Hello, I am unable to complete an assembly on the same machine and with the same parameters as soe previous runs but with a different set of input reads.
The program runs for many hours and then gives a seg fault error: Rank 20: assembler memory usage: 7002348 KiB Rank 39: assembler memory usage: 7002340 KiB Rank 39: gathering scaffold links [1/539] [1/776] Rank 39: assembler memory usage: 7002340 KiB Rank 17: gathering scaffold links [1/576] [1/545] Rank 17: assembler memory usage: 7006448 KiB [vgncompute1:71378] *** Process received signal *** [vgncompute1:71378] Signal: Segmentation fault (11) [vgncompute1:71378] Signal code: Address not mapped (1) [vgncompute1:71378] Failing at address: 0x16d6b0 [vgncompute1:71378] [ 0] /lib64/libpthread.so.0() [0x3b9b80f500] [vgncompute1:71378] [ 1] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(_ZNK4Read6lengthEv+0) [0x50a9b0] [vgncompute1:71378] [ 2] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x9f) [0x49c09f] [vgncompute1:71378] [ 3] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(_ZN11ComputeCore10runVanillaEv+0x61) [0x532351] [vgncompute1:71378] [ 4] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(_ZN11ComputeCore3runEv+0x6e) [0x53379e] [vgncompute1:71378] [ 5] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(_ZN7Machine5startEv+0x1697) [0x4487a7] [vgncompute1:71378] [ 6] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray(main+0x3a) [0x443bba] [vgncompute1:71378] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3b9ac1ecdd] [vgncompute1:71378] [ 8] /mnt/Nexenta/archive/Software/RAY/Ray-v2.1.0/Ray() [0x443a89] [vgncompute1:71378] *** End of error message *** Rank 24: gathering scaffold links [1/507] [1/856] Rank 24: assembler memory usage: 7002352 KiB -------------------------------------------------------------------------- mpiexec noticed that process rank 39 with PID 71378 on node vgncompute1.uvm.edu exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- The command used to run is: -bash-4.1$ cat RayCommand.txt mpiexec -n 40 Ray \ -mca \ btl \ ^sm \ -disable-recycling \ -o \ coco_filtered.200.NCBI \ -p \ /mnt/Nexenta/archive/BC_Projects/BCProject-1-Launen-Metagenomics/analysis_recovered_reads/filtered-reads/coco/coco_filtered_left.fastq \ /mnt/Nexenta/archive/BC_Projects/BCProject-1-Launen-Metagenomics/analysis_recovered_reads/filtered-reads/coco/coco_filtered_right.fastqa \ -k \ 31 \ -minimum-contig-length \ 200 ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
