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Old   February 2, 2011, 23:47
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  #81
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Chris Sideroff
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After a little more digging ...

First I added the '-v' flag to the rpmbuild command in $WM_THIRD_PARTY_DIR/tools/makeThirdPartyFunctionsForRPM to get some more info.

After rerunning AllMake.stage2, the following line output seems to indicate the problem:

Code:
Found '/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64' in installed files; aborting
After learning a little more about building rpms, this error indicates that the BUILDROOT dir is being included in the files to be added to the RPM - which rpmbuild does not like (here's one of the sites that mention this: http://www.ibm.com/developerworks/library/l-rpm1/).

I checked the openmpi spec file and its set up no different the other third party packages so I'm a bit baffled why only openmpi fails to create the RPMs. Furthermore, no 'openmpi-1.4.3' dir is created in $WM_THIRD_PARTY_DIR/packages, where there are respective dirs for the others. Ultimately, this would be better answered by Martin.

Edit: I thought I'd make a quick note. I'm installing it all in a system dir and not my home dir. Not sure if that could be a/the reason.
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Old   February 3, 2011, 23:24
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  #82
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Martin Beaudoin
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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

Quote:
Originally Posted by cnsidero View Post
After a little more digging ...

First I added the '-v' flag to the rpmbuild command in $WM_THIRD_PARTY_DIR/tools/makeThirdPartyFunctionsForRPM to get some more info.

After rerunning AllMake.stage2, the following line output seems to indicate the problem:

Code:
Found '/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILDROOT/openmpi-1.4.3-linux64GccDPOpt.x86_64' in installed files; aborting
After learning a little more about building rpms, this error indicates that the BUILDROOT dir is being included in the files to be added to the RPM - which rpmbuild does not like (here's one of the sites that mention this: http://www.ibm.com/developerworks/library/l-rpm1/).

I checked the openmpi spec file and its set up no different the other third party packages so I'm a bit baffled why only openmpi fails to create the RPMs. Furthermore, no 'openmpi-1.4.3' dir is created in $WM_THIRD_PARTY_DIR/packages, where there are respective dirs for the others. Ultimately, this would be better answered by Martin.

Edit: I thought I'd make a quick note. I'm installing it all in a system dir and not my home dir. Not sure if that could be a/the reason.
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Old   February 4, 2011, 11:01
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Chris Sideroff
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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.

Quote:
Originally Posted by mbeaudoin View Post
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
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Old   February 15, 2011, 07:51
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  #84
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Marcus Ende
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Hello Chris,

I've the same problems with OpenMPI under RHEL 6.0. So after tries I found out that the
/usr/lib/rpm/check-buildroot has some problems. I deactivated this script and now the installing works fine.

My way for deactivation was to insert following line in the .spec-file (I tried openmpi-1.5.spec) at the end of the %install section.

echo " PINC : \$PINC"
echo " PLIBS : \$PLIBS"
endif
DOT_CSH_EOF
export QA_SKIP_BUILD_ROOT=1 <== this line was inserted

%clean
rm -rf %{buildroot}

Maybe it helps.

Marcus
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Old   February 15, 2011, 10:49
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Hello,

I was able to replicate the problem which is specific to the compilation of openmpi-1.4.3 on RHEL 6.0.

In order to fix the problem, I had to modify the .spec file, but the overall solution is a bit cleaner (I think) than what was done before.

This modification is also solving one of the problem David Boger reported earlier about linking with the openmpi ".la" files. So two fixes for the price of one, ain't bad...

Now I need to test this fix on other platforms just to make sure I am not introducing problems on OpenSUSE or Ubuntu or Fedora or Mac OS X, which obviously would be counterproductive.

Thank you all for your patience.

Martin
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Old   March 6, 2011, 13:08
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I'm trying to compile the extended package using the ThirdParty directory I already have in place for 1.6.x. So far all the errors I hit were simply resolved by modifying prefs.sh to let extend know where to find scotch, metis, etc. I hit the first real roadblock with mesquite.

Mesquite is not included in the original ThirdParty package, so I downloaded the source and did ./configure, ./make without any issues. Yet I still got a lot of errors like the following:
Code:
/home/daniel/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linux64GccDPOpt/include/Mesquite_all_headers.hpp:33:23: fatal error: MsqIRel.hpp: No such file or directory
The solution is to run wmakeLnInclude in the mesquite directory, and then add mesquite/lnInclude to prefs.sh as the include directory. Then compiling works, but linking fails, because OpenFoam expects to find libmesquite.a instead of the libmsqutil.a built earlier. Fixed easily with a symbolic link, and now I can finally continue building the rest of the extend package
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Old   March 15, 2011, 12:09
Default Error when building thirdParty at stage 3
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Sebastian Saegeler
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Dear all!

I have tried to get OF-1.6-ext run on our campus computer SGI Altix 4700 without any success. To be honest, I am not so deep in the knowlege whith all that so I hope anybody of you can help.

I successfully compiled OF-1.6.x. But as mentioned I am getting stuck with the ext-version.

One prob seems to be the thirdParty package. I am getting errors when executing stage 3. I have generated and attachted a log-file. Please have a look on it and hopefully one of you guys has got an idea what I am doing wrong


Sebastian
Attached Files
File Type: txt log.stage3.txt (77.8 KB, 10 views)
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Old   March 15, 2011, 12:13
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are u using icc or gcc? I saw both in your log file
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Old   March 15, 2011, 12:22
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Sebastian Saegeler
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Hi! I am using icc. Version 11.1
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Old   March 15, 2011, 12:43
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Chris Sideroff
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Quote:
Originally Posted by lakeat View Post
are u using icc or gcc? I saw both in your log file
I believe 'gcc' is being used by the make/configure scripts for the original source packages for each component. I don't believe these are controlled by OpenFOAM's specification of the compiler. If you want to change those you'll have to manually modify the config files for each package to use 'icc'.

Specifically about the errors, there are two. First, there are several instances similar to the following:

Code:
ld: ../obj/linux64_2.4-itanium-glibc_2.2.4/release-shared/ADF_internals.o: @gprel relocation against dynamic symbol disk_cache
Upon digging through Intel's compiler notes for IA-64 on Linux, it suggests using the follow compiler options to remedy this:

-i_dynamic -nofor_main

The second:

Code:
make[2]: mpicc: Command not found
Means it can't find the mpi compiler. It's either provided with OpenMPI or MPICH. You're going to have to find out where those are installed and make sure it's included in the PATH.

This will require a little digging so you're going to have to "get dirty" to straighten it out or possibly consult with someone internally who can work with you.

Last edited by cnsidero; March 15, 2011 at 18:41.
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Old   March 21, 2011, 12:57
Default Floating Point Exception
  #91
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Hello again. Thanks for your answers.

Finally we made it - and it was really cruel! Fortunately I got some help from an expert of the Leibniz Rechenzentrum in Munich. We had to change a lot to get this new ThirdParty compiled on our system.

After successful compilation without any error I just wanted to start a tutorial. I did the one of rhoPisoFoam/ras und just got an floating point exception!

Create time

Create mesh for time = 0

Reading thermophysical properties

Selecting thermodynamics package hPsiThermo<pureMixture<constTransport<specieThermo <hConstThermo<perfectGas>>>>>

Reading field U

Reading/calculating face flux field phi

Creating turbulence model

Selecting turbulence model type RASModel
Selecting RAS turbulence model kOmegaSST
Floating point exception


The other tutorials I have tested seem to work. But I want to use a solver, written by a collegue and its the same problem ...

I cannot find anything here in the forum, can anybody help please?


Thanks,
Sebastian
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Old   March 22, 2011, 04:53
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Well, seems there is something wrong with the kOmegaSST ...
In combination with some other turbulence models I have tested it works quite well...
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Old   March 25, 2011, 03:39
Default Trouble compiling OpenFoam 1.6-ext
  #93
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Hi to everyone,

I am trying to compile OpenFoam 1.6-ext to my PC Ubuntu 8.10 (x64), more for experimentation and to see its extended capabilities, in comparison to the standard 1.7.x. I have successfully installed OpenFOAM 1.7.x, but I am facing a lot of trouble compiling OpenFOAM 1.6-ext.

First of all, I have to say that I have all the required libraries, such as those mentioned at #45 post of this thread (bison, flex, ...........etc). Also I have included in bashrc the line :

. $HOME/OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc
and commented out the respective line for OpenFOAM 1.7.x.

The main problem is when compiling Third Party. I cant succesfully compile scotch. I get the error log I have attached below (err_thirdparty.log).

Of course trying to compile OpenFOAM .16.ext fails with tons of errors such as /usr/bin/ld: cannot find -lfiniteVolume.

I attach the error log of the thirdparty only since I belive that these errors are those which cause the problem.

Any ideas are welcome.
Attached Files
File Type: txt err_thirdparty.txt (96.2 KB, 2 views)
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Old   April 8, 2011, 05:34
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Hello everybody!

I have as well some problems in compiling OF-1.6-ext on openSUSE 11.2 64. First i cloned the repository and edited the bash to my local directory. Then i ran thae AllMake in the ThirdParty-Dir and get the attached error - Scotch cannot be compiled. I found in several other topics, that i need the package "patch", which I installed. However it doesn't work.
Has anyone any ideas what might be wrong? When compiling the OF1.6-ext I get lots of errors that some -lsomething cannot be found.

Thanks in advance!
Attached Files
File Type: gz err.tar.gz (1.8 KB, 1 views)
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Old   April 8, 2011, 05:59
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I searched quite a long time before I posted the last message.. anyway after posting I found out that these packages where missing:
libtool
autoconf

obviously it didn't worked before.. now scotch is compiled!

[edit]After compiling OF1.6-ext i always got the error "error while loading shared libraries: libscotch.so" no such file or directory when running blockMesh or any solver.
I solved that by copying the libscotch.so to the binaries.. maybe this is not elegant but after hours of searching i didn't care any longer:

Quote:
cp OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/scotch_5.1.10b/lib/libscotch.so OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/
Greetings

Last edited by lindstroem; April 8, 2011 at 08:36.
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Old   May 16, 2011, 12:06
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  #96
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Hello everybody!

I am trying to compile OpenFoam 1.6-ext on my PC Ubuntu 11.04 (x64). The compilation of OpenFoam was successfull as well as Third Party from stage 0 to 3. The problem occurs by compilation of Third Party Stage-4 (exactly ParaView-3.8.1) with following error:

,
.
.
Linking CXX shared library ../../bin/libvtkParallel.so
[ 45%] Built target vtkParallel
Scanning dependencies of target GenericFilteringCxxTests
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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
make[1]: *** Waiting for unfinished jobs....
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[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MIPFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MIPFourDependentFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MIPFourDependentCropping FS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MIPFourDependentNoCroppi ngFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MIPNoCroppingFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPCroppingFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPFourDependentFS.cxx .o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPFourDependentCroppi ngFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPFourDependentNoCrop pingFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_MinIPNoCroppingFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_ParallelProjectionFS.cxx .o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_PerspectiveProjectionFS. cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_ScaleBiasFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_OneComponentFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_FourComponentsFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_NoShadeFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkGPUVolumeRayCastMapper_ShadeFS.cxx.o
[ 45%] Building CXX object VTK/VolumeRendering/CMakeFiles/vtkVolumeRendering.dir/vtkVolumeRenderingInstantiator.cxx.o
Linking CXX shared library ../../bin/libvtkVolumeRendering.so
[ 45%] Built target vtkVolumeRendering
make: *** [all] Error 2
error: Bad exit status from /home/eol/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.PlemeD (%build)


RPM build errors:
Bad exit status from /home/eol/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.PlemeD (%build)
Installing package: ParaView-3.8.1
Uninstalling ParaView-3.8.1 using RPM: ParaView-3.8.1-linux64GccDPOpt.x86_64
Installing ParaView-3.8.1 using RPM file: /home/eol/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/ParaView-3.8.1-linux64GccDPOpt.x86_64.rpm
error: open of /home/eol/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/ParaView-3.8.1-linux64GccDPOpt.x86_64.rpm failed: No such file or directory
Done installing package ParaView-3.8.1

========================================
Done ThirdParty AllMake: Stage4
========================================

========================================
Done ThirdParty Allwmake
========================================




Has anyone any ideas what might be wrong?
Thanks in advance!
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Old   May 16, 2011, 12:07
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Daniel WEI (老魏)
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I met the same error, ubuntu 11.04 (64bits)
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Old   May 16, 2011, 12:36
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Quote:
Originally Posted by lakeat View Post
I met the same error, ubuntu 11.04 (64bits)
Did you find a solution?
I have installed following packages:

sudo apt-get install binutils-dev flex bison git-core build-essential python-dev libreadline5-dev wget zlib1g-dev cmake libpng12-dev libxt-dev libxi-dev libxrender-dev libxrandr-dev libxcursor-dev libxinerama-dev libfreetype6-dev libfontconfig1-dev libglib2.0-dev freeglut3-dev libqt4-dev qt4-dev-tools

sudo apt-get install bison flex build-essential git gitk git-gui rpm
sudo apt-get install libxt-dev
sudo apt-get install zlib1g-dev
sudo apt-get install gnuplot python-numpy
sudo apt-get install binutils-dev
sudo apt-get install libtool autoconf

as well as I have set in ".bashrc" at the end:

. $HOME/OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc
export QT_BIN_DIR=/usr/bin
export QT_DIR=/usr
export WM_64=on
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/$USER/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/qt-everywhere-opensource-src-4.7.0/lib/

and in "AllMake.stage4":

export QT_THIRD_PARTY=1

after:

echo ========================================
echo Starting ThirdParty AllMake: Stage4
echo ========================================
echo

I belive that I have all required libraries.

Last edited by jajcevic; May 19, 2011 at 17:42.
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Old   May 16, 2011, 12:39
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Daniel WEI (老魏)
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nope...
Usually, what I will do is to use system software manager to install the paraview package, by doing this, all requirements of paraview can be automatically fullfilled and then I do Allwmake.
But this time, it failed.
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Old   May 16, 2011, 12:47
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Quote:
Originally Posted by lakeat View Post
nope...
Usually, what I will do is to use system software manager to install the paraview package, by doing this, all requirements of paraview can be automatically fullfilled and then I do Allwmake.
But this time, it failed.
My first step was also installation of paraview via "Ubuntu Software Centar" . I suppose we are missing a package or there is a package conflict.
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