OpenFoam installation on CentOs 6.5 without root access
 

Dear Foamers,
I want to compile openFoam 2.3.0 on my University cluster without root access, the operating system of the cluster is CentOs 6.5 and the gcc version is 4.4.7, while i think the minimum gcc version is 4.7 for OpenFoam 2.3.0!
Is there a way to upgrade the gcc version and compile OpenFoam from source code without any root access( The administrator told me to compile anything from source code just in my home folder!) ?
The cluster operating system properties are as follows:
Thank you all for your ideas in advance!
Regards,
Arsalan.

Quick question: Have you tried following the instructions given here: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5 :confused:
If not, then since you do not have root access, you can skip the first 3 steps.

And since you're trying to install on a cluster, you can also skip steps 16 to 18.

Hi Bruno,
Actually i didn't try that because i know that the gcc version on this cluster is 4.4.7 while the minimum gcc version that required for OpenFoam 2.3.0 is 4.7, so i thought that this method does not lead to the good results!
However, if you think that this could be useful, I'll do it and post the results here.
I also read the other posts of you about this problem that you have advised to skip from steps that required root access and post the results, so this is my fault that i did not do it.

Thank you very much for your quick answer.
Regards,
Arsalan.

Quick comment: Like I wrote, if you follow my instructions, hopefully it will build as intended.
Regardless of whether it works or it does not work, then please let me know. Because if it doesn't, it is still possible to build it, because you already have the GCC 4.4 stack installed in that machine.

Hi Bruno,
Unfortunately because of the new year holidays i don't have access to the system for two weeks, so I'll do it at the first time after the holidays and post the results here, and i hope that you could help me for build it.

Thank you very much for your attention.
Regards,
Arsalan.

Hi Bruno,
I tried to following the instructions given in the wiki to build OpenFOAM and as expected it didn't work and failed at initial steps (i skipped the first 3 steps). Here is the first error in step 7 :
However, i continued the process to the final step and uploaded the make.log file in my dropbox for more information.
here is the make.log file download link :
https://www.dropbox.com/s/vnui9qvpde...og.tar.gz?dl=0

(i couldn't attach make.log file here because of the forum's limit of 195.3 KB for gz filetype.)

Thank you very much for your attention.

Regards,
Arsalan.

Hi Arsalan,

You will have to either check the instructions page for the cluster you're using, or you need to contact the administrators for the cluster to figure out which MPI toolbox they are using.

I was hoping they were using CentOS' own Open-MPI, but they are apparently using something else. And using the custom Open-MPI that OpenFOAM has got will likely not work in the cluster you're using.

Therefore, you need to ask and/or figure out which MPI the cluster is using and how it's activated, so that you can build OpenFOAM in a way that it can use it.

In addition, there is a particular error that implies that the custom GCC version failed to build properly, namely step #10 failed to work properly. Please check the log file "mkgcc.log" located at "ThirdParty-2.3.0", it should tell us why it didn't work.

Best regards,
Bruno

Hi Bruno,
I asked the administrators for which mpi version they are using and they told me that using the following command, is it helpful to you?
And for the error to building custom GCC version at step #10, the makegcc.log file is as follows :

Probably this is because that the connection is refused in step #8, as it shown below :

Thank you very much again for your attention, i really need this installation because of the high CPU time of simulations for my master thesis.

King regards,
Arsalan.

Quick answer: OK, now we're getting closer. Using the instructions on the wiki as a reference: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.5 - do the following steps differently from the wiki:

1. Steps 1 to 4 can be ignored.
2. I'm guessing that step #5 worked as intended.
3. Step #6 is still needed.
4. In step #7, you should replace this command:
   
   Code:

   ---

   module load openmpi-x86_64

   ---

   With this command:
   
   Code:

   ---

   module load mpi/openmpi/gcc/1.8

   ---

   Note: there are 2 places where you need to do that change.
5. In step #8, you will have to do the download manually, instead of relying on wget.
   • The first two you can download directly from here: https://github.com/wyldckat/scripts4OpenFOAM3rdParty/
   • The other two from here: https://github.com/wyldckat/ThirdPar.../tree/binutils
6. You can replace step #9 with this command:
   
   Code:

   ---

   module load cmake/2.8.12.2

   ---

7. You can try step #10.
   • If the download fails with getGcc, then you will have to download using the files from the download links given by that script.
8. Same applies to step #11, namely getBinutils might fail to download the necessary package.
9. Same applies for step #12, namely getBoost might fail to download the package.
10. Steps #14 and #15 should work as intended.
11. You can skip steps #16 and #17, because I'm guessing that you will not do post-processing with ParaView within the cluster.

Hopefully this will work as intended.

---

edit: Arsalan made another post a bit related to this topic, but it was more in regards to running in the cluster after the installation went well, therefore it was moved to here: http://www.cfd-online.com/Forums/ope...ble-basis.html

step 10
 

Hi bruno,
I have exactly the same question!(but I'm tryin to install openfoam-2.4.0 on centos6.5) and I get the same error in step 10
could u plz explain how can I download the files?and which files?
I downloaded gcc-4.8.4 gmp-5.1.2 mpfr-3.1.2 mpc-1.0.1 files from

http://mpfr.loria.fr/mpfr-3.1.2/mpfr-3.1.2.tar.bz2
ftp://208.118.235.20/gnu/gcc/gcc-4.8.4/gcc-4.8.4.tar.gz
https://gmplib.org/download/gmp-5.1.2/gmp-5.1.2.tar.bz2
http://www.multiprecision.org/mpc/do...c-1.0.1.tar.gz

and then extracted them in ThirdParty-2.4.0 and ran step 10 but it didn't work and I got the same error:

No such file or directory
Error building: gmp-5.1.2

thanks in advance :)

done!
 

Hi I found the solution arsalan.dryi sent me the correct links
thanks :)

Hi guys,

I have installed the OpenFOAM 3.0.0 in a cluster (Centos 6.7) and i can run it on a single processor (6 cores). However, when i try to run it in through the qsub in got an error:

rhoCentralFoam: command not found.

Does anyone knows what should i do?

Thank you in advance

Ok, at first you should load up OpenFOAM's environment at your qsub file, for detailed information read this thread : http://www.cfd-online.com/Forums/ope...ble-basis.html

Regards,
Arsalan.

Hi Arsalan,

Thank you for your suggestion. I have tried that but it still not recognise the OpenFOAM as loaded and i don't know why.My error is:

gcc: error: unrecognized command line option '--showme:link'
/opt/gridengine/default/spool/compute-0-0/job_scripts/768: line 53: rhoCentralFoam: command not found

Can you think why i got this error?

Thanks again

Ok, please attach your job script and use the "module avail" command and post the result here for more detailed information.

Regards.

When i press module avail i get :

[cc535@rocks OpenFOAM]$ module avail

-------------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------------
dot module-git module-info modules null opt-python use.own

--------------------------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------------------------
mpich-x86_64 openmpi-x86_64

Thanks

Hi,

I managed to find that the problem is with the parallel environment since openmpi is not install. Do you know if i can run in parallel with MPICH?how?

Thanks again

Hi, I'm trying to install openfoam v3.0.1 in my home directory, and I use this instruction page http://openfoamwiki.net/index.php/In...HEL#CentOS_6.7
But I got errors:
It seems there is something wrong with "mpicc". Should I change the commands in step 7?
there is some information maybe helpful

Hi,

First of all from what i can see you are trying to load the openmpi-x86_64 but it doesn't exist. Please try to contact the administrator (if its not you) and install the openmpi-x86_64. After that, when you press module avail you will see that the openmpi-x86_64 is on the available modules.In addition i think that there is not any mpicc installed. Try first installing the openmpi-x86_64 and then we can see the other errors.

Chariton

Thank you for your reply, Chariton! I sent an email to the administrator, but no reply yet. I'll post results after I solve the 'openmpi-x86_64' problem.

Hi,Chariton, below is the commands I used in compiling openfoam v3.0.1 in my /home directory.
It works well, I can calculate my case using it, but there are fatal errors in log.make file like this

I don't know what's the purpose of CGAL.

I also want to install openfoam in centOS with no root access and I also skiiped the first three steps. But the system shows the following error with .tar file.
[chayanit@un03 OpenFOAM]$ tar -xzf OpenFOAM-2.3.0.tgz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

Hi everyone, I'm also trying to install OF5.0 on my institute cluster in home folder. I also don't have root access. I have followed all the instruction given in this link, https://openfoam.org/download/5-0-source/. After running ./Allwake command I'm getting following error
In file included from UOPwrite.C:30:0:
PstreamGlobals.H:42:17: fatal error: mpi.h: No such file or directory
#include <mpi.h>
^
compilation terminated.
make: *** [/data/me16d023/OpenFOAM/OpenFOAM-5.0/platforms/linux64GccDPInt32OptSYSTEMOPENMPI/src/Pstream/mpi/UOPwrite.o] Error 1

Anybody have solution ? Please help me.

Quick answer: The Institute cluster should have a way to load/activate the MPI version that could be used with OpenFOAM. My guess is that if you run the following command:
you should get a complete list of the available modules in that cluster. Among them, search for one that states "openmpi" in some way. Then you can load the respective version, by using the associated name, for example, the name "openmpi/1.10.1" would be activated by running this command:
then try building OpenFOAM once again.

Thank you sir. It work for me.

Hi Ebrahim
can you plz send me those links?
Thanks in advance

Hi Bruno,


I followed your instructions to install OF3.0.1 on the cluster without root access given in this link.


https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL


SInce the OS of my university cluster is CentOS Linux release 7.8.2003 (Core). I followed the post#3 i.e for CentOS 7.1

I skipped step 1, 2 and 3.
Step 4, 5, 6, 7 worked normally.



For step 8, I first loaded

based on the available MPI on the cluster as below


and executed
I also changed the alias in step 8 accordingly



Then I proceeded to compile further. I didn't have any error or warning. However. the final compilation with ./Allwmake failed.

The first error says

I have no idea what this means but I suspect it is from the loading of OpenMPI.

Would you please have a look at the log file of the compilation I have attached. I would sincerely appreciate your help.


Best regards,
James

Hi,

I need to install openfoam6 on a cluster without root access. Is there any useful website to guide me?

Thanks