On 31 janvier 2014 09:16, Scott Monsma [smon...@lucigen.com] wrote: > À : denovoassembler-users@lists.sourceforge.net > Objet : [Denovoassembler-users] different machine, new openmpi 1.6.5 build, > new problem > > Hi all, I installed on a new machine with a fresh build of openmpi 1.6.5, and > had one successful assembly with Ray 2.3- but all subsequent attempts have > resulted in an ORTE error (below). I tried rebuilding openmpi but that did > not change the error. Any ideas on this one? > > > Here’s the Ray command with the same inputs that ran successfully the first > time: > > scott@biolinux2[Ray-2.3.0] mpiexec -n 7 Ray -o test3 -p > TaqFragment_S2_L001_R1_001.fastq TaqFragment_S2_L001_R2_001.fastq -k 31 > > and here’s the end of the error output: > > > [biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past > end of buffer in file ../../../orte/util/nidmap.c at line 398 > [biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past > end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at > line 62 > [biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past > end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at > line 173
Hi, I never saw this Open-MPI message. Did you compile Ray with the same version of Open-MPI that you are using to run your job ? I found this http://comments.gmane.org/gmane.comp.clustering.open-mpi.user/14711 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_base_build_nidmap failed > --> Returned value Data unpack would read past end of buffer (-26) instead > of ORTE_SUCCESS > -------------------------------------------------------------------------- > [biolinux2:05099] [[57821,1],0] ORTE_ERROR_LOG: Data unpack would read past > end of buffer in file ../../../orte/runtime/orte_init.c at line 132 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_set_name failed > --> Returned value Data unpack would read past end of buffer (-26) instead > of ORTE_SUCCESS > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init failed > --> Returned "Data unpack would read past end of buffer" (-26) instead of > "Success" (0) > -------------------------------------------------------------------------- > *** The MPI_Init() function was called before MPI_INIT was invoked. > *** This is disallowed by the MPI standard. > *** Your MPI job will now abort. > [biolinux2:5099] Abort before MPI_INIT completed successfully; not able to > guarantee that all other processes were killed! > -------------------------------------------------------------------------- > mpiexec has exited due to process rank 0 with PID 5099 on > node biolinux2 exiting improperly. > ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
