Versions Compared

Old Version 23

changes.mady.by.user Indy Siva

Saved on

compared with

New Version 24

changes.mady.by.user Indy Siva

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Table of Contents

Introduction

OpenFOAM is a framework for developing application executables that use packaged functionality contained within a collection of approximately 100 C+ libraries. OpenFOAM is shipped with approximately 250 pre-built applications that fall into two categories: solvers, that are each designed to solve a specific problem in fluid (or continuum) mechanics; and utilities, that are designed to perform tasks that involve data manipulation.

Source: https://cfd.direct/openfoam/user-guide/

...

No Format
Initial Prep:
=============
 
Copy the images into the local container folder:
 
mkdir ~/Container
cp /sw/Containers/singularity/images/openfoam7-paraview56_latest.sif ~/Container/

Shell into the container and create launcher script:
====================================================
 
Initial setup
 
1. shell into the container
=============================
For example:

singularity  shell -B /scratch/s12345:/scratch --pwd /scratch/s12345:/scratch --pwd /scratch  /export/home/s12345/Container/openfoam7-paraview56_latest.sif
 
e.g:

singularity  shell -B /scratch/s5126720:/scratch --pwd /scratch/s5126720:/scratch --pwd /scratch  /export/home/s5126720/Container/openfoam7-paraview56_latest.sif
 
2. Create a variable file you can source

Copy the bashrc file to scratch
cp   /opt/openfoam7/etc/bashrc /scratch

Modify the /scratch/bashrc file to suit your environment.

 
Once in the shell, create a variable file with contents like this:
 
vi /scratch/openFOAMenv.sh
export LD_LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LIBRARY_PATH
export PATH=/opt/openfoam7:/opt/openfoam7/bin:/opt/paraviewopenfoam56/bin:$PATH
export   LDFLAGS=-L/opt/paraviewopenfoam56/lib:$LDFLAGS
export   PKG_CONFIG_PATH=/sw/library/loki/0.1.7/lib/pkgconfig:$PKG_CONFIG_PATH
export   INCLUDE=/opt/paraviewopenfoam56/include:$INCLUDE
export   CPLUS_INCLUDE_PATH=/opt/paraviewopenfoam56/include:$CPLUS_INCLUDE_PATH
export   CPATH=/opt/paraviewopenfoam56/include:$CPATH
export   C_INCLUDE_PATH=/opt/paraviewopenfoam56/include:$C_INCLUDE_PATH
export   FPATH=/opt/paraviewopenfoam56/include:$FPATH
export   CFLAGS=-I/opt/paraviewopenfoam56/include:$CFLAGS
export   CPPFLAGS=-I/opt/paraviewopenfoam56/include:$CPPFLAGS
export   CXXFLAGS=-I/opt/paraviewopenfoam56/include:$CXXFLAGS
export   FCFLAGS=-I/opt/paraviewopenfoam56/include:$FCFLAGS
export   FFLAGS=-I/opt/paraviewopenfoam56/include:$FFLAGS
source /optscratch/openfoam7/etc/bashrc


3. Manual Test Run
===================
 
source /scratch/openFOAMenv.sh 
foamInfo -help

For example:
 
Singularity openfoam7-paraview56_latest.sif:/opt/openfoam7> foamInfo -help

Usage: foamInfo [OPTIONS] <name>
options:
  -all     | -a        list all tutorials that use <name> (otherwise maximum 10)


4. Create a Launcher Script;
===========================
Once you are happy that all step 1 ,2 and 3 works, you can create a launcherScript
While still inside the shell:
 
vi /scratch/openfoamLauncher.sh
 
An example of the content is this:

export LD_LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LIBRARY_PATH
export PATH=/opt/openfoam7:/opt/openfoam7/bin:/opt/paraviewopenfoam56/bin:$PATH
export   LDFLAGS=-L/opt/paraviewopenfoam56/lib:$LDFLAGS
export   PKG_CONFIG_PATH=/sw/library/loki/0.1.7/lib/pkgconfig:$PKG_CONFIG_PATH
export   INCLUDE=/opt/paraviewopenfoam56/include:$INCLUDE
export   CPLUS_INCLUDE_PATH=/opt/paraviewopenfoam56/include:$CPLUS_INCLUDE_PATH
export   CPATH=/opt/paraviewopenfoam56/include:$CPATH
export   C_INCLUDE_PATH=/opt/paraviewopenfoam56/include:$C_INCLUDE_PATH
export   FPATH=/opt/paraviewopenfoam56/include:$FPATH
export   CFLAGS=-I/opt/paraviewopenfoam56/include:$CFLAGS
export   CPPFLAGS=-I/opt/paraviewopenfoam56/include:$CPPFLAGS
export   CXXFLAGS=-I/opt/paraviewopenfoam56/include:$CXXFLAGS
export   FCFLAGS=-I/opt/paraviewopenfoam56/include:$FCFLAGS
export   FFLAGS=-I/opt/paraviewopenfoam56/include:$FFLAGS
source /opt/openfoam7/etcscratch/bashrc
cd /scratch
#Put your run instructions/command below.
foamInfo -help

>>>>>>>>>>>>> 

make it executable:
chmod +x /scratch/openfoamLauncher.sh

Run it manually and check if it gives the expected reults:

Check if it gives the expected results:
/scratch/openfoamLauncher.sh
(OR: try cd /scratch;./openfoamLauncher.sh)

5. Running it as a batch job:
==============================

Exit the shell and create this pbs script anywhere in space:
 
vi pbs.01
 
>>>>>>>>> 
#!/bin/bash 
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -N TestOpenFoam
#PBS -q workq
#PBS -l select=1:ncpus=1:mem=2gb,walltime=3:00:00
cd  $PBS_O_WORKDIR
#An example is as below. Modify accordingly to suit your needs
singularity  exec -B /scratch/s5126720:/scratch --pwd /scratch/s5126720:/scratch --pwd /scratch  /export/home/s5126720/Container/openfoam7-paraview56_latest.sif "/scratch/openfoamLauncher.sh"
exit
sleep 2
>>>>>> 
 
Submit the job and check the results.
 
qsub pbs.01

...