Nothing immediate comes to mind - all sbatch does is create an allocation and then run your script in it. Perhaps your script is using a different “mpirun” command than when you type it interactively?
> On Feb 14, 2017, at 5:11 AM, Anastasia Kruchinina > <nastja.kruchin...@gmail.com> wrote: > > Hi, > > I am trying to use MPI_Comm_spawn function in my code. I am having trouble > with openmpi 2.0.x + sbatch (batch system Slurm). > My test program is located here: > http://user.it.uu.se/~anakr367/files/MPI_test/ > <http://user.it.uu.se/%7Eanakr367/files/MPI_test/> > > When I am running my code I am getting an error: > > OPAL ERROR: Timeout in file > ../../../../openmpi-2.0.1/opal/mca/pmix/base/pmix_base_fns.c at line 193 > *** An error occurred in MPI_Init_thread > *** on a NULL communicator > *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, > *** and potentially your MPI job) > -------------------------------------------------------------------------- > 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_dpm_dyn_init() failed > --> Returned "Timeout" (-15) instead of "Success" (0) > -------------------------------------------------------------------------- > > The interesting thing is that there is no error when I am firstly allocating > nodes with salloc and then run my program. So, I noticed that the program > works fine using openmpi 1.x+sbach/salloc or openmpi 2.0.x+salloc but not > openmpi 2.0.x+sbatch. > > The error was reproduced on three different computer clusters. > > Best regards, > Anastasia > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users
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