On 20/11/13 03:55 PM, jjv5 wrote: > Hello, > > I am unable to complete a run due to a segmentation fault. I have run > with odd kmer values from 21 - 31 and each run dies in the contig > generation step after writing 28,000 contigs. > > The output header is: > > Ray version 2.2.0-rc0
Hello, Can you reproduce this with a stable release like 2.2.0 or 2.3.0 ? > License for Ray: GNU General Public License version 3 > RayPlatform version: 1.2.0-devel > License for RayPlatform: GNU Lesser General Public License version 3 > > MAXKMERLENGTH: 128 > Maximum coverage depth stored by CoverageDepth: 4294967295 > MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes > FORCE_PACKING = n > ASSERT = n > HAVE_LIBZ = y > HAVE_LIBBZ2 = n > PROFILER_COLLECT = n > 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++ 4.4.7 20120313 (Red Hat 4.4.7-3) > MPI I/O: n > > > The runs are on an EC2 cr1.8xlarge instance with 32 cores and 244G of memory. > > > The only part of the output that looks like an error is the final few lines: > > *** > Step: Generation of contigs > Date: Wed Nov 20 20:05:42 2013 > Elapsed time: 23 seconds > Since beginning: 1 hours, 11 minutes, 47 seconds > *** > > Rank 0 objectName: 19 => peakCoverage: 32 blockSize: 2591 > [master:09843] *** Process received signal *** > [master:09843] Signal: Segmentation fault (11) > [master:09843] Signal code: Address not mapped (1) > [master:09843] Failing at address: 0x20008 > [master:09843] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060) > [0x7fb582e97060] > [master:09843] [ 1] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(_ZNK4Read6lengthEv+0) > [0x544920] > [master:09843] [ 2] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x9f) > [0x4b860f] > [master:09843] [ 3] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(_ZN11ComputeCore3runEv+0xb0) > [0x56f970] > [master:09843] [ 4] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(_ZN7Machine5startEv+0x14c2) > [0x46b412] > [master:09843] [ 5] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(_ZN11RankProcessI7MachineE3runEv+0x190) > [0x468680] > [master:09843] [ 6] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray(main+0xc5) > [0x465d95] > [master:09843] [ 7] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fb582b0930d] > [master:09843] [ 8] > /mnt/Nexenta/archive/Software/RAY/Ray-Dev/ray/Ray() [0x465bc9] > [master:09843] *** End of error message *** > -------------------------------------------------------------------------- > mpiexec noticed that process rank 31 with PID 9843 on node master > exited on signal 11 (Segmentation fault). > > > I suppose I am just running out of memory? Is there a way to monitor > that during a run? Could it be something else? > > Thanks for your help. > > > Jim > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
