On 08/11/13 11:54 AM, Rob Egan wrote: > Hi Sébastien, > Correct, the contigs are not paired, but the error occurred after the 'Step' > summary for Estimation of outer distances for paired reads. I'm not sure > what step it was trying to perform when the Bus error happens. >
I think this is similar to the problem described in https://github.com/sebhtml/ray/issues/163 > If you'd like some test data, I'd be happy to try and get a small data set to > behave poorly. Test data would be nice. But I won't have the time to look at it in the next couple of weeks. > > -Rob > > > On Wed, Nov 6, 2013 at 1:57 PM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > On 04/11/13 11:52 PM, Rob Egan wrote: > > Hello Sébastien, > > > Hi Rob, > > > Regarding the maximum read length, I've found 16kb to be the limit > not 64kb as you posted previously. > > I've been trying to run Ray iteratively by including the cleaned up > and shredded contigs (to less then 50kb) from the previous assembly as one of > the inputs, and am running into a problem after the "Estimation of outer > distances for paired reads" step. > > > This is strange because your contigs are not paired, right ? > > > I tried in on 2.2.0, 2.3.0 and the latest version from github: > v2.3.0-1-g2b0a6a5. Through trial and error, I discovered that if I include > shredded contigs greater than ~16kb, > then it segfaults, > > > In the log you provided below, I see a "Bus Error". > > > but if they are 16000 bases or less, then everything completes > successfully. (I did not find the actual limit) > > > That is informative to know that 16000 is *the* current limit. > > > > It looks to me that MPI_Test is being called with a NULL pointer for > the request, but in looking at the code, I can't see where that would happen. > > > That would be in RayPlatform, in RingAllocator.cpp ("void > RingAllocator::__checkDirtyBuffer(int index){"). > > But the index is bounded inside a loop, so that's weird. > > > This is the command: mpirun -bynode -pernode -bycore -bind-to-core > -npernode 16 --mca oob_tcp_if_exclude ib0 memtime > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray -o R > ay-jgi_job_wrapper.sh-7460945-__k51.d -k 51 -minimum-contig-length > 250 -bloom-filter-bits 0 -read-write-checkpoints > /scratch/Ray-jgi_job_wrapper.__sh-7460945-k51.d.ckpt \é > > -disable-network-test -i 1m.fastq -s 400.fastq -s > unmap-min5-contigShreds.fastq.__fasta > > And here are some excerpts from the log: > > > 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: 160 > Maximum coverage depth stored by CoverageDepth: 4294967295 > MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes > FORCE_PACKING = n > ASSERT = n > HAVE_LIBZ = y > HAVE_LIBBZ2 = y > 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 1.6.4 > Compiler: GNU gcc/g++ 4.8.1 > MPI I/O: n > > …. > > *** > Step: Estimation of outer distances for paired reads > Date: Mon Nov 4 14:24:38 2013 > Elapsed time: 33 seconds > Since beginning: 52 minutes, 29 seconds > *** > > …. > > Rank 6 starts on seed 2526, length is 454, flow 0 [2526/6125] > Rank 12 traversed 2436293 nucleotide symbols > Rank 12: assembler memory usage: 766920 KiB > Rank 12 starts on seed 2138, length is 520, flow 0 [2138/6278] > Rank 10: assembler memory usage: 753516 KiB > Rank 10 starts on seed 2486, length is 455, flow 0 [2486/6164] > Rank 13 traversed 2319776 nucleotide symbols > Rank 13: assembler memory usage: 758376 KiB > Rank 13 starts on seed 2089, length is 501, flow 0 [2089/6150] > Rank 2: assembler memory usage: 756088 KiB > Rank 2 starts on seed 2657, length is 437, flow 0 [2657/6068] > [mc0555:08747] *** Process received signal *** > [mc0555:08747] Signal: Bus error (7) > [mc0555:08747] Signal code: (128) > [mc0555:08747] Failing at address: (nil) > [mc0555:08747] [ 0] /lib/libpthread.so.0(+0xeff0) > [0x2acd0fc8bff0] > [mc0555:08747] [ 1] > /global/common/genepool/usg/__hpc/openmpi/gnu4.6/1.6.4/ib___ofed2/lib/libmpi.so.1(ompi___request_default_test+0x24) > [0x2acd0e7b2fb4] > [mc0555:08747] [ 2] > /global/common/genepool/usg/__hpc/openmpi/gnu4.6/1.6.4/ib___ofed2/lib/libmpi.so.1(MPI___Test+0x6c) > [0x2acd0e7d48cc] > [mc0555:08747] [ 3] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN13RingAllocator17cleanDirtyB__uffersEv+0x8c) > [0x59dbfc] > [mc0555:08747] [ 4] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN15MessagesHandler12sendMessa__gesEP12StaticVectorP13RingAllo__cator+0x39) > [0x5b73c9] > [mc0555:08747] [ 5] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN11ComputeCore12sendMessagesE__v+0x156) > [0x5ba236] > [mc0555:08747] [ 6] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN11ComputeCore15runWithProfil__erEv+0x534) > [0x5bc754] > [mc0555:08747] [ 7] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN11ComputeCore3runEv+0xaa) > [0x5bf16a] > [mc0555:08747] [ 8] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(___ZN7Machine5startEv+0x1416) > [0x477e96] > [mc0555:08747] [ 9] > /usr/common/jgi/assemblers/__Ray/2.3.0/Ray(main+0x297) [0x4757c7] > [mc0555:08747] [10] /lib/libc.so.6(__libc_start___main+0xfd) > [0x2acd0feb7c8d] > [mc0555:08747] [11] /usr/common/jgi/assemblers/__Ray/2.3.0/Ray() > [0x4727f1] > [mc0555:08747] *** End of error message *** > Killed [7] > > > > On Wed, Aug 28, 2013 at 6:13 AM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.__ca <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> wrote: > > On 28/08/13 04:15 AM, Hornung, Bastian wrote: > > Hi Sébastien, > > > > the assembly is now running, so it seems to be working, > thanks :). > > Thank you for testing the patch. > > I merged it in the master branch. > > > https://github.com/sebhtml/__ray/commit/__20d20c1cef4136281b46e14115631a__2326920550 > > <https://github.com/sebhtml/ray/commit/20d20c1cef4136281b46e14115631a2326920550> > > > > > Bastian > > > > __________________________________________ > > From: Sébastien Boisvert [sebastien.boisvert.3@ulaval.__ca > <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>] > > > Sent: Tuesday, August 27, 2013 4:37 PM > > To: Hornung, Bastian > > Cc: denovoassembler-users@lists.__sourceforge.net > <mailto:denovoassembler-users@lists.sourceforge.net> > <mailto:denovoassembler-users@__lists.sourceforge.net > <mailto:denovoassembler-users@lists.sourceforge.net>> > > > Subject: Re: [Denovoassembler-users] maximum read length for > ray > > > > (Please use the list) > > > > Hello, > > > > I think I found the problem. > > > > > > Can you try with the enclosed patch ? > > > > > > To build Ray v2.2.0 with this patch: > > > > > > wget > http://sourceforge.net/__projects/denovoassembler/__files/Ray-v2.2.0.tar.bz2 > <http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2> > > wget > https://raw.github.com/__sebhtml/patches/master/ray/__Ray-v2.2.0-fix-for-amos-and-__long-reads.patch > > <https://raw.github.com/sebhtml/patches/master/ray/Ray-v2.2.0-fix-for-amos-and-long-reads.patch> > > > > tar -xjf Ray-v2.2.0.tar.bz2 > > cd Ray-v2.2.0 > > patch -p1 < ../Ray-v2.2.0-fix-for-amos-__and-long-reads.patch > > > > make -j 20 > > > > mkdir -p ~/software/ray/2.2.0-1-long-__reads-amos > > cp Ray~/software/ray/2.2.0-1-__long-reads-amos > > > > > > > > > > -Sébastien > > > > On 27/08/13 03:58 AM, Hornung, Bastian wrote: > >> Okay, that's then obviously not the problem. > >> I've for testing purposes installed a version locally, once > with different parameters, afterwards with the standard parameters, and > loaded the PacBio data into it. And it runs. > >> If I now try it again on our server (both the local linux > machine as well as the server are Ubuntu 12.04), no matter if I freshly > compile it or use the already present installation (also without any > different installation parameters) I get again a stack overflow warning, see > the command line output: > >> > >> > >> Rank 0 is fetching file > /home/bastian/data/RAW/test___illumina_read_1/NG-5257_test___read_1.fastq > with lazy loading (please wait...) > >> Rank 3 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R2_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 2 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R1_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 1 is fetching file > /home/bastian/data/RAW/test___illumina_read_2/NG-5257_test___read_2.fastq > with lazy loading (please wait...) > >> Rank 4 is fetching file > /home/bastian/data/RAW/PacBio/__all_ccs.fastq with lazy loading (please > wait...) > >> Rank 4: File /home/bastian/data/RAW/PacBio/__all_ccs.fastq > (Number 4) has 3699 sequences > >> Rank 2: File > /home/bastian/data/RAW/test1___GTCCGC_L008_R1_001_AC0RCJACXX.__filt.fastq > (Number 2) has 9886736 sequences > >> Rank 3: File > /home/bastian/data/RAW/test1___GTCCGC_L008_R2_001_AC0RCJACXX.__filt.fastq > (Number 3) has 9886736 sequences > >> Rank 0: File > /home/bastian/data/RAW/test___illumina_read_1/NG-5257_test___read_1.fastq > (Number 0) has 34807392 sequences > >> Rank 1: File > /home/bastian/data/RAW/test___illumina_read_2/NG-5257_test___read_2.fastq > (Number 1) has 34807392 sequences > >> Rank 0 wrote > /home/bastian/data/RAW/test___illumina_untrimmed_matepair___pacbio_ray_k31/__NumberOfSequences.txt > >> Rank 0 wrote > /home/bastian/data/RAW/test___illumina_untrimmed_matepair___pacbio_ray_k31/__SequencePartition.txt > >> > >> *** > >> Step: Counting sequences to assemble > >> Date: Tue Aug 27 09:42:39 2013 > >> Elapsed time: 18 seconds > >> Since beginning: 18 seconds > >> *** > >> > >> > >> Rank 0 is adding sequences to > /home/bastian/data/RAW/test___illumina_untrimmed_matepair___pacbio_ray_k31/AMOS.afg > >> > >> Rank 0 is fetching file > /home/bastian/data/RAW/test___illumina_read_1/NG-5257_test___read_1.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test___illumina_read_1/NG-5257_test___read_1.fastq > with lazy loading (please wait...) > >> adRank 0 is fetching file > /home/bastian/data/RAW/test___illumina_read_2/NG-5257_test___read_2.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test___illumina_read_2/NG-5257_test___read_2.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R1_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R1_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R2_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/test1___GTCCGC_L008_R2_001_AC0RCJACXX.__filt.fastq > with lazy loading (please wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/PacBio/__all_ccs.fastq with lazy loading (please > wait...) > >> Rank 0 is fetching file > /home/bastian/data/RAW/PacBio/__all_ccs.fastq with lazy loading (please > wait...) > >> *** stack smashing detected ***: Ray terminated > >> [ssb3:23288] *** Process received signal *** > >> [ssb3:23288] Signal: Segmentation fault (11) > >> [ssb3:23288] Signal code: (128) > >> [ssb3:23288] Failing at address: (nil) > >> > >> I have no idea what's going on. > >> I doubt that I can run the assembly on my local machine, > don't think I have enough RAM here. > >> There shouldn't be any difference between the 2 machines, > that's what puzzles me. > >> > >> Any ideas? > >> > >> Bastian > >> > >> > >> __________________________________________ > >> From: Sébastien Boisvert [sebastien.boisvert.3@ulaval.__ca > <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>] > > >> Sent: Monday, August 26, 2013 3:12 PM > >> To: Hornung, Bastian > >> Cc: denovoassembler-users@lists.__sourceforge.net > <mailto:denovoassembler-users@lists.sourceforge.net> > <mailto:denovoassembler-users@__lists.sourceforge.net > <mailto:denovoassembler-users@lists.sourceforge.net>> > > >> Subject: Re: [Denovoassembler-users] maximum read length for > ray > >> > >> On 26/08/13 04:56 AM, Hornung, Bastian wrote: > >>> Hi @all, > >>> > >>> I'd have a technical question about ray: What is the > maximum read length, which can be used? > >>> I ask because I get a stack overflow (or rather a message > that the process has been aborted before it could happen) when I try to run > ray with PacBio data (up to 2kb in that set, IIRC), and wonder what the > maximum is what ray can take. > >>> > >> > >> It is 65536 nucleotides. > >> > >>> Best regards, > >>> > >>> Bastian > >>> > >>> > >>> > ------------------------------__------------------------------__------------------ > >>> Introducing Performance Central, a new site from > SourceForge and > >>> AppDynamics. 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