openfoam

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

https://www.openfoam.com

Software Description

OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with it\'s open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox.

Mesabi

OpenFOAM v6 is available on Mesabi. Several working examples are posted, which illustrate how to run interactive with graphics using ParaFOAM, and how to run non- interactively in the PBS batch queue.

Run Interactively with Graphics

In a terminal window on an MSI NICE or NX desktop

ssh -X mesabi 
/home/dhp/public/sing/openfoam6/run

This will start  an instance of the openfoam6-paraview54 singularity container. At the prompt in this container, enter you can  get and run backward facing step with simpleFoam with:

cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily . 
cd pitzDaily
blockMesh 
simpleFoam

View results with Paraview

export HOME=$myhome
paraFoam

Exit container

exit

Run in PBS batch

From a login shell on Mesabi, get a copy of the  OpenFOAM v6 tutorial pitzDaily example, PBS run script, and submit it to the queue:

cp -r /panfs/roc/msisoft/openfoam/6.0/pitzDaily_v6 . 
cd pitzDaily_v6 cp /panfs/roc/msisoft/openfoam/6.0/pbs_run . 
qsub pbs_run

NOTES

Problem size

This is a tiny example which runs for a very short time.  The PBS resource request only asks for 2 cores and 10 min of run time.    In fact, it's running OpenFOAM single-threaded, and only asks for 2 cores to ensure it has enough memory.  To run larger problems, request all 24 cores on a node and a longer wall clock time. For example, to run for as long as 6 hours and have the full memory of the Mesabi compute node, use a resource request like

#PBS -l nodes=1:ppn=24,pmem=2580mb,walltime=06:00:00

Customize problem

This example runs blockMesh, simpleFoam, and foamToVTK non-interactively in a PBS job, using a singularity container. It does so by first creating a bash script (sing_input.sh) and then running the container on this script with

singularity exec $container_file $wrkdir/sing_input.sh

You can modify run_pbs to run your own OpenFOAM commands for your own use case.

Working directory

This example is setup to work as-is for any user, so you do not need to make any modifications to see it run.  It has you copy the OpenFOAM v6 tutorial pitzDaily directory to a location anywhere under your home directory.  You then use this directory as a working directory (i.e.,. where you run your job, and OpenFOAM does its work). The PBS script (see the file pbs_run copied below) generates a path to the working directory in the shell variable wrkdir with

wrkdir=$HOME/$(echo $PWD | cut -d'/' -f8-)

You can leave this as is if you want to have your PBS run script in the OpenFOAM project directory.

Example PBS Batch File (pbs_run)

#!/bin/bash -l 
#PBS -l nodes=1:ppn=2,pmem=2580mb,walltime=00:10:00 
#PBS -j oe

cd $PBS_O_WORKDIR

# Construct working directory path that will be valid in container 
wrkdir=$HOME/$(echo $PWD | cut -d'/' -f8-)

# Create bash shell scripti with commands you want to run in container 
echo "#!/bin/bash -l

# Set OpenFOAM6 environment, and working directory, inside of container 
source /opt/openfoam6/etc/bashrc 
cd $wrkdir

# Your OpenFOAM commands go here (must be non-interactive) 
blockMesh 
simpleFoam
foamToVTK 
" > sing_input.sh 
chmod 755 sing_input.sh

module load singularity
container_file=/panfs/roc/msisoft/openfoam/6.0/openfoam6-paraview54.simg
singularity exec $container_file $wrkdir/sing_input.sh

General Linux

MSI currently provide OpenFOAM outside of the module system. See the additional tabs on this page for instructions on how to access this software on Mesabi.

Not a Module

This software is not provided as a module. See the associated documentation for access instructions.