Hi, One thing that would help us figure out this issue would be to generate a stack trace with line number (your stack trace does not include line numbers).
For instance: $ ulimit -c unlimited $ mpiexec -n 32 Ray -k 31 -p 40xillumina_1.fastq 40xillumina_2.fastq -s depth10_001.fastq -o Ray_Hybrid $ which Ray $ gdb path/to/Ray gdb> core-file core.123456 gdb> backtrace On 21 mars 2014 02:24, Timothy Price [marthmaster...@yahoo.com] wrote: > À : denovoassembler-users@lists.sourceforge.net > Objet : [Denovoassembler-users] Segmentation Fault > > Hello Ray users, > > I am currently running assemblies of simulated data of human chromosome 21 > with Ray to see what sort of 'hybrid' coverage is needed to effectively > assemble primate genomes. With this trial, I use simulated short (250 insert > size) Illumina reads and simulated PacBio reads, attempting to leverage Ray's > ability to use different NGS reads. However, I am getting a persistent error > even before producing contigs--somewhere while estimating outer differences > of the paired reads. I have checked to make sure that the MPI used is the > same as Ray was compiled with, which seems like it was an issue in another > archived post, so this is not the issue. Below is the command and the > produced error file. > > Any troubleshooting suggestions would be most appreciated! > > Thanks, > Ryan > > #!/bin/bash > #PBS -l nodes=4:ppn=8 > #PBS -l mem=60g > #PBS -l walltime=02:00:00:00 > #PBS -q hpc-uni > > module unload compiler/gnu/4.5 > module load compiler/gnu/4.5 > module unload mpi/openmpi/1.4.3-gnu-4.5 > module load mpi/openmpi/1.4.3-gnu-4.5 > module unload bio/ray/2.3.0 > module load bio/ray/2.3.0 > > mpiexec -n 32 Ray -k 31 -p 40xillumina_1.fastq 40xillumina_2.fastq -s > depth10_001.fastq -o Ray_Hybrid > > Error File: > > Ray does parallel de novo genome assemblies of next-gen sequencing data. > > INFO: Please read module help and references therein for additional infos. > > [n030102:23315] *** Process received signal *** > [n030102:23315] Signal: Segmentation fault (11) > [n030102:23315] Signal code: (128) > [n030102:23315] Failing at address: (nil) > [n030102:23315] [ 0] /lib64/libpthread.so.0 [0x2b299ef6ebe0] > [n030102:23315] [ 1] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0 > [0x2b299c816c04] > [n030102:23315] [ 2] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0 > [0x2b299c8a5c03] > [n030102:23315] [ 3] /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0 > [0x2b299c89cd30] > [n030102:23315] [ 4] > /opt/bwgrid/mpi/openmpi/1.4.3-gnu-4.5/lib/libmpi.so.0(MPI_Isend+0x173) > [0x2b299c7f5eb3] > [n030102:23315] [ 5] > Ray(_ZN15MessagesHandler12sendMessagesEP12StaticVectorP13RingAllocator+0xbb) > [0x5bcecb] > [n030102:23315] [ 6] Ray(_ZN11ComputeCore12sendMessagesEv+0x156) [0x5c04e6] > [n030102:23315] [ 7] Ray(_ZN11ComputeCore15runWithProfilerEv+0x5d1) [0x5c4491] > [n030102:23315] [ 8] Ray(_ZN11ComputeCore3runEv+0xbc) [0x5c5bdc] > [n030102:23315] [ 9] Ray(_ZN7Machine5startEv+0x1766) [0x47e506] > [n030102:23315] [10] Ray(main+0x28e) [0x47959e] > [n030102:23315] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b299f198994] > [n030102:23315] [12] Ray(_ZNSt8ios_base4InitD1Ev+0x39) [0x479209] > [n030102:23315] *** End of error message *** > -------------------------------------------------------------------------- > mpiexec noticed that process rank 22 with PID 23315 on node n030102 exited on > signal 11 (Segmentation fault). ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
