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An object-oriented Computational Fluid Dynamics(CFD) toolkit

Description

OpenFOAM core is an extensible framework written in C++, i.e. it provides a sufficient abstraction for a programmer to build their own code for an underlying mathematical model. 

Prerequisites

OpenFOAM is a free, open source software which is released under the GNU-GPL license

Modules

The following versions of OpenFOAM are installed in HLRN system

OpenFOAM versionOpenFOAM module fileRequirementsHLRN Site
v4openfoam/gcc.9/4gcc/9.2.0, openmpi/gcc.9/3.1.5Berlin, Goettingen
v5openfoam/gcc.9/5gcc/9.2.0, openmpi/gcc.9/3.1.5-
v6openfoam/gcc.9/6gcc/9.2.0, openmpi/gcc.9/3.1.5-
v7openfoam/gcc.9/7gcc/9.2.0, openmpi/gcc.9/3.1.5-
v1912openfoam/gcc.9/v1912gcc/9.2.0, openmpi/gcc.9/3.1.5-

The module name is openfoam. Other versions may be installed. Inspect the output of :            module avail openfoam

Example Jobscripts

#!/bin/bash#SBATCH --time 1:00:00
#SBATCH --nodes 1 
#SBATCH --tasks-per-node 96 
#SBATCH -p standard96
#SBATCH --job-name=of_test_job
#SBATCH --output=outlog/ol-%x.%j.out
#SBATCH --error=outlog/ol-%x.%j.err

export I_MPI_FALLBACK=0
export I_MPI_DEBUG=6
export I_MPI_FABRICS=shm:ofi
export I_MPI_OFI_PROVIDER=psm2
export I_MPI_PMI_LIBRARY=libpmi.so

#--------------------------------------

module load gcc/9.2.0
module load openmpi/gcc.9/3.1.5
module load openfoam/gcc.9/5
# Working Directories
#---------------------
WORKDIR=$TMPDIR/openfoam# initialize OpenFOAM environment
source $WM_PROJECT_DIR/etc/bashrc
. ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions  # Tutorial run functions
#---------------

cd $WORKDIR

# run OpenFOAM in parallel
#--------------------------
runApplication decomposePar
runParallel pimpleFoam

#clean the work directory
#----------------------------
rm -rf processor*

1

Some important advice when running OpenFOAM on a supercomputer

OpenFOAM produces lots of small files. This default behavior jams no only your job but slows down the parallel file system (Lustre) for all HLRN users. Also, you can quickly generate more files than allowed by our quota system (hlrnquota).

To reduce this meta data strain and optimize your OpenFOAM job for this supercomputer we strongly recommend the following steps:

  • Always, to avoid that each processor writes in its own file please use collated file I/O.
    This feature was released 2017 for all OpenFOAM versions.
    [ESI www.openfoam.com/releases/openfoam-v1712/parallel.php]
    [Foundation www.openfoam.org/news/parallel-io]

    OptimisationSwitches
    {
        fileHandler collated; // all processors share a file
    }

    to the $WM_PROJECT_DIR/etc/controlDict file, or the per-user override in the /.OpenFOAM/v#/controlDict file or per-case override in the $FOAM_CASE/system/controlDict file.

  • Always, set

    runTimeModifiable false;

    to reduce I/O activity. Only set "true" (default), if it is strictly necessary to re-read dictionaries (controlDict, ...) each time step.

  • Possibly, do not save every time step:
    [www.openfoam.com/documentation/guides/latest/doc/guide-case-system-controldict.html]
    [www.cfd.direct/openfoam/user-guide/v6-controldict]

    writeControl	timeStep;
    writeInterval	100;
  • Possibly, save only the latest n time steps (overwrite older ones), such as:

    purgeWrite	1000;
  • Typically, only a subset of variables is needed frequently (post-processing). The full set of variables can be saved less frequently (e.g., restart purposes). This can be achieved with [https://wiki.bwhpc.de/e/OpenFoam]:

    writeControl    clockTime;
    writeInterval   21600; // write ALL variables every 21600 seconds = 6 h
    
    functions
    {
        writeFields
        {
            type writeObjects;
            libs ("libutilityFunctionObjects.so");
    
            objects
            (
    	    T U // specified variables
            );
    
            outputControl timeStep;
            writeInterval 100; // write specified variables every 100 steps
        }
    }
  • In case your HLRN run accidentally generated thousands of small files, please pack them (at least the small-size metadata files) into a single file afterwards:

    tar -xvzf singlefile.tar.gz -C /folder/subfolder/location/

    Thanks a lot for your contribution making HLRN a great place for all...

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