CFD Online Discussion Forums - [foam-extend.org] Error compiling OpenFOAM-1.6-ext

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Hello,

I took a look at your compilation log files, and you have a bunch of errors you need to solve, one by one, first one first, and not only the last error you are reporting.

Some comments:

- You are probably missing some -dev packages for OpenGL. Try compiling Paraview as a stand-alone package using the instructions provided by Kitware. It might help pinpointing the missing packages.

- Some of your compiler settings seems to be off. Your installation of 1.7.1 is probably conflicting.

From your log file:
/home/tibornyers/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/libccmio-2.6.1/libadf/..//config/linux_2.4-x86-glibc_2.3.2/qmake: error while loadi
ng shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory

- You are having problems downloading packages from the Internet

From your log:
Download mesquite-2.1.2.tar.gz from : http://software.sandia.gov/~jakraft/mesquite-2.1.2.tar.gz
--2011-06-17 09:30:39-- http://software.sandia.gov/~jakraft/mesquite-2.1.2.tar.gz
Resolving software.sandia.gov... failed: Name or service not known.
wget: unable to resolve host address `software.sandia.gov'

So basically, instead of focusing on the last error message you've got, open your log file with a text editor, and go hunting for the string "error". Solve the problem you find one by one, first problem first.

Martin

Quote:

Originally Posted by Toorop (Post 313057)

Some progress, finally! ;)
With the instructions you suggested - QT_BIN_DIR and the soft linking between make and gmake - I was able to compile the ThirdParty package except for paraview. I have the same error now as post #96.

I have update the scripts as well cuz some urls in the AllMake scripts of the ThirdParty are out of date, maybe it helped as well, I'm not sure.

If I compile the 1.6ext with the current state, I get some solvers, which is great. I also receive some errors and the compilation stops at some point.

Thank you all for the great help!

Quote:

Originally Posted by ubald (Post 312047)

Sadly I Stage3 as problem downloading:

Updating the ThirdParty environment variables before building package metis-5.0pre2
Download metis-5.0pre2.tar.gz from : http://glaros.dtc.umn.edu/gkhome/fet...5.0pre2.tar.gz
--2011-06-15 10:33:05-- http://glaros.dtc.umn.edu/gkhome/fet...5.0pre2.tar.gz
Résolution de glaros.dtc.umn.edu... 160.94.77.162
Connexion vers glaros.dtc.umn.edu|160.94.77.162|:80...connecté.
requête HTTP transmise, en attente de la réponse...404 Not Found
2011-06-15 10:33:05 ERREUR 404: Not Found.

I ad to download it from an other source:
ftp://ftp.uni-frankfurt.de/pub/Mirrors2/gentoo.org/distfiles/metis-5.0pre2.tar.gz

The location of metis-5.0pre2 seems to have change.
It can be fixed by editing ThirdParty/AllMake.stage3
line 62 and change the url from
http://glaros.dtc.umn.edu/gkhome/fet...5.0pre2.tar.gz
to
http://glaros.dtc.umn.edu/gkhome/fet...5.0pre2.tar.gz

That is adding the OLD/

Btw I also had to do :sudo ln -s /usr/bin/make /usr/bin/gmake

Then running AllMake and sourcing again and trying to compile OF16ext and sourcing once more and then compiling again and it worked.
Running Ubuntu 11.04

/Eysteinn

Hello,

Yup, that tutorial seems to be in problem.

You can get a pretty good overview of the list of tutorials currently in problem here:

http://openfoam-extend.sourceforge.n...enFOAM-1.6-ext

Of course, depending on your system, even on your compiler, your mileage may vary.

I invite you to run the test harness on your machine, and to post the results on the openfoam-extend CDash service.

Just take a look here for a starter on the test harness: OpenFOAM-1.6-ext/testHarness/README.txt

Martin

Quote:

Originally Posted by ubald (Post 312638)

But the tutorial test tutorials/incompressible/icoDyMFoam/turboPassageRotating
dos not seam to work properly did any bothy had this problem ??

(I modify it to run on 2 processor change decomposePar and Allrun -> runParallel icoDyMFoam 2)

Maybe, there is something I did rung in decomposing in t processor ??!!
the other work correctly : mixer2D movingBlockRBF movingConeTopo mixerGgi

Regards

Hi Martin,

Thanks for taking the time to have a look at my logs.

I have resolved the errors on the first 4 of the ThirdParty AllMake stages (0-3). So there's no package downloading woe any more as I said @ 120. The ParaView compiling fails like jajcevic reported some pages before.

Code:

Linking CXX executable ../../../../bin/GenericFilteringCxxTests

../../../../bin/libvtkRendering.so.pv3.8: undefined reference to `vtkOSOpenGLRenderWindow::New()'

collect2: ld returned 1 exit status

make[2]: *** [bin/GenericFilteringCxxTests] Error 1

make[1]: *** [VTK/GenericFiltering/Testing/Cxx/CMakeFiles/GenericFilteringCxxTests.dir/all] Error 2

...

[ 45%] Built target vtkVolumeRendering

make: *** [all] Error 2

error: Bad exit status from $HOME/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.eJh8MM (%build)

What modifications do the paraFoam script needs so one could use the pre-built ParaView 3.10.1?

Thanks!

Dear forum,

I am trying to compile OF-1.6-ext. My ThirdParty is done, but I get linking errors while building src:

Code:

+ wmake libso meshTools

make: *** No rule to make target `lnInclude/pointIndexHit.H', needed by `directMapped/directMappedPolyPatch/directMappedWallPolyPatch.dep'.  Stop.

I already tried to remove src/OpenFOAM/lnInclude, but the same error comes back.

What can I do to make correct links?

Hello Foamers,

I found a compact, and thus very helpful procedure for compiling OpenFOAM-1.6-ext on OpenSuse 11.4 64bit.

http://www.cfd-online.com/Forums/ope...1-4-64bit.html

I proceeded all the steps and it went well until step 16. But as soon as I execute the global Allwmake script in the $WM_PROJECT_DIR I got a lot errors. All the OpenFOAM files/libraries which are needed for compilation are not found. The error is for all libs the same as the following:

g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/meshTools/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/incompressible/LES/LESModel -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/LES/LESdeltas/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/transportModels -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -IlnInclude -I. -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC Make/linux64GccDPOpt/yPlusLES.o -L/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \
-lincompressibleLESModels -lincompressibleTransportModels -lfiniteVolume -lOpenFOAM -liberty -ldl -lm -o /home/lga19/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/yPlusLES
/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld: cannot find -lincompressibleLESModels
collect2: ld returned 1 exit status
make[3]: *** [/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/yPlusLES] Error 1
make[2]: *** [yPlusLES] Error 2
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/meshTools/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/transportModels -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/incompressible/RAS/derivedFvPatchFields/wallFunctions/nutWallFunctions -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/compressible/RAS/derivedFvPatchFields/wallFunctions/mutWallFunctions -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/basic/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -IlnInclude -I. -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC Make/linux64GccDPOpt/yPlusRAS.o -L/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \
-lincompressibleTransportModels -lincompressibleRASModels -lbasicThermophysicalModels -lspecie -lcompressibleRASModels -lfiniteVolume -lmeshTools -lsampling -lOpenFOAM -liberty -ldl -lm -o /home/lga19/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/yPlusRAS
/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/bin/ld: cannot find -lincompressibleTransportModels
collect2: ld returned 1 exit status
make[3]: *** [/home/lga19/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/yPlusRAS] Error 1
make[2]: *** [yPlusRAS] Error 2
make[2]: Target `application' not remade because of errors.
make[1]: *** [wall] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [postProcessing] Error 2
make: Target `application' not remade because of errors.

This must be some very "global" error. Has anybody an idea?

Thank you in advance for any hint,
Toni

Hello,

When I update my version with git pull, I sometimes have incorrect symbolic links. My "agricultural" solution is to delete the .dep file and lnInclude folder in question, and then recompiling works (wmake make the delete files again correctly). This is a nasty job, because I have to watch the printout of the compilation, interrupt it when an error occurs and then find the files.

Another solution is to delete ALL of the .dep files an lnInclude folders, and the compile everything again.

Is there a more intelligent way to deal with this?

Quote:

Originally Posted by boger (Post 292659)

When installing from an rpm (specifically for openmpi, although I suspect the same will be true for any rpm), I get this error:

Code:

error: can't create transaction lock on /var/lock/rpm/transaction

As a summary for the problem discussed in the posts #74-#79, I solved this by creating a file "~/.rpmmacros" with text

Code:

%_rpmlock_path %{_dbpath}/__db.000

I finished building the ThirdParty and src, but when I run applications/Allwmake, I get errors for libmesquite:

Code:

+ wmake all solvers

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/PODSolver' is up to date.

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/dnsFoam' is up to date.

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/potentialFoam' is up to date.

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/laplacianFoam' is up to date.

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/sixDOFSolver' is up to date.

make[2]: `/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/scalarTransportFoam' is up to date.

g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/engine/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/specie/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/basic/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/reactionThermo/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/compressible/turbulenceModel -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/laminarFlameSpeed/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/sampling/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -IlnInclude -I. -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude   -fPIC Make/linux64GccDPOpt/XiFoam.o -L/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \

         -lengine -lcompressibleTurbulenceModel -lcompressibleRASModels -lcompressibleLESModels -lbasicThermophysicalModels -lreactionThermophysicalModels -lspecie -llaminarFlameSpeedModels -lfiniteVolume -lmeshTools -llduSolvers -lOpenFOAM -liberty -ldl   -lm -o /home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/XiFoam

g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -IXiModels/XiModel -IXiModels/XiEqModels/XiEqModel -IXiModels/XiGModels/XiGModel -IPDRModels/dragModels/PDRDragModel -IlaminarFlameSpeed/SCOPE -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/engine/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/sampling/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/specie/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/basic/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/reactionThermo/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/turbulenceModels/compressible/RAS/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/thermophysicalModels/laminarFlameSpeed/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/finiteVolume/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/dynamicFvMesh/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/dynamicMesh/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/meshTools/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/triSurface/lnInclude -IlnInclude -I. -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude   -fPIC Make/linux64GccDPOpt/XiModel.o Make/linux64GccDPOpt/newXiModel.o Make/linux64GccDPOpt/fixed.o Make/linux64GccDPOpt/algebraic.o Make/linux64GccDPOpt/transport.o Make/linux64GccDPOpt/XiEqModel.o Make/linux64GccDPOpt/newXiEqModel.o Make/linux64GccDPOpt/Gulder.o Make/linux64GccDPOpt/instabilityXiEq.o Make/linux64GccDPOpt/SCOPEBlendXiEq.o Make/linux64GccDPOpt/SCOPEXiEq.o Make/linux64GccDPOpt/XiGModel.o Make/linux64GccDPOpt/newXiGModel.o Make/linux64GccDPOpt/KTS.o Make/linux64GccDPOpt/instabilityG.o Make/linux64GccDPOpt/PDRkEpsilon.o Make/linux64GccDPOpt/PDRDragModel.o Make/linux64GccDPOpt/newPDRDragModel.o Make/linux64GccDPOpt/basic.o Make/linux64GccDPOpt/basicXiSubXiEq.o Make/linux64GccDPOpt/basicXiSubG.o Make/linux64GccDPOpt/SCOPELaminarFlameSpeed.o Make/linux64GccDPOpt/PDRFoam.o -L/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt \

         -lengine -lmeshTools -lcompressibleTurbulenceModel -lcompressibleRASModels -lbasicThermophysicalModels -lreactionThermophysicalModels -lspecie -llaminarFlameSpeedModels -lfiniteVolume -ldynamicFvMesh -llduSolvers -lOpenFOAM -liberty -ldl   -lm -o /home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/applications/bin/linux64GccDPOpt/PDRFoam

/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linux64GccDPOpt/lib/libmesquite.so.0: undefined reference to `std::_List_node_base::_M_unhook()@GLIBCXX_3.4.14'

/home/jmatthei/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linux64GccDPOpt/lib/libmesquite.so.0: undefined reference to `std::_List_node_base::_M_hook(std::_List_node_base*)@GLIBCXX_3.4.14'

collect2: ld returned 1 exit status

What gcc version are you using?

Hello l_r_mcglashan

isn't it possible to define the compiler in file

~/OpenFOAM/OpenFOAM-1.6-ext/etc/settings.sh

by setting the following variable?

compilerInstall=System

or

compilerInstall=OpenFOAM

I am indeed using the system compiler:
gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3

How was mesquite compiled? It looks like GLIBCXX_3.4.14 comes with a later gcc version. Try googling it.

Hi,
I got the following error with AllMake.stage3.
Any idea?

Package name :
Package URL :
RPM spec file name:
Additional flags :
Updating the ThirdParty environment variables before building package
Making package using RPM.
rpm_build: missing SPEC file for package scotch-5.1.10b. Aborting.
Installing package:
Uninstalling using RPM: -linux64GccDPOpt.x86_64
Installing using RPM file: /home/bannari/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/-linux64GccDPOpt.x86_64.rpm
erreur: échec de l'ouverture de /home/bannari/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/-linux64GccDPOpt.x86_64.rpm: Aucun fichier ou dossier de ce type
Done installing package

Package name :
Package URL :
RPM spec file name:
Additional flags :
Updating the ThirdParty environment variables before building package
Making package using RPM.
rpm_build: missing SPEC file for package ParMetis-3.1.1. Aborting.
Installing package:
Uninstalling using RPM: -linux64GccDPOpt.x86_64
Installing using RPM file: /home/bannari/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/-linux64GccDPOpt.x86_64.rpm
erreur: échec de l'ouverture de /home/bannari/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/-linux64GccDPOpt.x86_64.rpm: Aucun fichier ou dossier de ce type
Done installing package

Hi Cris

Could please tell how you installed OpenFOAM-1.6-ext, I am having a lot of problems in Fedora 15, 64 bit

Thank you

Alberto

Quote:

Originally Posted by cnsidero (Post 293680)

Ya, it is fairly new - I am brave ;-). Actually I looked closer and Paraview was not getting built/installed correctly either. So perhaps there is something different in RHEL 6.0

FWIW, I managed to get 1.6-ext built and installed (not Paraview). In the mean time, I opt'd to use system OpenMPI instead in the provided package. Although this wasn't without it's difficulties. Redhat [I'm guessing] decided to either drop the openmpi-devel package and/or not include the compilation tools (e.g. mpiCC) in their openmpi package. So I had to build a new RPM from the SRPM provided on openmpi.org.

Hello Martin

Any news about installing OpenFOAM-1.6-ext on Fedora 15, 64-bit system, I have tried to install it, and it is being a nightmare!, I always get

gcc 4.6.1
WARNING: Conflicting installations:
OpenFOAM settings : /bin/gcc
current path : /usr/lib64/ccache/gcc
CRITICAL ERROR

Any help is welcome!

Thank you

Alberto

Quote:

Originally Posted by mbeaudoin (Post 293560)

Hello Chris,

The very long path you are seeing in the log file is fine. This is not the problem.

> I am running RHEL 6.0 x86_64.

This RedHat operating system is fairly new. The rpm based compilation recipe for the Third Party package was not tested on that system.

I guess something changed with the way rpms are build on RHEL 6.0, or something in the spec files is not general enough. However, according to your post, the fact that all the other Third party packages are successfully being built on the same system is a bit baffling...

I don't have access to a RHEL 6.0 x86_64 system, but maybe I can replicate the problem with the latest version of Fedora.

I know however that all is fine on a Fedora 14 32-bit system. I will check on a 64-bit system, just in case...

Martin

hi foamers i am installing oepnfoam 1.6-ext on opensuse 12.1

after some problems about misquite2.1.2 i changed as many people do to 2.99

then after thirdparty Allmake.stage3:

common.h:84:28: fatal error: mpi.h: No such file or directory

it seems that he is not finding the openMPI instalation but

thirdparty Allmake.stage3 gives:

========================================
Starting ThirdParty AllMake: Stage2
========================================

Package name : openmpi-1.4.3
Package URL : http://www.open-mpi.org/software/omp...i-1.4.3.tar.gz
RPM spec file name: openmpi-1.4.3.spec
Additional flags :
Updating the ThirdParty environment variables before building package openmpi-1.4.3
Package openmpi-1.4.3 is already installed
Done installing package

========================================
Done ThirdParty AllMake: Stage2
========================================

I have faced a similar problem in my installation. Namely,
"db/IOstreams/Pstreams/IPread.C:29:17: fatal error: mpi.h: No such file or directory"
Any ideas foamers?