On 17/11/13 09:20 AM, Hornung, Bastian wrote: > I'm not familiar with GitHub, and I think I just submitted it, but it doesn't > show up yet. > Any validation process necessary til an issue shows up, or am I just dumb > right now?
It is here: https://github.com/sebhtml/ray/issues/221 > > Regards, > > Bastian > ________________________________________ > From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] > Sent: Friday, November 15, 2013 5:59 PM > To: Hornung, Bastian > Cc: denovoassembler-users@lists.sourceforge.net > Subject: Re: [Denovoassembler-users] Ray doesn't run on 2 cores (only more or > less) > > 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, > > This is an interesting bug. > > I reproduced the problem: > > Works: > [boiseb01@ls30 Ray-2.3.0]$ mpiexec -n 1 ./Ray -p > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R1.fastq > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R2.fastq -o > 1-core > > > Does not work: > [boiseb01@ls30 Ray-2.3.0]$ mpiexec -n 2 ./Ray -p > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R1.fastq > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R2.fastq > > > Works: > [boiseb01@ls30 Ray-2.3.0]$ mpiexec -n 3 ./Ray -p > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R1.fastq > ~/data-for-system-tests/ecoli-MiSeq/MiSeq_Ecoli_MG1655_110527_R2.fastq -o > 3-core > > > Can you submit an issue on https://github.com/sebhtml/ray/issues/new . > > > I will add this to the 5 open issues for Ray 2.3.1 (see > https://github.com/sebhtml/ray/issues?milestone=8&state=open ) > > > seb > >> >> ************************************************** >> 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. 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