[federicabi]

Hi everyone!
I need to compile a custom version of OF3.0.1 on a HPC cluster (CentOS 7.1) and I have never done this before so I'm not familiar with environment variables and .pbs files. I try to explain what my problem is even if it is not easy at all.

I compiled without errors the standard version of OF3.0.1 in $HOME/Openfoam following this guide https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL. I put the modified src folder in $HOME/Openfoam/fbiano00-3.0.1 (my folder on the cluster) and I run wmake to compile it. No errors came out.

Now I need to submit my jobs using the modified OF version instead of the standard version.
I used this .pbs file to submit jobs with standard OF and I don't know how to modify it for my purpose.

Allrun_18.pbs

#!/bin/bash
#PBS -A azi_prod_0
#PBS -l walltime=15:00:00
#PBS -l select=2:ncpus=16:mpiprocs=16:mem=120GB
#PBS -N 18
#### File di output e di errore
#PBS -o job.out
#PBS -e job.err
#PBS -M federica.biano@gmail.com
#### Coda di sottomissione
echo "Job started at " `date`
#### change dir to your working directory
cd $PBS_O_WORKDIR
#### load bash shell cineca to set the module environment
source /cineca/prod/environment/module/3.1.6/none/init/bash
module purge
module load gnu/4.9.2
module load openmpi/1.8.4--gnu--4.9.2
module load profile/advanced
module load openfoam/3.0.1
jobid=`echo $PBS_JOBID | sed 's/[.].*//'`
name=18kn
./Allrun $name > OUT.$jobid.txt
echo "Job finished at " `date`
exit

Can you please help me? I can give you any other relevant information if you ask.
Thanks in advance

Federica

[wyldckat]

Greetings Federica,

I've moved your post from the Installation forum to the Solving forum, because this seems more related to running in the HPC environment. And since you've stated that it seems to have been installed without any error messages, then we might as well move to the next step.

From your description, it seems like you did not use any of the following commands before building your custom build of OpenFOAM 3.0.1:

module load gnu/4.9.2
module load openmpi/1.8.4--gnu--4.9.2
module load profile/advanced
module load openfoam/3.0.1

If so, then I expect that you can remove those 4 lines and replace them with these two:

module load openmpi-x86_64
source $HOME/OpenFOAM/OpenFOAM-3.0.x/etc/bashrc foamCompiler=ThirdParty WM_COMPILER=Gcc48 FOAMY_HEX_MESH=yes

These 2 essentially do the same as the other 4, but for your own installation.


However, I am a bit worried about the following statement that you wrote:

Originally Posted by federicabi

I put the modified src folder in $HOME/Openfoam/fbiano00-3.0.1 (my folder on the cluster) and I run wmake to compile it. No errors came out.

I didn't understand where the "src" folder came from and why you placed it inside that folder.

Best regards,
Bruno

[federicabi]

Hi Bruno!
Thank you for your reply! my apologies if I posted in the wrong section.
actually I replaced the four lines you mentioned with the two lines you suggested and it worked perfectly!

Regarding the src folder, I followed the procedure I used to compile a new OF library on my computer, but on the cluster, so since I modified a sixDoFRigidBodyMotion library, I recompile only that part of the OF source on my personal folder on the cluster. Indeed the src folder in my personal folder contains only the modified library.

I'm sorry if I'm not able to be more clear, I'm not an expert and I followed only the hints I found on this forum.

Anyway, thank you very much for your help!


Federica

[wyldckat]

Quick answers:

Originally Posted by federicabi

Thank you for your reply! my apologies if I posted in the wrong section.

No problem. I only pointed it out to make it clearer why I had moved the thread . Sometimes I also don't know for certain on which sub-forum a thread should be, since it's referring to several topics.

Originally Posted by federicabi

Regarding the src folder, I followed the procedure I used to compile a new OF library on my computer, but on the cluster, so since I modified a sixDoFRigidBodyMotion library, I recompile only that part of the OF source on my personal folder on the cluster. Indeed the src folder in my personal folder contains only the modified library.

I'm sorry if I'm not able to be more clear, I'm not an expert and I followed only the hints I found on this forum.

Mmm... well, this information is a bit important to understand other potential future problems.
Depending on the changes you've done, you might want to change the final name and location of the custom library. If you edit the file "Make/files" for this custom library and change the last line to use "FOAM_USER_LIBBIN" instead of "FOAM_LIBBIN" and if you use another name for the library, this way you can ensure that the original build of this library is not affected. Then don't forget to use the correct name in the dictionary files on the case.