CFD Online Discussion Forums - [OpenFOAM.org] Problems in Installing OpenFOAM-4.0 on CentOS SL RHEL

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louistse

September 20, 2016 06:03

Problems in Installing OpenFOAM-4.0 on CentOS SL RHEL

Hello, everyone. I am an MPhil student doing CFD. I encountered A LOT OF questions when I am trying to install OpenFOAM-4.0 on the computer cluster managed by the university. I followed the instructions given by the following website:
https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL

The main problem is, I do not have the permission to access the cluster as root, in other words, I cannot install the libraries by simply typing the commands like “sudo”. Is it possible for me to install every libraries, OpenFOAM itself and Thirdparty software in my home directory?

Besides, is it possible to get rid of the “root” problem if I do not install the Thirdparty software like Paraview, or if I install OpenFOAM® v1606+ ?? Or can I just install the OpenFOAM on the cluster, and do post-processing on my desktop computer?

I just know a little about linux, I don’t know what I can do if I cannot install OpenFOAM on the cluster. :confused: :confused:

FYI, the general information of the computer cluster
Operating System: CentOS 6.6 64-bit
Architecture: x86_64
Open MPI: v2.0.0
Python: v2.6.6
bison (GNU Bison): v2.4.1
flex: v2.5.35
GCC (GNU Compiler Collection): v4.4.7

wyldckat

September 24, 2016 15:40

Quick answer: You can simply try starting from step #4, namely you can try skipping the first 3 steps and see if it works: https://openfoamwiki.net/index.php/I...HEL#CentOS_6.8

If you have problems with the wget commands, then you can download manually the files with your Internet browser and then place the files where needed.

And yes, I do advise you to skip trying to build ParaView on the cluster, at least for now.

In addition, if your cluster is very well administered, you can try and check what other software packages are already available in it, but running:

Code:

module avail

Having GCC 4.5 or newer would make it easier for building OpenFOAM, because that would mean that you could skip a few steps in the instructions, namely the steps meant for compiling GCC 4.8.5.

louistse

September 26, 2016 23:47

Thanks for your reply.
I would like to ask if I do not install ParaView on the cluster, but OpenFOAM4.0 only, I believe it requires updating CMake and GCC 4.8.5, but how about Qt and GNU binutils?
What I am asking is, any steps on the website https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL I can skip in order to install OpenFOAM Only, but not ParaView.

Besides, I just checked the available packages using

PHP Code:


		
			
rpm -q

There are 13 packages listing in step 2 have been installed, and only 7 packages are not installed, they are
1. texinfo
2. gstreamer-plugins-base-devel
3. libGLU-devel
4. libXinerama-devel
5. libXrandr-devel
6. libXi-devel
7. libXcursor-devel

Do these packages matter for installing OpenFOAM? or just for ParaView? And If I really need to install these 7 packages, is it possible for me to download the packages in https://rpmfind.net/linux/rpm2html/s...os&arch=x86_64 and install them in my HOME directory?

wyldckat

September 27, 2016 16:36

Quick answers:

Quote:

Originally Posted by louistse (Post 619358)

Thanks for your reply.
I would like to ask if I do not install ParaView on the cluster, but OpenFOAM4.0 only, I believe it requires updating CMake and GCC 4.8.5, but how about Qt and GNU binutils?

CMake is also needed for building CGAL.
- But if you don't need foamyHexMesh on the cluster, then CGAL isn't needed either, therefore CMake won't be needed.
Qt is only needed for ParaView.
GNU binutils is probably not 100% necessary, but I've witnessed in the past that it was needed.
You need GCC 4.5 or newer for building OpenFOAM 4.0.

A more recent GCC version might be available in the cluster through module loading. As I mentioned in the previous post, please let us know what this command gives you, at least any mentions to GCC versions:

Code:

module avail

Quote:

Originally Posted by louistse (Post 619358)

There are 13 packages listing in step 2 have been installed, and only 7 packages are not installed, they are
1. texinfo
[...]

Most of them are only needed for ParaView.
"texinfo" is either needed for building GCC or binutils, I can't remember which one it was...

louistse

October 3, 2016 09:45

Sorry for late reply, because the cooling system of the computer cluster was not going well last week, and the university spent about 6 days to fix the problem, eventually it is back to normal now.

Here is the response for the command

Code:

module avail

PHP Code:


		
			
-------------------------- /usr/share/Modules/modulefiles --------------------------

dot              modules          rocks-openmpi

module-git       null             rocks-openmpi_ib

module-info      opt-python       use.own



--------------------------------- /etc/modulefiles ---------------------------------

openmpi-x86_64

It seems that the command does not give any information about GCC, isn't it? According to the official website of the university, the system default version of GCC is v4.4.7, and I am noticed that, I need to run

PHP Code:


		
			
source /usr/local/setup/gcc-g++-4.9.2.sh

in order to access GCC

cfdsolver1

October 3, 2016 11:58

As I know, official repositories of Redhat EL is 4.4.7 for gcc but it is possible to upgrade it from unofficial repositories but I am not sure if it is possible to do it.

I have installed OpenFOAM 4.0 on HPC running RHEL 5 and 6 without root access by using OpenFOAMWiki post. Also, you can install gcc on your local folder using this post:

http://stackoverflow.com/questions/9...t-shared-libra

What is the exact problem by installing gcc and binutils by using ThirdParty folder?

louistse

October 5, 2016 02:35

1 Attachment(s)

I have tried to install OpenFOAM v4.0 again following http://openfoamwiki.net/index.php/In...CentOS_SL_RHEL and since I do not have the root access, I skipped the first 3 steps, and started from step #4.

Until step #10, after I entered the command

Code:

./makeGcc -no-multilib > log.makeGcc 2>&1

GCC was not built successfully, and error comes up. Attached please find the log file.
I have no idea why the errors exist, is it something wrong with my account, or I didn't clean everything that I left in the previous installation process?

Thank you

cfdsolver1

October 5, 2016 06:36

Yes, if you clean it before you start it might be better. And also, according to log file, you do not have isl. it might be required to build gcc, I guess.

Quote:

Originally Posted by louistse (Post 620322)

Code:

./makeGcc -no-multilib > log.makeGcc 2>&1

wyldckat

October 6, 2016 15:29

Quick answer:

Quote:

Originally Posted by louistse (Post 620125)

[CODE]It seems that the command does not give any information about GCC, isn't it? According to the official website of the university, the system default version of GCC is v4.4.7, and I am noticed that, I need to run

Code:

source /usr/local/setup/gcc-g++-4.9.2.sh

in order to access GCC

This means that you no longer need to build a custom GCC, because you already have GCC 4.9.2!

This also means that you only need to do a small change to the instructions. In step #7, it tells you to use something like this:

Code:

source $HOME/OpenFOAM/OpenFOAM-4.0/etc/bashrc WM_COMPILER_TYPE=ThirdParty FOAMY_HEX_MESH=yes

Edit the file "~/.bashrc", find the line that as the command above and remove the "WM_COMPILER_TYPE=ThirdParty" entry. Then start a new terminal and run:

Code:

of40

to activate the OpenFOAM 4.0 environment.
The you can skip steps #10 and #11.

Next... are you going to need foamyHexMesh? I ask this because I have no idea if MPFR and GMP are already available on that machine.
If you need it, then we need to figure out if we need to use the custom build of MPFR and GMP that was built with makeGcc. Please run the following command to see if there is any installed in the same stack as GCC 4.9.2:

Code:

find /opt/rh/devtoolset-3 -name "libmpfr*"

If you don't need foamyHexMesh, then please edit the file "~/.bashrc" once again and remove "FOAMY_HEX_MESH=yes" as well. You can then skip step #12 as well.

louistse

October 7, 2016 03:37

I think I have installed OpenFOAM successfully, as it gives exactly the same output when I typed

Code:

icoFoam -help

in step #16

Thank you everyone !

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