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 (While shelled into the singularity container,, do this)

2a. Copy the bashrc file to scratch
cp   /opt/openfoam7/etc/bashrc /scratch
Modify the /scratch/bashrc file to suit your environment.

2b. (While shelled in, do this), create a variable file (openFOAMenv7.sh) with contents like this:

vi /scratch/openFOAMenv7.sh
#!/bin/bash
export PATH=/opt/openfoam7:/opt/openfoam7/bin:/opt/paraviewopenfoam56/bin:$PATH
export LD_LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/opt/paraviewopenfoam56/lib:$LIBRARY_PATH
export   LDFLAGS=-L/opt/paraviewopenfoam56/lib:$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 bashrc7  

3. Manual Test Run 
====================
 
(While shelled into the singularity container, do this)

source /scratch/openFOAMenv7.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)

If the output looks correct, go to the next step

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/openfoamLauncher7.sh
 
An example of the content is this: 
#!/bin/bash 
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 bashrc7
#Put your run instructions/command below.
foamInfo -help
cd s2940457/currentWaveFlume
chmod +x runCase
./runCase  >>>>>>>>>>>>> 

make it executable:
chmod +x /scratch/openfoamLauncher7.sh

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

Check if it gives the expected results:
/scratch/openfoamLauncher7.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:
 
mkdir /scratch/s2940457/pbs
cd /scratch/s2940457/pbs
vi openfoam7.pbs01

>>>>>>>>>  

!/bin/bash
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -N TestOpenFoam7
#PBS -q workq
#PBS -l select=1:ncpus=8: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/s2940457:/scratch --pwd /scratch/s2940457:/scratch --pwd /scratch  /export/home/s2940457/Container/openfoam7-paraview56_latest.sif "./openfoamLauncher7.sh"
exit
sleep 2 
>>>>>> 
 
Submit the job and check the results (output and error files).
 
qsub openfoam7.pbs01  


If all goes well, then the only file that needs to be edited in the future is the openfoamLauncher7.sh

To run in parallel, you may look at online documentation.
>>>>>>>>>>>>>>
e.g
How to run in parallel:
https://www.youtube.com/watch?v=YdYHDMygNPU
>>>>>>>>>>

source /usr/local/bin/s3proxy.sh
mkdir -p  $HOME/sw/Containers/openfoam8/
cd  $HOME/sw/Containers/openfoam8/
singularity pull  docker://public.docker.itc.griffith.edu.au/openfoam/openfoam8-paraview56


mkdir -p $HOME/OpenFOAM/${USER}-8
cd $HOME/OpenFOAM/${USER}-8
singularity  shell -B /export/home/${USER}:/home --pwd /export/home/${USER}:/home --pwd $HOME/OpenFOAM/${USER}-8 $HOME/sw/Containers/openfoam8/openfoam8-paraview56_latest.sif

Once inside the shell:

source /opt/openfoam8/etc/bashrc
mkdir -p $FOAM_RUN
#echo $FOAM_RUN
#/export/home/s5072653/run

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

To run it as a batch job, create a launcher script:
1. Launcher Script
>>>>>>>
vi ~/pbs/openfoam8Launcher.sh
#!/bin/bash 
source /opt/openfoam8/etc/bashrc
mkdir -p $FOAM_RUN
#cd ~/run
cd $FOAM_RUN
cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
cd pitzDaily
blockMesh
>>>>>>>>
#make it executable
chmod +7 ~/pbs/openfoam8Launcher.sh

2. pbs script

vi ~/pbs/openfoam8.pbs01
>>>>>
#!/bin/bash
#PBS -m abe
#PBS -M YourEmail@griffithuni.edu.au
#PBS -N TestOpenFoam8
#PBS -q workq
#PBS -l select=1:ncpus=8:mem=12gb,walltime=3:00:00
cd  $PBS_O_WORKDIR
#An example is as below. Modify accordingly to suit your needs
singularity  exec -B ~:/home --pwd ~:/home --pwd /home  $HOME/sw/Containers/openfoam8/openfoam8-paraview56_latest.sif "pbs/openfoam8Launcher.sh"
exit
sleep 2
>>>>>>>

Please submit the test pbs script to check functionality
cd ~/pbs
qsub openfoam8.pbs01