[anfho]

Hi,
finally, I could also get a hold of the cluster admin. And I have to apologize as I am a new user of this cluster, too. The admin told me that there was CentOS 5.4 installed. Is this the same as CentOS/SL 5.x? I got confused about the Linux versions. Because when I entered "gcc --version" I got the output: "gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46) Copyright (C) 2006 Free Software Foundation, Inc." Therefore I thought RHEL 4.1.2 would be installed.
But still - eventhough CentOS 5.4 is installed it is the old gcc 4.1.2 compiler. So is it possible to use CentFOAM and then do a work around of the "yum" command? Meaning, can I update the gcc compiler on CentOS 5.x eventhough I do not have the root rights?
Also, why does OpenCFD and everyone in this forum recommend to compile OpenFOAM with gcc? gcc is known to produce inefficient codes (at least that's what the cluster admin says). Wouldn't it be better to use icc or pgi? On the cluster there is icc 10.1 installed.
Thanks! Andreas

[anfho]

Is there a command to check the linux version?

[wyldckat]

Greetings to all!

I'm just dropping by to say that I've already answered Andreas in the other thread (namely "OpenFoam Installation in Redhat Enterprise linux 5 - post #15"), since the questions are nearly the same

Best regards,
Bruno

[linnemann]

Thx Bruno

Good stuff

[deepu134]

I have some basic background in CFD (mainly Fluent) and Linux (RHEL), and would not regard myself as an expert by any means.

I have root privileges on our Centos 5.5 (x 86 architecture, 64 bit) Linux server and want to install the entire openFOAM suite so that it is available to all users. I logged on as 'root' and ran the centFOAMInstall script and it appears that all packages were installed under /opt as desired.

[deepu134@arc1 opt]$ ls -al
total 36
drwxr-xr-x 7 root root 4096 Sep 21 13:45 .
drwxr-xr-x 24 root root 4096 Sep 21 16:40 ..
drwxrwxr-x 3 deepu134 deepu134 4096 Sep 21 13:42 engrid-1.2.0
drwxr-xr-x 4 root root 4096 Sep 21 13:45 gmsh-2.4.2
drwxr-xr-x 6 root root 4096 Sep 21 13:38 netgen-4.9.13
drwxr-xr-x 4 root root 4096 Sep 21 13:18 OpenFOAM
drwxr-xr-x 6 root root 4096 Sep 21 13:38 paraview-3.8.0

When I checked with 'OF17' and 'which gcc' as root, I received the following message, suggesting that it works.

[root@arc1 ~]# OF17
[root@arc1 ~]# which gcc
/opt/OpenFOAM/ThirdParty-1.7.1/platforms/linux64/gcc-4.4.4/bin/gcc

I then logged on as a regular user (deepu134), but was not able to run openFOAM.

[deepu134@arc1 ~]$ OF17
-bash: /opt/OpenFOAM/OpenFOAM-1.7.1/etc/bashrc: Permission denied

I checked the permissions for /opt/OpenFOAM/OpenFOAM-1.7.1/etc/bashrc, and this is what I found:

[deepu134@arc1 etc]$ ls -al
total 116
drwxr-xr-x 4 root root 4096 Sep 21 13:18 .
drwxr-xr-x 10 root root 4096 Sep 21 13:18 ..
-rw-r----- 1 1049 1049 2383 Jun 15 14:53 aliases.csh
-rw-r----- 1 1049 1049 2365 Jun 15 14:53 aliases.sh
drwxr-xr-x 5 root root 4096 Sep 21 13:18 apps
-rw-r----- 1 1049 1049 8337 Sep 21 13:18 bashrc
-rw-r----- 1 1049 1049 7754 Aug 24 08:35 cellModels
-rw-r----- 1 1049 1049 27486 Aug 24 08:52 controlDict
-rw-r----- 1 1049 1049 8686 Aug 24 08:47 cshrc
-rw-r----- 1 1049 1049 1904 Jun 22 07:30 prefs.csh-EXAMPLE
-rw-r----- 1 1049 1049 1891 Jun 22 07:30 prefs.sh-EXAMPLE
-rw-r----- 1 1049 1049 10332 Aug 6 05:52 settings.csh
-rw-r----- 1 1049 1049 10036 Aug 26 23:19 settings.sh
drwxr-xr-x 2 root root 4096 Sep 21 13:18 thermoData

Can somebody please clarify where I went wrong, and the best way to fix it so that the openFOAM suite is available to all users?

-Rishya

[linnemann]

Hi

You need to set the permissions to let users read/excecute OF stuff.

So go to /opt write

chmod -R 755 ./OpenFOAM

^

Then users have read/excecute permissions on all OpenFOAM related stuff.

Maybe you need to do this for paraview and other stuff as well.

[vishal]

Hi,

i too didn't get paraview in Thirdparty. rather i downloded compiled version of paraview.

download the 3.8.0 or modified version of paraview.

create .foam or .OpenFOAM file for ur case.

open paraview by execution of ./paraview in (bin folder contained in paraview).

and you can open your .foam file there.....!!!

[linnemann]

Hi

Yes as it says on the centFOAM wiki page

Note that from June 2010 Paraview will be a separate program from OpenFOAM and thus paraFoam will no longer work. This was a decision I've made since I feel the performance from the parallel reader found here is superior to the one in OpenFOAM. It also means that you can use Paraview without OpenFOAM and it allows me to keep Paraview more up to date. To use Paraview with the new reader just create an empty file in your case folder "touch casename.foam" and open this file using Paraview.

[vnpenguin]

Hi linnemann,
I use your build 1.7.1 from CentFOAM. Could you tell me openmpi-1.4.1 (in ThirdParty-1.7.1 package) was compiled with option "--with-sge" ?

Thank you for your very good job,

Regards,

[linnemann]

Hi

Yes it has support for SGE (its what I use :-) )

Best

[vnpenguin]

Originally Posted by linnemann

Hi

Yes it has support for SGE (its what I use :-) )

Best

Super! Thank you so much

[mirko]

Originally Posted by linnemann

Hi

Yes it has support for SGE (its what I use :-) )

Best

Small typo in centFOAMinstall:

One of the echo commands still refers to OF16

[Rebecca513]

Hi Linnemann,

I used your python script to install centFOAM.

Though I got some problems earlier, but OF and engrid seem to work well now. Still I have trouble opening gmsh, netgen, and paraview. I wonder whether I need to go through more compiling for those three or there might be other reasons.

Thank you!

Best,

H

[linnemann]

Hi

Unless you give me some details or terminal output that describes the error I will have a hard time helping you.

[Rebecca513]

Hi Linnemann,

Sure. For instance, when I tried to run 'start_gmsh', it gives

#!/bin/bash

export PATH=/home/hangdeng/centFOAM//gmsh-2.5.0/bin:$PATH

export LD_LIBRARY_PATH=/home/hangdeng/centFOAM//gmsh-2.5.0/lib:$LD_LIBRARY_PATH

/home/hangdeng/centFOAM//gmsh-2.5.0/bin/gmsh

For the other two, no response at all.

Thank you~

[linnemann]

ok.

Can you please verify that "start_gmsh" is executable by running

ll start_gmsh

This has to be done on the file so you have to cd to the dir where start_gmsh is by using

which start_gmsh

If its not executable run

chmod +x start_gmsh

on the file.

Then try again.

Please to the same for the other programs.

If in doubt post the output here.

[Rebecca513]

Hi,

First time, I got

[hangdeng@cee-5dpjzq1 gmsh-2.5.0]$ ll start_gmsh
-rw-rw-r-- 1 hangdeng hangdeng 199 Nov 1 11:08 start_gmsh
[hangdeng@cee-5dpjzq1 gmsh-2.5.0]$ which start_gmsh
/usr/bin/which: no start_gmsh in (/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/qt-4.6.4/bin:/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/bin:/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64/gcc-4.5.3/bin:/home/hangdeng/OpenFOAM/hangdeng-2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/site/2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/wmake:/platforms//qt-4.6.4/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/hangdeng/bin)

After running chmod
It becomes
[hangdeng@cee-5dpjzq1 gmsh-2.5.0]$ ll start_gmsh
-rwxrwxr-x 1 hangdeng hangdeng 199 Nov 1 11:08 start_gmsh
[hangdeng@cee-5dpjzq1 gmsh-2.5.0]$ which start_gmsh
/usr/bin/which: no start_gmsh in (/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/qt-4.6.4/bin:/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64Gcc45/openmpi-1.5.3/bin:/home/hangdeng/centFOAM//OpenFOAM/ThirdParty-2.0.x/platforms/linux64/gcc-4.5.3/bin:/home/hangdeng/OpenFOAM/hangdeng-2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/site/2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/platforms/linux64Gcc45DPOpt/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/bin:/home/hangdeng/centFOAM//OpenFOAM/OpenFOAM-2.0.x/wmake:/platforms//qt-4.6.4/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/hangdeng/bin)

And still it is not working:
[hangdeng@cee-5dpjzq1 gmsh-2.5.0]$ ./start_gmsh
/home/hangdeng/centFOAM//gmsh-2.5.0/bin/gmsh: error while loading shared libraries: libfltk_images.so.1.1: cannot open shared object file: No such file or directory

I was just reading your recent posts, and I realized that maybe it is because I used the py script on centOS6.0. I am sorry I should have mentioned this earlier.

start_gmsh was shellscript. But executable files in the folders like 'gmsh' did not respond at all~

[linnemann]

Hi

It complains that libfltk_images.so.1.1 cant be found.

This is a part of the fltk package and must be installed to run gmsh

yum install fltk

If its not in the std yum repos its part of atrpms.

http://atrpms.net/documentation/install/

Best

[Rebecca513]

I see, seems that I got some packages missing. I have fixed gmsh, will work on the other two programs.

Thank you Linnemann!

Best,
Hang

[Rebecca513]

Hi Linnemann,

I tried to fix all the missing packages. But there is a wired one I can't resolve.

When I try to open paraview in the terminal,

It says that libpython2.4.so.1.o can't be found.

But I have python 2.6.5 installed. And I searched online, there is no installation information of libpython2.4 on centOS available.

Maybe I am missing something else?

Thank you!

Best,

Hang