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Problem with paraFoam on a linux-64 bit

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Old   April 13, 2010, 15:16
Default Problem with paraFoam on a linux-64 bit
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Hi,

I recently downloaded OpenFOAM binaries, double precision, linux 64-bit (fedora 12). I have the solver I need running fine, but I've got a problem with paraview/parafoam. I already had paraview installed on the computer (which ran fine). running paraFoam in the appropriate directory, I get the error below. I still have my 'old' paraview in /usr/bin, and editing out the paraview lines in bashrc file ( $HOME/OpenFOAM/OpenFOAM-1.6/etc/bashrc ) --trying to use my local paraview, and not the one in ThirdParty ... -- I still get the error.

Ideas on how to fix greatly appreciated and I'll buy you a virtual beer.


Error:



/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libpqComponents.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libpqCore.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkPVServerManager.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libQVTK.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkViews.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkPVFilters.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkVolumeRendering.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkXdmf.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libXdmf.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkPVServerCommon.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkInfovis.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkWidgets.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libKWCommon.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkPVCommandOptions.so)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkGenericFiltering.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkHybrid.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkParallel.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkRendering.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkGraphics.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkImaging.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkIO.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkFiltering.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkCommon.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkDICOMParser.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtkmetaio.so.pv3.6)
/usr/lib64/paraview/paraview-real: /home/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib64/paraview/libvtksys.so.pv3.6)
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Old   April 13, 2010, 17:29
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Bruno Santos
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Greetings bunni,

If you had searched in cfd-online for "GLIBCXX_3.4.11" you would have found the fix

Anyway, here is the generic quick fix for that:
Code:
cd ~/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64
mv libstdc++.so.6 libstdc++.so.6.orig
ln -s `locate libstdc++.so.6.0 | grep "^/usr/lib" | head -n 1` libstdc++.so.6
mv libgcc_s.so.1 libgcc_s.so.1.orig
ln -s `locate libgcc_s.so. | grep "^/lib" | head -n 1` libgcc_s.so.1
Basically, it forces the proper libraries "libstdc++.so" and "libgcc_s.so" to be linked to the visible available gcc libraries.


The other solution is to change in "etc/settings.sh" the compiler option from OpenFOAM to System:
Code:
# Select compiler installation
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# compilerInstall = OpenFOAM | System
compilerInstall=System
CAUTION: OpenFOAM-1.6 will not build with gcc 4.4.? that comes with Fedora 12! Nonetheless, OpenFOAM-1.6.x will work properly with it.

Best regards,
Bruno
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Old   April 14, 2010, 11:56
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I tried looking, but was clearly looking for the wrong search terms, so thank you for your response.

Sadly, neither one of those things work, but progress is being made. I no longer get the long error message, but now paraview launches and crashes (core dump). The 2nd fix - moving to compilerInstall = System gives me a 'command not found error'. I will work at this some more.

I don't know whether or know OpenFOAM will build with gcc.4.4 - my attempts to build OpenFOAM ended in failure, so that is why I resorted to downloading the binaries. The solving aspect of it worked great, but not the paraview part

Last edited by bunni; April 14, 2010 at 12:21. Reason: updated info
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Old   April 14, 2010, 16:52
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Greetings bunni,

Well, for better or for worst, you're not the first one to get that very same issue on the first solution. I had hoped that it would work, although already suspected it, from what I've read, that Fedora is a bit quirky and seems to feel the need for more dedication from the user...

OK, as for the second fix, the idea is to use OpenFOAM's gcc version to build OpenFOAM, but use then change to the system's compiler for when working with the solvers and paraFoam. Wait, have you installed these packages (the 2 in bold, the rest is the install command to be executed in root mode):
Code:
yum install gcc-c++ binutils-devel
The problem might be that you were missing some libraries that come with g++ (OK, technically only the gcc-c++ will install the libraries, the other one is for building g++ stuff, is needed...). This is valid for the both solutions! I completely forgot about those two

Nonetheless, for building OpenFOAM with gcc-4.4.? in Fedora 12, you'll have to follow the instructions I've posted here: Problem Installing OF 1.6 Ubuntu 9.10 (64 bit) - How to use GCC 4.4.1 post #11
Unfortunately, OpenFOAM 1.6 will not build with gcc 4.4.? without some additional tweaking. So the quickest solution would be using OpenFOAM 1.6.x.
The longest solution, and it isn't a full proof one, is to follow the information available in the posts: here and here. Nonetheless, these make OpenFOAM 1.6 build-able, but I'm not 100% sure that the solvers that depend on these fixes will work, because by what I've seen in the code changes made in these posts and compared them to the actual code changes made by the OpenFOAM developers, the posted ones might lead to some "bad memory access" issues in some particular usage pattern

So, keep us posted on how you fixed the problem, or if you've run into any more problems with building OpenFOAM and/or running Paraview.

Best regards,
Bruno
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Old   April 14, 2010, 20:55
Default temporary solution (for those who may read this later)
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For the moment what seems to work is to not use paraFoam. Since I already had paraview installed, to view the files, I ran foamToVTK, and my version of paraview ( for me it was : /usr/bin/paraview), and open the *vtk files. It is not elegant, but it works, and I haven't got the time to do more at the moment, as the fixing I attempted to do seems to have broken or injured another program I need to use, so I'll be fixing that problem for awhile. Thank you for all your help, it is really nice of you and I appreciate it.
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