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[OpenFOAM.org] Problems installing OpenFOAM 2.3.0 on CentOS-6.6-x86-64 |
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November 22, 2015, 17:12 |
Problems installing OpenFOAM 2.3.0 on CentOS-6.6-x86-64
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#1 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
I followed the instructions on https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL
...for the CentOS 6.5 (mine is 6.6 if relevant). Hopefully I did it properly but here is the problem: I was about to try the tutorials (cavity flow) and when I type the blockMesh command: > blockMesh. Gives and error message: bash: blockMesh: command not found and when I type the full pathname: > ~/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/blockMesh there is an error message: /home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/blockMesh: error while loading shared libraries: libblockMesh.so: cannot open shared object file: No such file or directory Then I followed the advice of an experienced user given bellow, but that did not solve the issue either. Maybe I should remove and reinstall OpenFoam again. # last tip I tried: Your library has either failed to compile, or you are trying to execute the solver without sourcing the global /etc/bashrc configuration script. Execute . ~/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc in the terminal where you are trying to use blockMesh. Execute blockMesh again. If that failed, try to compile the libraries by executing cd $FOAM_SRC , then executing ./Allwmake. Once the build has finished Execute Allwmake in $FOAM_SRC again and observe the output: you should see a bunch of lines stating that different libraries are "up to date" . You should see no errors there. Received the "up to date" but also error messages. Hopefully you can give me a hand here. |
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November 22, 2015, 17:29 |
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#2 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
I repeated some of the installation steps again, went back to tutorials directory, and the blockMesh seems to be working now...
Here's the output text it generated in the command line, upon execution (cavity flow tutorial case): 0 constant system [username@localhost cavity]$ [username@localhost cavity]$ [username@localhost cavity]$ blockMesh /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.3.0 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.3.0-f5222ca19ce6 Exec : blockMesh Date : Nov 22 2015 Time : 23:23:37 Host : "localhost.localdomain" PID : 15508 Case : /home/username/OpenFOAM/username-2.3.0/run/tutorials/incompressible/icoFoam/cavity nProcs : 1 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Creating block mesh from "/home/username/OpenFOAM/username-2.3.0/run/tutorials/incompressible/icoFoam/cavity/constant/polyMesh/blockMeshDict" Creating curved edges Creating topology blocks Creating topology patches Creating block mesh topology Check topology Basic statistics Number of internal faces : 0 Number of boundary faces : 6 Number of defined boundary faces : 6 Number of undefined boundary faces : 0 Checking patch -> block consistency Creating block offsets Creating merge list . Creating polyMesh from blockMesh Creating patches Creating cells Creating points with scale 0.1 Block 0 cell size : i : 0.005 .. 0.005 j : 0.005 .. 0.005 k : 0.01 .. 0.01 Writing polyMesh ---------------- Mesh Information ---------------- boundingBox: (0 0 0) (0.1 0.1 0.01) nPoints: 882 nCells: 400 nFaces: 1640 nInternalFaces: 760 ---------------- Patches ---------------- patch 0 (start: 760 size: 20) name: movingWall patch 1 (start: 780 size: 60) name: fixedWalls patch 2 (start: 840 size: 800) name: frontAndBack End |
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November 22, 2015, 17:43 |
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#4 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
Thanks! This is what I get @ step 15:
[username@localhost cavity]$ icoFoam -help Usage: icoFoam [OPTIONS] options: -case <dir> specify alternate case directory, default is the cwd -noFunctionObjects do not execute functionObjects -parallel run in parallel -roots <(dir1 .. dirN)> slave root directories for distributed running -srcDoc display source code in browser -doc display application documentation in browser -help print the usage Using: OpenFOAM-2.3.0 (see www.OpenFOAM.org) Build: 2.3.0-f5222ca19ce6 |
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November 23, 2015, 13:18 |
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#5 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
I am having this issue trying to run Para View:
[username@localhost PV4Readers]$ paraFoam FATAL ERROR: ParaView reader module libraries do not exist Please build the reader module before continuing: cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers ./Allwclean ./Allwmake |
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November 23, 2015, 16:22 |
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#6 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Hi Milan,
I've got the feeling that you're reading the instructions at a very high speed I say this because the step #15 has 4 sub-steps and you only did the first sub-step. As for the latest issue, the fix should be just a matter of doing the commands the paraFoam script told you to do, namely: Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers wmSET $FOAM_SETTINGS ./Allwclean ./Allwmake Code:
cd $WM_PROJECT_DIR ./Allwmake > make.log 2>&1 gzip < make.log > make.log.gz pwd If you don't know where the file is located, the last command will have told the full folder path inside which the file is located. Best regards, Bruno --------------- Sorry, I only saw just now what you wrote me via PM: Quote:
I've taken a better look at the code and I believe the following commands will help solve the problem: Code:
foam sed -i -e 's/#\(export ParaView_VERSION=4.1.0\)/\1/' etc/config/paraview.sh foam3rdParty mv platforms/linux64Gcc48/paraview-4.1.0 platforms/linux64Gcc48/ParaView-4.1.0 wmSET $FOAM_SETTINGS which paraview Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers wmSET $FOAM_SETTINGS ./Allwclean ./Allwmake |
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November 24, 2015, 04:11 |
make.log.gz
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#7 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
here's the make.log.gz after the first part of the instructions above
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November 24, 2015, 04:28 |
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#8 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
The first segment returns this in the command line:
[username@localhost ThirdParty-2.3.0]$ mv platforms/linux64Gcc48/paraview-4.1.0 platforms/linux64Gcc48/ParaView-4.1.0 mv: cannot stat `platforms/linux64Gcc48/paraview-4.1.0': No such file or directory [username@localhost ThirdParty-2.3.0]$ [username@localhost ThirdParty-2.3.0]$ wmSET $FOAM_SETTINGS [username@localhost ThirdParty-2.3.0]$ which paraview /usr/bin/which: no paraview in (/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/gperftools-svn/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/cmake-2.8.12.1/bin:/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/bin:/home/username/OpenFOAM/username-2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/site/2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/bin:/home/username/OpenFOAM/OpenFOAM-2.3.0/wmake:/usr/lib64/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/username/bin) ...while the second segments returns: [username@localhost PV4Readers]$ cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers [username@localhost PV4Readers]$ wmSET $FOAM_SETTINGS [username@localhost PV4Readers]$ ./Allwclean + wclean libso vtkPV4Readers wclean vtkPV4Readers + PV4blockMeshReader/Allwclean + rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4blockMeshReader*' + rm -rf PV4blockMeshReader/Make + wclean libso vtkPV4blockMesh wclean vtkPV4blockMesh + PV4FoamReader/Allwclean + rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4FoamReader*' + rm -rf PV4FoamReader/Make + wclean libso vtkPV4Foam wclean vtkPV4Foam [username@localhost PV4Readers]$ ./Allwmake ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 Indeed there is no ParaView-4.1.0 in the last directory: [username@localhost PV4Readers]$ pwd /home/username/OpenFOAM/OpenFOAM-2.3.0/applications/utilities/postProcessing/graphics/PV4Readers [username@localhost PV4Readers]$ ls Allwclean Allwmake log.make log.makePV PV4blockMeshReader PV4FoamReader vtkPV4Readers what do you recommend me to do? Thanks |
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November 24, 2015, 05:06 |
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#9 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
PS. Looks like the make command is missing the path, it returns there is no ParaView-4.1.0 in the path: [username@localhost PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 ...well there it is not - because it the proper path is one up, at: /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48 [username@localhost linux64Gcc48]$ cd /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48 [username@localhost linux64Gcc48]$ ls boost_1_54_0 CGAL-4.3 cmake-2.8.12.1 ParaView-4.1.0 qt-4.8.4 scotch_6.0.0 |
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November 24, 2015, 15:51 |
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#10 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Hi Milan,
Sorry, but I wasn't able to answer during the day. Something really strange is going on with your installation of ParaView. The good news is that the "make.log" file tells us that everything has been built with success, therefore OpenFOAM is ready to be used. As for ParaView, please do the following commands: Code:
foam3rdParty ./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV 2>&1 gzip < log.makePV > log.makePV.gz pwd With any luck, then try again: Code:
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers wmSET $FOAM_SETTINGS which paraview ./Allwclean ./Allwmake Best regards, Bruno |
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November 25, 2015, 13:12 |
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#11 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
Thank you for the support.
Well, I did as you wrote above. Bellow is the log.makePV.gz file. After running the second part I get something like before: [username@localhost PV4Readers]$ cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers [username@localhost PV4Readers]$ wmSET $FOAM_SETTINGS [username@localhost PV4Readers]$ [username@localhost PV4Readers]$ which paraview ~/build/paraview/bin/paraview [username@localhost PV4Readers]$ [username@localhost PV4Readers]$ ./Allwclean + wclean libso vtkPV4Readers wclean vtkPV4Readers + PV4blockMeshReader/Allwclean + rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4blockMeshReader*' + rm -rf PV4blockMeshReader/Make + wclean libso vtkPV4blockMesh wclean vtkPV4blockMesh + PV4FoamReader/Allwclean + rm -f '/home/username/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libPV4FoamReader*' + rm -rf PV4FoamReader/Make + wclean libso vtkPV4Foam wclean vtkPV4Foam [username@localhost PV4Readers]$ ./Allwmake ERROR: ParaView not found in /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 Last night I followed another advice I received, to download the paraview binaries. Here it is: ,,Get the paraview binaries: http://www.paraview.org/download/ Download the linux 64 or 32 bit binary (depending on your OS installation), save it somewhere in your home folder, e.g. ~/build/, unpack it, rename the folder to ~/build/paraview and extend the PATH export PATH=~/build/paraview/bin:$PATH in ~/.bashrc. That's it. You con't have to compile paraview or install it any other way. I'm using Arch Linux and the binary is working fine.'' I did so, and now I can run the paraview (say tutorial case cavity)by typing: touch $FOAM_RUN/tutorials/incompressible/icoFoam/cavity/case.foam paraview $FOAM_RUN/tutorials/incompressible/icoFoam/cavity/case.foam The which command above indeed returns: [username@localhost PV4Readers]$ which paraview ~/build/paraview/bin/paraview Would be nice to resolve the "ParaFoam" compilation problem above though, since I plan to use this OS further on another computer....just to have the same OS as on a powerful cluster which will be available to me from time to time, where the CentOS 6.6 and OF 2.3 are installed currently. Sorry for taking your time, Milan |
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November 25, 2015, 13:14 |
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#12 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
the log.makePV.gz
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November 26, 2015, 03:15 |
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#13 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Hi Milan,
If you have a pre-built installation, you can try using: Code:
paraFoam -builtin As for the custom installation, I've examined the "log.makePV.gz" and it only fails when it reaches the installation step, with the following message: Code:
Install the project... -- Install configuration: "Release" CMake Error at cmake_install.cmake:36 (FILE): file cannot create directory: /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/share/paraview-4.1. Maybe need administrative privileges. make: *** [install] Error 1 --- Installation complete for paraview-4.1.0 Set environment variables: export ParaView_DIR=/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 export PATH=$ParaView_DIR/bin:$PATH export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1 --- Done Code:
foam3rdParty rm -r platforms/linux64Gcc48/ParaView-4.1.0/ ./makeParaView4 -no-config -no-make -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV2 2>&1 gzip < log.makePV2 > log.makePV2.gz pwd Then take a look at the lines I mentioned above from "log.makePV" and compare with what you now get in "log.makePV2". If you can't figure out what the problem is, please attach the file "log.makePV2.gz". Best regards, Bruno edit: sorry, wrote this post in a hurry, hope to not have missed any important detail... Last edited by wyldckat; November 26, 2015 at 03:16. Reason: see "edit:" |
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November 26, 2015, 06:33 |
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#14 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
Thanks!
Here is what is written at the bottom of the log.makePV2 [100%] Built target paraview [100%] Built target paraview-launcher Install the project... -- Install configuration: "Release" CMake Error at cmake_install.cmake:36 (FILE): file cannot create directory: /home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0/share/paraview-4.1. Maybe need administrative privileges. make: *** [install] Error 1 --- Installation complete for paraview-4.1.0 Set environment variables: export ParaView_DIR=/home/username/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 export PATH=$ParaView_DIR/bin:$PATH export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1 --- Done Should I run this as administrator? |
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November 26, 2015, 06:35 |
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#15 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
the log.makePV2.gz
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November 27, 2015, 04:53 |
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#16 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Hi Milan,
Building as root (admin) is unlikely to solve the problem. It might have been the origin of the problem in the first place. Please do the following commands: Code:
foam3rdParty ls -l platforms/linux64Gcc48/ > filelist.txt ls -l platforms/linux64Gcc48/ParaView-4.1.0 >> filelist.txt ls -l platforms/linux64Gcc48/ParaView-4.1.0/share >> filelist.txt gzip < build/linux64Gcc48/ParaView-4.1.0/cmake_install.cmake > paraview410.cmake_install.cmake.gz gzip < filelist.txt > filelist.txt.gz pwd The "ls -l" commands will tell us who created the original folders and their permissions. The "cmake_install.cmake" will tell us if the file is corrupted. Best regards, Bruno |
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November 28, 2015, 12:59 |
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#17 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
Thanks!!!
here they are |
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November 28, 2015, 13:24 |
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#18 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Hi Milan,
Interesting, seems that somehow "platforms/linux64Gcc48/ParaView-4.1.0" is a file instead of a folder... which I didn't expected in the instructions I gae before . But at least the "cmake_install.cmake" file seems OK. Please run these commands: Code:
foam3rdParty rm platforms/linux64Gcc48/ParaView-4.1.0 ls -l platforms/linux64Gcc48/ParaView-4.1.0 If the second command tells you the path/file/folder doesn't exist, then run: Code:
./makeParaView4 -no-config -no-make -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV3 2>&1 gzip < log.makePV3 > log.makePV3.gz pwd If it still has the same problem, then I need the file "log.makePV3.gz", at least in case the message is different. Best regards, Bruno |
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November 28, 2015, 14:42 |
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#19 |
Member
Milan
Join Date: Dec 2013
Posts: 38
Rep Power: 12 |
First part, no error message and third command returs:
[username@localhost ThirdParty-2.3.0]$ ls -l platforms/linux64Gcc48/ParaView-4.1.0 ls: cannot access platforms/linux64Gcc48/ParaView-4.1.0: No such file or directory * Should I run the second part and send you the log.makePV3.gz or no? |
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centos 6.6 |
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