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 ************************************************** 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
