[andrewmichael]

Hello everyone,

I am trying to submit a job for OpenFOAM on an HPC facility. I have a problem
when the parallel simulation starts, in the log file I receive this:

--> FOAM FATAL ERROR:
[3] UPstream::init(int& argc, char**& argv) : environment variable
MPI_BUFFER_SIZE not defined[5]

From what I found online the problem is that OpenFOAM uses an MPI
platform and have to load an MPI module to solve this. In my job file,
I had used this command to load OpenFOAM to run on an MPI platform:
module load apps/openfoam/4.1/gcc-6.2-openmpi-2.0.1.

My job file is this one:

#! /bin/bash
#$ -o Openfoam_ReconstructLog.txt
#$ -j y
#$ -m bea -M ambota1@sheffield.ac.uk
#$ -pe openmpi-ib 27 (tried even with -pe mpi command)
#$ -l h_rt=03:00:00
#$ -l rmem=16G

module load apps/openfoam/4.1/gcc-6.2-openmpi-2.0.1
fluentMeshToFoam Wing1to28_structured_refine.msh
decomposePar -force
mpirun -np 27 simpleFoam -parallel > Residuals &

[ykanani]

Originally Posted by andrewmichael

Hello everyone,

I am trying to submit a job for OpenFOAM on an HPC facility. I have a problem
when the parallel simulation starts, in the log file I receive this:

--> FOAM FATAL ERROR:
[3] UPstream::init(int& argc, char**& argv) : environment variable
MPI_BUFFER_SIZE not defined[5]

From what I found online the problem is that OpenFOAM uses an MPI
platform and have to load an MPI module to solve this. In my job file,
I had used this command to load OpenFOAM to run on an MPI platform:
module load apps/openfoam/4.1/gcc-6.2-openmpi-2.0.1.

My job file is this one:

#! /bin/bash
#$ -o Openfoam_ReconstructLog.txt
#$ -j y
#$ -m bea -M ambota1@sheffield.ac.uk
#$ -pe openmpi-ib 27 (tried even with -pe mpi command)
#$ -l h_rt=03:00:00
#$ -l rmem=16G

module load apps/openfoam/4.1/gcc-6.2-openmpi-2.0.1
fluentMeshToFoam Wing1to28_structured_refine.msh
decomposePar -force
mpirun -np 27 simpleFoam -parallel > Residuals &

Hi,
You also need to load appropriate openMPI module as well. Have you done that? it seems you need to load openMPI version 2.0.1 which should be available. Typically the openfoam module itself should take care of that. You can check by loading openfoam module in the login node and then check "module list" to see the currently loaded modules.

Typically each HPC has it's own configuration, module, etc. So one could expect to get more accurate answer and solve the issue in shorter timeframe by contacting the technical support team of the HPC.

Regards,

[andrewmichael]

when I load the OpenFOAM module, the mpi platform is automatically loaded too. That's the problem, I tried to load a separated mpi module as you said but it did not worked.

Best wishes,
Andrei

[ykanani]

Originally Posted by andrewmichael

when I load the OpenFOAM module, the mpi platform is automatically loaded too. That's the problem, I tried to load a separated mpi module as you said but it did not worked.

Best wishes,
Andrei

If the MPI is appropriately loaded, then the following environmental variables typically are set properly:

MPI_ARCH_PATH
MPI_BUFFER_SIZE
FOAM_MPI

after loading openfoam module, you can view the value of those variable by using echo command, e.g. echo $MPI_BUFFER_SIZE and it will show you their values. If you see nothing, it means that they are not properly set by the modules that you have loaded.

It will help if you could post the following information after loading the module:

echo $MPI_BUFFER_SIZE
echo $FOAM_MPI
echo $MPI_ARCH_PATH

Again, I strongly recommend you to contact the technical support of your HPC system since they themselves have installed openfoam and know the appropriate procedure to use it.

Regards,