.3 > MPI I/O: n > > > > And then nothing happens. > If I change n to 1 or 3 it will run, but with 2 it just stalls. > (why am I running an assembly on 2 cores? Because I run 5 in parallel, and I > have more time than computing power) > > > As said, not sure if it's really relevant, but better to report than to > ignore. > > Best regards, > > Bastian > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
