At least I'm not the only one. Although I get the same error only with higher kmers (works for me til 49).
I suspected that it might have something to do with the compilation setup, but the only differences I see that you've compiled ray with libz, with a different gcc (I have 4.6.3), and I have a higher max kmer value (201), everything else seems to be the same. Don't think it's the memory. My assemblies are rather small, memory shouldn't be a problem at all for me. ________________________________________ From: jjv5 [j...@jjv5.net] Sent: Wednesday, November 20, 2013 9:55 PM To: denovoassembler-users@lists.sourceforge.net Subject: [Denovoassembler-users] Seg fault at exact place in many runs 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 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
