On 09/05/13 05:58 PM, Cedar Hesse wrote: > Hello, > I recently started using Ray in an attempt to assemble a metatranscriptome. > I have tried multiple assemblies and repeatedly get a segmentation fault. > The fault happens after contigs are written and the AMOS file is generated, > however I don't think Ray gets to the scaffolding stage or any downstream > plugins >(gene ontology, etc...). Below is my RayCommand.txt file and the last few >lines of stdout showing the segfault.
Does it work if you omit the -amos option ? > > RayCommand.txt > ################################### > mpiexec -n 25 Ray \ # This was also run with "--mca btl ^sm" > and the same segfault > -p \ > TAH-19.1_rejected_reads.fastq \ > TAH-19.2_rejected_reads.fastq \ > -p \ > TAH-20.1_rejected_reads.fastq \ > TAH-20.2_rejected_reads.fastq \ > -p \ > TAH-21.1_rejected_reads.fastq \ > TAH-21.2_rejected_reads.fastq \ > -p \ > TAH-22.1_rejected_reads.fastq \ > TAH-22.2_rejected_reads.fastq \ > -p \ > TAH-23.1_rejected_reads.fastq \ > TAH-23.2_rejected_reads.fastq \ > -p \ > TAH-24.1_rejected_reads.fastq \ > TAH-24.2_rejected_reads.fastq \ > -o \ > ray_assembly_new \ > -show-memory-usage \ > -write-contig-paths \ > -amos \ > -search \ > /dbase/Ray/EMBL_CDS_Sequences \ > -gene-ontology \ > /dbase/Ray/OntologyTerms.txt \ > /dbase/Ray/Annotations.txt > ################################### > > STDOUT > #################################### > Rank 0 objectName: 20 => peakCoverage: 125 blockSize: 1305 > Rank 0 objectName: 0 => peakCoverage: 192 blockSize: 1538 > Rank 0 objectName: 12 => peakCoverage: 37 blockSize: 1486 > Rank 0 objectName: 19 => peakCoverage: 107 blockSize: 1490 > Rank 0 objectName: 16 => peakCoverage: 82 blockSize: 1880 > [metatron:01941] *** Process received signal *** > [metatron:01941] Signal: Segmentation fault (11) > [metatron:01941] Signal code: Address not mapped (1) > [metatron:01941] Failing at address: 0xb0c68 > [metatron:01941] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f8cd6851cb0] > [metatron:01941] [ 1] Ray(_ZNK4Read6lengthEv+0) [0x549160] > [metatron:01941] [ 2] > Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x88) > [0x4b8208] So the problem occurs when receiving a message during the computation. > [metatron:01941] [ 3] Ray(_ZN11ComputeCore10runVanillaEv+0xb4) [0x5867c4] > [metatron:01941] [ 4] Ray(_ZN11ComputeCore3runEv+0x89) [0x58c019] > [metatron:01941] [ 5] Ray(_ZN7Machine5startEv+0x1876) [0x46d056] > [metatron:01941] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a6df] > [metatron:01941] [ 7] Ray(main+0xc7) [0x465477] > [metatron:01941] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f8cd64a476d] > [metatron:01941] [ 9] Ray() [0x466a81] > [metatron:01941] *** End of error message *** > [metatron][[32923,1],0][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],4][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],8][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],9][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],12][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],14][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],23][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],2][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],21][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],1][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],3][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],5][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],6][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],7][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],10][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],11][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],13][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],15][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],17][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],18][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],19][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],20][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [metatron][[32923,1],22][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > -------------------------------------------------------------------------- > mpiexec noticed that process rank 24 with PID 1941 on node metatron exited on > signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > #################################################### > > Any help? Which version of Ray are you using ? How many reads do you have ? > Thanks, > -Cedar ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
