Thanks Sebastien, I think you are right- I rebuilt Ray by make MPICXX=/usr/local/bin/mpicxx
This is running without error now. Thanks again! Cheers- Scott > On Feb 1, 2014, at 8:33 AM, "Sébastien Boisvert" > <sebastien.boisver...@ulaval.ca> wrote: > > >> 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
