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  • Ray : Segmentation fault (11)

    Hello,

    I am trying to run Ray to do hybrid assembly of Illumina (paired end data) and Roche 454 data. I am running the program on server with 64 cores and 512GB RAM

    I ran the sample data in Ray; which is working fine.
    When I give my data, the program is producing Contigs.fasta output but, giving error before scaffolding.

    I ran the following command
    $ mpiexec -n 20 ray-build/Ray -k 31 -p mp_R1_trimmed_q20_p100_clipped.fastq mp_R2_trimmed_q20_p100_clipped.fastq -s 454.fastq -o kmer_31_out

    After contig buildng program gave the following fault while scaffolding

    *** Process received signal ***
    Signal: Segmentation fault (11)
    Signal code: Address not mapped (1)
    Failing at address: 0x15b710
    [ 0] /lib64/libpthread.so.0() [0x3dbd00f500]
    [ 1] ray-build/Ray(_ZNK4Read6lengthEv+0) [0x50a9b0]
    [ 2] ray-build/Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x9f) [0x49c09f]
    [ 3] ray-build/Ray(_ZN11ComputeCore10runVanillaEv+0x61) [0x532351]
    [ 4] ray-build/Ray(_ZN11ComputeCore3runEv+0x6e) [0x53379e]
    [ 5] ray-build/Ray(_ZN7Machine5startEv+0x1697) [0x4487a7]
    [ 6] ray-build/Ray(main+0x3a) [0x443bba]
    [ 7] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3dbc41ecdd]
    [ 8] ray-build/Ray() [0x443a89]
    *** End of error message ***
    --------------------------------------------------------------------------
    mpiexec noticed that process rank 19 with PID 21982 on node pragnya exited on signal 11 (Segmentation fault).
    --------------------------------------------------------------------------

    I tried to run the program with different number of ranks and kmers. But still stoping at scaffolding stage.

    Can anyone please help

  • #2
    Ray:segmentation fault (11)

    So, a question as
    I am having the same problem.
    I think its an open mpi error.
    Run Top - do you see if all 20 cores are running Ray?

    In my case, only one is running causing the error.

    Double check and get back to me?

    cheers
    Rick

    Comment


    • #3
      RE : Ray : Segmentation fault (11)

      Hi,

      As you suggested, it is an open mpi fault. But when I run the program I see 20 cores being used for initial period of about 1 hour. The program stops after the contig building. The contigs are not scaffolded because of this error

      Comment


      • #4
        Hi,
        I have the same problem. Has anyone managed to solve it?

        Interesting fact is that I have managed to finish many samples with the same machine, mpi, settings, comparable complexity and size... This one refuses to cooperate.

        Regards

        Comment

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