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Subject: Re: [OMPI users] Odd and long error with OpenMPI and OpenFOAM.
From: Ralph Castain (rhc_at_[hidden])
Date: 2013-10-27 10:13:45


Please look at the following:

http://www.open-mpi.org/faq/?category=rsh#ssh-keys

http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path

Note that you also need to add your OpenFOAM installation to the LD_LIBRARY_PATH.

On Oct 27, 2013, at 5:48 AM, Tommi Laiho <tommilaiho_at_[hidden]> wrote:

>
> Hi,
>
> I have been trying to setup Open MPI with OpenFOAM211. I have compiled the Open MPI by myself but it went very smoothly so I guess the compilation went correctly. However I am not a true expert of the field.
>
> I have bridged modem having different IP's with different machines right now. I should at first connect two computers with Open MPI in order to run 14 cores with OpenFOAM 211. The OpenFOAM 211 is same version now in both computers which I will call as master and slave and also OpenMPI is same in both computers. This time master machine is CAELinux Ubuntu 10.04 LTS and slave is Ubuntu Studio 12.04 LTS. I have read many articles and also FAQ but now I cant progress any more by myself, I need some help. Thank you for understanding.
>
> So when I run this code:
>
> /opt/openmpi-1.6.5/bin/mpirun -hostfile /home/tommi2/Desktop/machinefile -np 14 /opt/openfoam211/platforms/linux*/bin/pisoFoam -parallel
>
> and give a password for my slave machine I will get this long, very long error by OpenFOAM211 and Open MPI. In order to be honest I don't fully understand its whole meaning. Here is goes:
>
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> /opt/openfoam211/platforms/linux64GccDPOpt/bin/pisoFoam: error while loading shared libraries: libincompressibleTurbulenceModel.so: cannot open shared object file: No such file or directory
> [caelinux:05633] [[49395,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/util/nidmap.c at line 371
> [caelinux:05633] [[49395,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
> [caelinux:05633] [[49395,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line 173
> --------------------------------------------------------------------------
> 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
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> 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
> --------------------------------------------------------------------------
> [caelinux:05633] [[49395,1],1] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/runtime/orte_init.c at line 132
> --------------------------------------------------------------------------
> 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)
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** before MPI was initialized
> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> [caelinux:5633] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
> *** An error occurred in MPI_Init
> *** before MPI was initialized
> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> [caelinux:5634] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
> [caelinux:05634] [[49395,1],3] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/util/nidmap.c at line 371
> [caelinux:05634] [[49395,1],3] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
> [caelinux:05634] [[49395,1],3] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line 173
> [caelinux:05634] [[49395,1],3] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/runtime/orte_init.c at line 132
> --------------------------------------------------------------------------
> 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)
> --------------------------------------------------------------------------
> [caelinux:05635] [[49395,1],5] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/util/nidmap.c at line 371
> [caelinux:05635] [[49395,1],5] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
> [caelinux:05635] [[49395,1],5] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line 173
> [caelinux:05635] [[49395,1],5] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/runtime/orte_init.c at line 132
> --------------------------------------------------------------------------
> 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)
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** before MPI was initialized
> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> [caelinux:5635] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
> [caelinux:05636] [[49395,1],7] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/util/nidmap.c at line 371
> [caelinux:05636] [[49395,1],7] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../orte/mca/ess/base/ess_base_nidmap.c at line 62
> [caelinux:05636] [[49395,1],7] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../../../../orte/mca/ess/env/ess_env_module.c at line 173
> [caelinux:05636] [[49395,1],7] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ../../../orte/runtime/orte_init.c at line 132
> --------------------------------------------------------------------------
> 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)
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** before MPI was initialized
> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> [caelinux:5636] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 5633 on
> node caelinux exiting improperly. There are two reasons this could occur:
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [caelinux:05630] 3 more processes have sent help message help-orte-runtime.txt / orte_init:startup:internal-failure
> [caelinux:05630] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> [caelinux:05630] 3 more processes have sent help message help-orte-runtime / orte_init:startup:internal-failure
>
>
> So I will also give my OpenFOAM decomposeParDict setup for 14 cores:
>
>
> /*--------------------------------*- C++ -*----------------------------------*\
> | ========= | |
> | \\ / F ield | OpenFOAM Extend Project: Open Source CFD |
> | \\ / O peration | Version: 1.6-ext |
> | \\ / A nd | Web: www.extend-project.de |
> | \\/ M anipulation | |
> \*---------------------------------------------------------------------------*/
> FoamFile
> {
> version 2.0;
> format ascii;
> class dictionary;
> object decomposeParDict;
> }
> // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
> numberOfSubdomains 14;
> method hierarchical;
> //method metis;
> //method parMetis;
> simpleCoeffs
> {
> n (4 1 1);
> delta 0.001;
> }
> hierarchicalCoeffs
> {
> n (14 1 1);
> delta 0.001;
> order xyz;
> }
> manualCoeffs
> {
> dataFile "cellDecomposition";
> }
> metisCoeffs
> {
> //n (5 1 1);
> //cellWeightsFile "constant/cellWeightsFile";
> }
> // ************************************************************************* //
>
>
> just in case there is a fault in that. Please help me I am totally confused and thanks in advance.
>
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