On 15/03/13 02:47 PM, jjv5 wrote: > 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 \
It should be mpiexec -n 40 --mca btl ^sm Ray ... and not mpiexec -n 40 Ray -mca btl ^sm > -disable-recycling \ This bug (infinite looping) was fixed in the development branch. > -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 > \ Is this a type or your file is really called coco_filtered_right.fastqa ? You should use symbolic links instead of these long VFS paths. > -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 > ------------------------------------------------------------------------------ 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
