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[OpenFOAM.org] Installation Quirks on Centos 6.6 |
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February 18, 2015, 10:14 |
Installation Quirks on Centos 6.6
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#1 |
New Member
Enrico Carrara
Join Date: Feb 2015
Posts: 3
Rep Power: 11 |
Hello,
I installed OpenFOAM 2.3.1 on CentOS 6.6 following this procedure except that I installed in /opt/OpenFOAM and not in $HOME/OpenFOAM. I did that by modifying bashrc manually and commenting/uncommenting relevant foamInstall. At the end of procedure I noticed two possible quirks: 1) blockMesh and other binaries are installed in /opt/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64Gcc48DPOpt/bin while PATH is set to /opt/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin i.e. there is a "48" missing in the path. This seems due to incorrect setting of WM_COMPILER variable in bashrc. If not corrected, blockMesh cannot be found 2) When paraFoam is executed it gives /usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.15' not found How can I fix this? Thanks in advance |
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February 18, 2015, 15:12 |
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#2 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,974
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Greetings Enrico,
By compiling directly at "/opt/OpenFOAM", you have put in danger your whole system . Because one wrong character while following the instructions, is all that it takes to damage your CentOS installation. As for the first problem you're seeing: please study again step #7. As for the second problem: it's probably related to the first one. Best regards, Bruno
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February 19, 2015, 04:40 |
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#3 |
New Member
Enrico Carrara
Join Date: Feb 2015
Posts: 3
Rep Power: 11 |
Thank you, Bruno, for your prompt answer.
Thanks also for caring about the sanity of my whole system: I am aware of the risks, and this is exactly why I am doing these installation experiments on a safe and expendable environment and not on a production line with service level guarantees. Concerning step #7, I guess you refer to the command line on paragraph 2.2 "CentOS 6.5", branch "x86_64": source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty \ WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI that is what I actually did. Indeed, in my installation I have a lot of "linux64Gcc48DPOpt" and "linux64Gcc48" directories and this name, as far as I understand, comes from the composition of several environment variables, WM_COMPILER among them. It is not clear to me why bashrc seems not to set WM_COMPILER to a consistent value ("Gcc48" instead of "Gcc"), if due. Concerning the error on libstdc++.so.6, googling a bit I could find several sites (e.g. http://qt-project.org/forums/viewthread/25550 and https://www.centos.org/forums/viewtopic.php?t=5807) where various explanations are given for similar problems. What I noticed is that my LD_LIBRARY_PATH (set with the of231 alias) does not contain the path to the version of libstdc++.so.6 required by paraFoam and the underlying Qt library, that is not the native CentOS 6.6 version. Of course, I could solve my problem setting LD_LIBRARY_PATH in .bashrc as follows: module load openmpi-x86_64 source /opt/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc $FOAM_SETTINGS LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/platforms/linux64/gcc-4.8.4/lib64:$LD_LIBRARY_PATH but I deem this solution sub-optimal for many reasons, first of all because it is not what is indicated in the instructions. Is there anyone who experienced the same problems and found a more satisfactory solution? Cordially, Enrico P.S. For more information, this is what I have in my library path: LD_LIBRARY_PATH= /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48/boost_1_54_0/lib: /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48/CGAL-4.3/lib: /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48/gperftools-svn/lib: /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48/ParaView-4.1.0/lib/paraview-4.1: /opt/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64Gcc48DPOpt/lib/openmpi-system: /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48DPOpt/lib/openmpi-system: /usr/lib64/openmpi/lib: /home/eca/OpenFOAM/eca-2.3.1/platforms/linux64Gcc48DPOpt/lib: /opt/OpenFOAM/site/2.3.1/platforms/linux64Gcc48DPOpt/lib: /opt/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64Gcc48DPOpt/lib: /opt/OpenFOAM/ThirdParty-2.3.1/platforms/linux64Gcc48DPOpt/lib: /opt/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64Gcc48DPOpt/lib/dummy |
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February 19, 2015, 18:43 |
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#4 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,974
Blog Entries: 45
Rep Power: 128 |
Quick answer: Replace this line you have:
Code:
source /opt/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc $FOAM_SETTINGS Code:
source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI |
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February 20, 2015, 03:50 |
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#5 |
New Member
Enrico Carrara
Join Date: Feb 2015
Posts: 3
Rep Power: 11 |
Thanks for your invaluable help, Bruno,
Now it seems to work, and I prefer this solution by far. Only I had to tweak the line a bit: In my .bashrc I had to put source /opt/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI instead of: source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI I'll fix it for all users, and voilą! Cordially Enrico |
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