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Installing OpenFOAM 2.4.0 on CentOS 6.6

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Old   July 22, 2015, 06:40
Default Installing OpenFOAM 2.4.0 on CentOS 6.6
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Well, that explains it all, even the guys at SF encounter nasty bugs!.

Thanks, I've been following your 2.3.1 guide with smalls modifications because the 2.4.0 one wasn't out yet. Are the changes in step 17 critical (CentOS 6.6)?

Sorry if this is off-topic, but there's no discussion thread up yet, feel free to move or delete the post if needed.
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Old   July 25, 2015, 08:54
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Hi Kyrox,

I've moved your post from the other thread http://www.cfd-online.com/Forums/ope...oam-2-3-x.html - so that we can now have a thread for discussing how to install OpenFOAM 2.4.0 on CentOS 6.6.

As for your question: Step #17 (fixing and installing ParaView 4.1.0) changed a bit between 2.3.1 and 2.4.0, because the file "etc/tools/ParaView4Functions" is already fixed. The other remaining fix relates to being able to build ParaView with both the MPI and Python options.

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Old   February 7, 2016, 04:53
Default Installing OpenFoam 2.4 on CentOS 6.7
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Hi,

I am new to OF... i am trying to install OF on CentOs 6.7 i686 , i used the procedure on wiki for OF 2.4 on CentOs 6.6.
I think that OF is installed correctly (hope so !), however Paraview (ParaFoam) is not installed , when running it i have this error message:

Code:
$ paraFoam

FATAL ERROR: ParaView reader module libraries do not exist

Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
The last lines of "log.makePV" are:

Code:
[ 16%] Building CXX object VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o
In file included from /usr/include/GL/glx.h:333,
                 from /home/Donminoti/OpenFOAM/ThirdParty-2.4.0/ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx:31:
/usr/include/GL/glxext.h:480: error: ‘GLintptr’ has not been declared
/usr/include/GL/glxext.h:480: error: ‘GLintptr’ has not been declared
/usr/include/GL/glxext.h:480: error: ‘GLsizeiptr’ has not been declared
/usr/include/GL/glxext.h:481: error: ‘GLintptr’ has not been declared
/usr/include/GL/glxext.h:481: error: ‘GLintptr’ has not been declared
/usr/include/GL/glxext.h:481: error: ‘GLsizeiptr’ has not been declared
make[2]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o] Error 1
make[1]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/all] Error 2
make: *** [all] Error 2
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/home/Donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done
Any help would be appreciated ,
Thanks

Last edited by wyldckat; February 7, 2016 at 12:19. Reason: Added [CODE][/CODE] markers
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Old   February 7, 2016, 12:26
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Quick answer @donminoti: I see that you've followed these instructions: https://openfoamwiki.net/index.php/I...HEL#CentOS_6.6 - I'm just adding this link-back, because I forgot to mention it in an earlier post.

This is odd, very odd. Please try the following commands:
Code:
cd $WM_THIRD_PARTY_DIR
sed -i -e 's=//#define GLX_GLXEXT_LEGACY=#define GLX_GLXEXT_LEGACY=' \
  ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx
Then please continue from sub-step #17.2 on the wiki page.

edit: Hopefully this will fix the problem. I find this odd, because I didn't need this fix when I tested with CentOS 6.6. I'll have to try it out with 6.7.

Last edited by wyldckat; February 7, 2016 at 12:27. Reason: see "edit:"
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Old   February 7, 2016, 15:23
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Thank you for the replay... i have try what you've suggested .... on the log.makePV it seems to go untill the end ( 100%) but still with error :

#########
.
.
[100%] Built target vtkParaViewDocumentation
Linking CXX executable ../../bin/paraview
/home/Donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/qt-4.8.6/lib/libQtCLucene.so.4: undefined reference to `std::__detail::_List_node_base::_M_unhook()@GLIBC XX_3.4.15'
/home/Donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/qt-4.8.6/lib/libQtCLucene.so.4: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__de tail::_List_node_base*)@GLIBCXX_3.4.15'
collect2: ld returned 1 exit status
make[2]: *** [bin/paraview] Error 1
make[1]: *** [Applications/ParaView/CMakeFiles/paraview.dir/all] Error 2
make: *** [all] Error 2
---
Installation complete for paraview-4.1.0
Set environment variables:

export ParaView_DIR=/home/Donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/ParaView-4.1.0
export PATH=$ParaView_DIR/bin:$PATH
export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
---
Done
#####################

When builling Paraview i have this error message

[....PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/ParaView-4.1.0
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Old   February 7, 2016, 15:31
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Quick answer: Those are signs of using the wrong GCC version, possibly due to something having gone wrong when you initialized the OpenFOAM environment. Please to the following commands and please tell me what they give you:
Code:
grep of240 $HOME/.bashrc
which gcc
which g++
gcc --version
g++ --version
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Old   February 7, 2016, 17:10
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Thank you for the reply, the output are bellow... actually it shows GCC 4.4.7 !!!!, then GCC 4.8 was not installed !!!

grep of240 $HOME/.bashrc
alias of240='module load openmpi-i386; source $HOME/OpenFOAM/OpenFOAM-2.4.0/etc/bashrc WM_NCOMPPROCS=2 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI WM_ARCH_OPTION=32'

which gcc
/usr/bin/gcc

which g++
/usr/bin/g++
gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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Old   February 7, 2016, 17:32
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Quick answer: OK, not to worry for now. We should have the log file "mkgcc.log" that tells us what happened when building GCC 4.8. Please run the following command:
Code:
foam3rdParty
tail -n 20 mkgcc.log
and tell me what it gives you.

It's a fairly long log file, so compressing it might still result in a very large file, but you can still try it:
Code:
gzip < mkgcc.log > mkgcc.log.gz
then attach the file "mkgcc.log.gz" to your next post.
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Old   February 7, 2016, 17:40
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thanks again for your help.
i went to ThirdParty-2.4.0 folder , and ran the command :tail -n 20 mkgcc.log. bellow is the output

in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/donminoti/OpenFOAM/ThirdParty-2.4.0/build/linux/gcc-4.8.4/i686-pc-linux-gnu/libatomic'
make[3]: Leaving directory `/home/donminoti/OpenFOAM/ThirdParty-2.4.0/build/linux/gcc-4.8.4/i686-pc-linux-gnu/libatomic'
make[2]: Leaving directory `/home/donminoti/OpenFOAM/ThirdParty-2.4.0/build/linux/gcc-4.8.4/i686-pc-linux-gnu/libatomic'
make[1]: Leaving directory `/home/donminoti/OpenFOAM/ThirdParty-2.4.0/build/linux/gcc-4.8.4'
+ echo 'Built: gcc-4.8.4'
Built: gcc-4.8.4
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Old   February 7, 2016, 18:19
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Mmm... so all signs point to GCC having been built without problems. Then there is likely a glitch in the "settings.sh" file.

OK, I need two things:
  1. Run the following commands:
    Code:
    foam
    export > log.foamEnv
    pwd
    The file "log.foamEnv" will be located at the folder indicated by the last command. I need this file, to ascertain what might have gone wrong in the OpenFOAM environment that is loaded on the current shell.
  2. Then run the following command:
    Code:
    grep gcc-4.8 etc/config/settings.sh
    If it's correctly configured, it should give you this:
    Code:
    gcc_version=gcc-4.8.4
    If not, it possibly will give you this:
    Code:
    gcc_version=gcc-4.8.2
    which would explain why the wrong GCC version is being found.
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Old   February 7, 2016, 18:35
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it gives
gcc_version=gcc-4.8.4

seems to be good
the file is in attachment

Thanks
Attached Files
File Type: gz log.foamEnv.gz (2.2 KB, 1 views)
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Old   February 7, 2016, 19:14
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This is really strange... what do the following commands give you?
Code:
foam3rdParty
ls -l platforms/linux/gcc-4.8.4/
ls -l platforms/linux/gcc-4.8.4/bin
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Old   February 8, 2016, 16:21
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Hi,
sorry,

ls -l platforms/linux/gcc-4.8.4/
total 24
drwxrwxr-x. 2 donminoti donminoti 4096 Feb 6 08:18 bin
drwxrwxr-x. 4 donminoti donminoti 4096 Feb 6 08:18 i686-pc-linux-gnu
drwxrwxr-x. 3 donminoti donminoti4096 Feb 6 08:17 include
drwxrwxr-x. 3 donminoti donminoti 4096 Feb 6 08:18 lib
drwxrwxr-x. 3 donminoti donminoti 4096 Feb 5 23:40 libexec
drwxrwxr-x. 6 donminoti donminoti 4096 Feb 5 23:41 share

ls -l platforms/linux/gcc-4.8.4/bin
total 78080
-rwxr-xr-x. 1 donminoti donminoti 3483448 Feb 6 08:18 addr2line
-rwxr-xr-x. 2 donminoti donminoti 3623703 Feb 6 08:18 ar
-rwxr-xr-x. 2 donminoti donminoti 5086489 Feb 6 08:18 as
-rwxr-xr-x. 4 donminoti donminoti 2539012 Feb 5 23:40 c++
-rwxr-xr-x. 1 donminoti donminoti 3442690 Feb 6 08:18 c++filt
-rwxr-xr-x. 1 donminoti donminoti 2533626 Feb 5 23:41 cpp
-rwxr-xr-x. 1 donminoti donminoti 78000 Feb 6 08:18 elfedit
-rwxr-xr-x. 4 donminoti donminoti 2539012 Feb 5 23:40 g++
-rwxr-xr-x. 3 donminoti donminoti 2531166 Feb 5 23:41 gcc
-rwxr-xr-x. 2 donminoti donminoti 109142 Feb 5 23:41 gcc-ar
-rwxr-xr-x. 2 donminoti donminoti 109102 Feb 5 23:41 gcc-nm
-rwxr-xr-x. 2 donminoti donminoti 109114 Feb 5 23:41 gcc-ranlib
-rwxr-xr-x. 1 donminoti donminoti 1323184 Feb 5 23:41 gcov
-rwxr-xr-x. 1 donminoti donminoti 3933616 Feb 6 08:18 gprof
-rwxr-xr-x. 4 donminoti donminoti 2539012 Feb 5 23:40 i686-pc-linux-gnu-c++
-rwxr-xr-x. 4 donminoti donminoti 2539012 Feb 5 23:40 i686-pc-linux-gnu-g++
-rwxr-xr-x. 3 donminoti donminoti 2531166 Feb 5 23:41 i686-pc-linux-gnu-gcc
-rwxr-xr-x. 3 donminoti donminoti 2531166 Feb 5 23:41 i686-pc-linux-gnu-gcc-4.8.4
-rwxr-xr-x. 2 donminoti donminoti 109142 Feb 5 23:41 i686-pc-linux-gnu-gcc-ar
-rwxr-xr-x. 2 donminoti donminoti 109102 Feb 5 23:41 i686-pc-linux-gnu-gcc-nm
-rwxr-xr-x. 2 donminoti donminoti 109114 Feb 5 23:41 i686-pc-linux-gnu-gcc-ranlib
-rwxr-xr-x. 4 donminoti donminoti 4827499 Feb 6 08:18 ld
-rwxr-xr-x. 4 donminoti donminoti 4827499 Feb 6 08:18 ld.bfd
-rwxr-xr-x. 2 donminoti donminoti 3509636 Feb 6 08:18 nm
-rwxr-xr-x. 2 donminoti donminoti 4218294 Feb 6 08:18 objcopy
-rwxr-xr-x. 2 donminoti donminoti 4934220 Feb 6 08:18 objdump
-rwxr-xr-x. 2 donminoti donminoti 3623698 Feb 6 08:18 ranlib
-rwxr-xr-x. 1 donminoti donminoti 896173 Feb 6 08:18 readelf
-rwxr-xr-x. 1 donminoti donminoti 3473656 Feb 6 08:18 size
-rwxr-xr-x. 1 donminoti donminoti 3471884 Feb 6 08:18 strings
-rwxr-xr-x. 2 donminoti donminoti 4218289 Feb 6 08:18 strip
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Old   February 8, 2016, 17:28
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I will try to make another clean installation and let you know. ..
Thank you for your help
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Old   February 13, 2016, 14:19
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Hi wyldckat,
to give a feedback....
I have re-installed the CentOs and OpenFoam 2.4, this time CentOs 6.5 ( last time it was 6.7) ... but still the same problem with paraview ( paraFoam).
again i was obliged to add (the commande below) , before step 17 / 2.....!
#########"
cd $WM_THIRD_PARTY_DIR sed -i -e 's=//#define GLX_GLXEXT_LEGACY=#define GLX_GLXEXT_LEGACY=' \ ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx
#########""

the paraFoam command , gives:

##########"
FATAL ERROR: ParaView reader module libraries do not exist

Please build the reader module before continuing:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
./Allwclean
./Allwmake
#########

the last lines of log.makePv , are:
##########
100%] Built target vtkParaViewDocumentation
Linking CXX executable ../../bin/paraview
/home/donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/qt-4.8.6/lib/libQtCLucene.so.4: undefined reference to `std::__detail::_List_node_base::_M_unhook()@GLIBC XX_3.4.15'
/home/donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/qt-4.8.6/lib/libQtCLucene.so.4: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__de tail::_List_node_base*)@GLIBCXX_3.4.15'
collect2: ld returned 1 exit status
make[2]: *** [bin/paraview] Error 1
make[1]: *** [Applications/ParaView/CMakeFiles/paraview.dir/all] Error 2
make: *** [all] Error 2
---
Installation complete for paraview-4.1.0
Set environment variables:

export ParaView_DIR=/home/donminoti/OpenFOAM/ThirdParty-2.4.0/platforms/linuxGcc48/ParaView-4.1.0
export PATH=$ParaView_DIR/bin:$PATH
export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
#########

Something is wrong with the OpenFoam 2.4 and CentOs 6.x...

Thanks
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Old   February 14, 2016, 16:36
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Hi donminoti,

This is reminding me of a problem that happened some months ago with another forum member. There was an important detail he didn't mention or that I didn't notice earlier. Let me see if I can find it...

OK, the first thread I found was this one: http://www.cfd-online.com/Forums/ope...tos-6-5-a.html - please check if you are doing anything similar to the descriptions given by the forum member kpsl.

Then there is this thread: http://www.cfd-online.com/Forums/ope...u-12-04-a.html

And finally, there is also this post: http://www.cfd-online.com/Forums/ope...tml#post369975 - post #12

Please let me know if there is any specific personal configuration that you do in your CentOS installations. For example, if you use any customized ".bash*" scripts that contain aliases or environment variables that might be interfering with the installation.

Best regards,
Bruno
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Old   February 29, 2016, 22:18
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Hi
Sorry to bother you , but I was having the same issue, but I followed you directions in this post and I got the para-view . Unfortunately, when I tried to run it I get the following error message:
Code:
[bashar@basharhpc ~]$ of240
[bashar@basharhpc ~]$ paraFoam
WARN file does not exist:
    ./system/controlDict
    ./system/fvSchemes
    ./system/fvSolution
created temporary 'bashar.OpenFOAM'


--> FOAM FATAL IO ERROR: 
cannot find file

file: /home/bashar/system/controlDict at line 0.

    From function regIOobject::readStream()
    in file db/regIOobject/regIOobjectRead.C at line 73.

FOAM exiting
I hope anyone have a clue about this error

Last edited by wyldckat; March 6, 2016 at 12:45. Reason: Added [CODE][/CODE] markers
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Old   March 1, 2016, 08:24
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Hi,

Actually, i was unable to correctly install OF 2.4 on Centos 6.6, i am using Ubuntu for the moment.
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Old   March 6, 2016, 12:48
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Quick answer @Bashar1978:
Quote:
Originally Posted by Bashar1978 View Post
Code:
--> FOAM FATAL IO ERROR: 
cannot find file

file: /home/bashar/system/controlDict at line 0.

    From function regIOobject::readStream()
    in file db/regIOobject/regIOobjectRead.C at line 73.

FOAM exiting
I hope anyone have a clue about this error
The error message is telling you that there is no file in the folder "/home/bashar/system/controlDict". This means that you are executing the command in the wrong folder.
Please follow the tutorials in the OpenFOAM User Guide more carefully.

If you don't know where to find the OpenFOAM User Guide, I'll quote myself:
Quote:
Originally Posted by wyldckat View Post
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Old   May 13, 2016, 04:57
Question same problem as donminoti
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Hello!

I have the same problem as donminoti. Is there still no solution for the issue with ParaView-4.1.0 installation on (CentOS6.6)/CentOS6.7??

kr,
Johannes

Last edited by jfw_cfd; May 30, 2016 at 07:14.
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