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@msn.com> 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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