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OpenFOAM-1.6 install cookbook

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Old   October 30, 2009, 15:47
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  #101
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Nugroho Adi
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Hei

i dont have problem within my Ubuntu 9.10.

my OF 1.6.x and 1.5-dev work well.


of16x@user-laptop:~$ gcc -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: ../configure --enable-languages=c,c++ --with-pkgversion=OpenFOAM --enable-__cxa_atexit --enable-libstdcxx-allocator=new --with-system-zlib --prefix=/home/dm2/henry/OpenFOAM/ThirdParty/gcc-4.3.3/platforms/linux --with-mpfr=/home/dm2/henry/OpenFOAM/ThirdParty/mpfr-2.4.1/platforms/linux --with-gmp=/home/dm2/henry/OpenFOAM/ThirdParty/gmp-4.2.4/platforms/linux
Thread model: posix
gcc version 4.3.3 (OpenFOAM)


of16x@user-laptop:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 9.10
Release: 9.10
Codename: karmic

i used Mads script when i install OF 1.6.x
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Old   October 30, 2009, 15:48
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Yeah, it's using the /usr/bin/cmake.

Could be me, not the script though. I just tried it on Debian Lenny. No luck there either. Exactly the same errors when compiling.

A manual makeParaFoam, that wouldn't even start in Ubuntu 9.10, makes it further this time...

Code:
[ 35%] Building CXX object Utilities/VTKClientServer/Filtering/CMakeFiles/vtkFilteringCS.dir/vtkFilteringCSInit.o
Linking CXX shared library ../../../bin/libvtkFilteringCS.so
[ 35%] Built target vtkFilteringCS
make: *** [all] Error 2
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Old   October 30, 2009, 16:19
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Mahaputra, did you install 9.10 and then OpenFOAM, or did you have OpenFOAM running already and then upgrade? Because in that case, you would have skipped the problematic compilation (once it's compiled there shouldn't been an issue).

Menorka, is there another error further up in the log?
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Old   October 30, 2009, 16:28
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Quote:
Originally Posted by akidess View Post
Mahaputra, did you install 9.10 and then OpenFOAM, or did you have OpenFOAM running already and then upgrade? Because in that case, you would have skipped the problematic compilation (once it's compiled there shouldn't been an issue).

Menorka, is there another error further up in the log?
Indeed there was. Missed this...
Code:
[ 34%] Building CXX object VTK/Rendering/CMakeFiles/vtkRendering.dir/vtkGraphicsFactory.o
In file included from /home/linus/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/VTK/Rendering/vtkGraphicsFactory.cxx:65:
/home/linus/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/VTK/Rendering/vtkXRenderWindowInteractor.h:37:74: error: X11/StringDefs.h: No such file or directory
/home/linus/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/VTK/Rendering/vtkXRenderWindowInteractor.h:38:73: error: X11/Intrinsic.h: No such file or directory
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Old   October 30, 2009, 16:32
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hehe

I had my OpenFOAM running already and then upgrade to 9.10

sorry, not solve the problem
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Old   October 30, 2009, 17:39
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Installed xorg-dev and paraFoam compiled without a hitch. Thanks to everyone for all your help and an extra thanks to Mads for putting up this script!
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Old   October 31, 2009, 09:13
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Hi Mads;
Thank you for your cookbook .
I was able to install OF on a fresh 9.04 ubuntu without any problem.
It was great.

Tnx.

Mostafa
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Old   November 1, 2009, 13:55
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Quote:
Originally Posted by menorka View Post
Can't get paraFoam to work despite running the old script.
I'm sure the "installation script" is fine. However, I have used the guide found here http://ubuntuforums.org/showthread.php?t=156298 on both 1.5 and 1.6 without much trouble. I have never recompiled the tarballs downloaded from sourceforge. In release 9.10 though, I had to install libqt4-dev (and I chose also cmake and build-essential in case I had to rebuild something), else I would get an error, and then paraFoam and everything else works like a charm.

NOTE: I do have to use the "export LANG=C" before running paraFoam, as my system is not set up to use English as native language. Thereby the decimal is "," and not "." - which has proven to be a problem for the PV3FoamReader plugin.
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Old   November 2, 2009, 03:43
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Kjetil, the guide you are referring to, is not doing exactly the same as the script. The guide you mention, is merely downloading already compiled binaries and this normally works effortless. This thread, however, is going full monty :-) and compiles OpenFOAM from source.

/Mads
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Old   November 2, 2009, 14:01
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I followed everything as suggested on the OpenFOAM website for the current release (1.6), but I have a problem with the installation.

With order:

I've downloaded:
- OpenFOAM-1.6.General.gtgz
- ThirdParty-1.6.General.gtgz

I am trying to install OpenFOAM 1.6 on Ubuntu 9.10 Karmic Koala, 64 bit version.

When I update the environment variables by sourcing the $HOME/.bashrc file by typing in the terminal:

Code:
* . $HOME/.bashrc
I receive this message:

Code:
Warning in /home/MyUserName/OpenFOAM/OpenFOAM-1.6/etc/settings.sh:
    Cannot find /home/MyUserName/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64 installation.
    Please install this compiler version or if you wish to use the system compiler,
    change the 'compilerInstall' setting to 'System' in this file
On Karmic the gcc version that I am using is gcc-4.4.1 (which I think is the latest one for the moment): how can I use this compiler to make OpenFOAM work?
What actions/commands should I use?
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Old   November 2, 2009, 16:50
Default installation solved for OpenFOAM 1.6.x at ubuntu 9.10 amd64
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hi

i had similiar problems then you guys. therefore i checked some other forums in the www and mixed a working solution.

thanks to the authors:

Piotr Prusinski

Alberto Passalacqua


quote begins:

Installing OpenFOAM 1.6.x and keeping it up to date
Aug.14, 2009 in CFD, OpenFOAM

OpenCFDTM regularly releases updates for OpenFOAMTM using a GIT repository, which can be conveniently used both for a fresh installation and to keep your current OpenFOAM installation up to date.

First installation

* Create a directory called OpenFOAM in your home directory: mkdir ~/OpenFOAM
* Enter the OpenFOAM directory: cd ~/OpenFOAM
* Download the OpenFOAM sources from the GIT repository: git clone git://repo.or.cz/OpenFOAM-1.6.x.git

* Download the third party packages from the OpenCFD website. If you are using a 64-bit system, you need to download also the 32-bit version of the third party package, containing cmake.
* Extract the third party packages corresponding to your architecture (32 or 64 bit) in the ~/OpenFOAM directory. If you use a 64 bit system, extract the 32-bit version of the third party packages in another directory from ~/OpenFOAM, and move the cmake directory to the ThirdParty directory into your ~/OpenFOAM directory.

-----> or just type sudo apt-get install cmake


* Create a symbolic link called ThirdParty-1.6.x pointing to ThirdParty-1.6: ln -s ~/OpenFOAM/ThirdParty-1.6/ ~/OpenFOAM/ThirdParty-1.6.x
* Open your ~/.bashrc file in a text editor and add the line: . $HOME/OpenFOAM/OpenFOAM-1.6.x/etc/bashrc

So, I found the source of my problem. And there is even quite simple solution for it. The problem is not the lacking of some libraries but wrong linking. So what you need to do is just:

Code:

cd /home/USER_NAME/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/lib64

sudo mv libstdc++.so.6 libstdc++.so.6.orig
sudo ln -s /usr/lib/libstdc++.so.6.0.10 libstdc++.so.6

sudo mv libgcc_s.so.1 libgcc_s.so.1.orig
sudo ln -s /lib/libgcc_s.so.1


Of course be carefull and check the version of libstdc++.so.6.0.x before typing and put your USER_NAME in the path.

* Enter the ThirdParty-1.6.x directory: cd ~/OpenFOAM/ThirdParty-1.6.x

* Rebuild Paraview with the following commands (you need qt4 development libraries installed in your system. Check the README file coming with OpenFOAM for a list of working versions)
o rm -rf paraview-3.6.1/platforms
o ./makeParaView



cd $FOAM_UTILITIES/postProcessing/graphics/PV3FoamReader
Code:

./Allwclean
./Allwmake


* Enter the ~/OpenFOAM/OpenFOAM-1.6.x directory: cd ~/OpenFOAM/OpenFOAM-1.6.x
* Rebuild OpenFOAM typing ./Allwmake

Once OpenFOAM 1.6.x is built for the first time, you can easily keep it up to date using GIT.

Update an existing installation of OpenFOAM 1.6.x.

* Enter the ~/OpenFOAM directory: cd ~/OpenFOAM
* Check for updates: git pull
* If there are updates, rebuild OpenFOAM as follows:
o cd ~/OpenFOAM/OpenFOAM-1.6.x
o ./Allwmake

These operations should be repeated often, in order to keep an up to date installation of OpenFOAM and obtain the latest bug fixes.

Enjoy :-)

OpenFOAMTM and OpenCFDTM are registered trademarks of OpenCFD Ltd.
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Old   November 2, 2009, 17:30
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Quote:
Originally Posted by dhondupant View Post

* Create a symbolic link called ThirdParty-1.6.x pointing to ThirdParty-1.6: ln -s ~/OpenFOAM/ThirdParty-1.6/ ~/OpenFOAM/ThirdParty-1.6.x
* Open your ~/.bashrc file in a text editor and add the line: . $HOME/OpenFOAM/OpenFOAM-1.6.x/etc/bashrc

So, I found the source of my problem. And there is even quite simple solution for it. The problem is not the lacking of some libraries but wrong linking. So what you need to do is just:

Code:

cd /home/USER_NAME/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/lib64

sudo mv libstdc++.so.6 libstdc++.so.6.orig
sudo ln -s /usr/lib/libstdc++.so.6.0.10 libstdc++.so.6

sudo mv libgcc_s.so.1 libgcc_s.so.1.orig
sudo ln -s /lib/libgcc_s.so.1


Of course be carefull and check the version of libstdc++.so.6.0.x before typing and put your USER_NAME in the path.
Technically this is not correcting a link, but replacing the gcc and stdc libraries with your system version. This doesn't really make sense to me, because now you are mixing libraries from your system gcc (4.4) with OpenFOAM's gcc (4.3). I'm glad it works, but I'm not sure it's the root of the problem or that it doesn't come with side effects. It's certainly not something I'd put in the cookbook script per default...
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Old   November 5, 2009, 07:11
Default Ubuntu Netbook Remix works fine but Debian 5.0 32 Bit have Problems
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Hi
thanks for the script. It worked fine for my Acer Netbook (only for fun) but my old workstation has the following problem:
------------------------------------------------------
Retrieveing OpenFOAM...
------------------------------------------------------
Initialized empty Git repository in /home/achim/OpenFOAM/OpenFOAM-1.6.x/.git/
warning: remote HEAD refers to nonexistent ref, unable to checkout.

./install: line 43: /home/achim/OpenFOAM/OpenFOAM-1.6.x/etc/bashrc: Datei oder Verzeichnis nicht gefunden

I changed only
git clone git://repo.or.cz/OpenFOAM-1.6.x.git
to
git clone http://repo.or.cz/r/OpenFOAM-1.6.x.git
because it never worked with the first one - maybe because of the firewall.
Have you an idea why the script does not work here?
Regards
Achim
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Old   November 5, 2009, 19:45
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Quote:
Originally Posted by af631717 View Post
Hi
thanks for the script. It worked fine for my Acer Netbook (only for fun) but my old workstation has the following problem:
------------------------------------------------------
Retrieveing OpenFOAM...
------------------------------------------------------
Initialized empty Git repository in /home/achim/OpenFOAM/OpenFOAM-1.6.x/.git/
warning: remote HEAD refers to nonexistent ref, unable to checkout.

./install: line 43: /home/achim/OpenFOAM/OpenFOAM-1.6.x/etc/bashrc: Datei oder Verzeichnis nicht gefunden

I changed only
git clone git://repo.or.cz/OpenFOAM-1.6.x.git
to
git clone http://repo.or.cz/r/OpenFOAM-1.6.x.git
because it never worked with the first one - maybe because of the firewall.
Have you an idea why the script does not work here?
Regards
Achim
i had this same problem as i mentioned above in this thread and was just going to ask about it again as well as it's bugging me... i realise its more a git problem than an openfoam problem.

i also have a firewall that is quite strict, i wonder if that's the reason? it seems like both the links work but only for some and not others.

i'm sure the answer will be trivial and obvious to someone - please enlighten us
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Old   November 16, 2009, 00:30
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Thanks. I had just gotten OpenFOAM compiling on 9.04 days before 9.10 came out. Your suggestions worked like a charm (using system libs).
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Old   November 17, 2009, 16:56
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Hi All -

I'm trying to install OF 1.6 on a fairly fresh Ubuntu 9.04 64 bit system using Mads' 64 bit script. Everything went well, no critical errors. But, when executing blockMesh in the cavity directory it complains it can't find *mpi.o.0 (forget exactly). So:

sudo apt-get -install openmpi

and that problem went away (only later I discovered Allwmake should have installed it). But then another problem arose, which I will just quote from dandiwijaya, since I saw the identical behavior. (see quote below)

I tried installing a few packages listed in this thread (most were already installed):
How to Install OpenFOAM on 64 Ubuntu 9.04

Then tried running Allwmake again - nothing compiled, nothing changed. FoamInstallationTest indicates just the one critical error, that being the compiler conflict.

It seems that these problems are cropping up on Ubuntu 64 bit installs. Is it a linking problem? Does anybody know what is going on?

Thanks in advance!

Philip

Quote:
Originally Posted by dandiwijaya View Post
Hi all
I was just installing openFoam and try installing using the your script .The installation successful, but when I try blockmesh at cases cavity at tutorials there is perform the following message appears:

--> FOAM FATAL ERROR:
Failed writing polyMesh.

From function blockMesh
in file blockMeshApp.C at line 346.

one more thing, when I try to check the installation after trying the case had the following message appears:

Third party software
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
gcc 4.3.3
WARNING: Conflicting installations:
OpenFOAM settings : /home/dandiwijaya/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux/bin/gcc
current path : /usr/bin/gcc
CRITICAL ERROR

gzip 1.3.12 /bin/gzip
tar 1.20 /bin/tar
Aborted
icoFoam 1.6.x .../OpenFOAM-1.6.x/applications/bin/linuxGccDPOpt/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.

The foam installation contains 1 critical error(s).

Review the output for warning messages and consult
the installation guide for trouble shooting.

Last edited by PJC; November 18, 2009 at 11:58. Reason: clarity
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Old   November 20, 2009, 21:29
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Greetings Mads,

Just to give you a head's up: I've modified your 32bit cookbook script to run in Mandriva 2010. I posted here, for someone who is starting to use Linux.

Which brings me to to a couple of suggestions, which are in the modification I made:
  1. imbue the use of multi-core build options (set WM_NCOMPPROCS), as defined in the script $WM_THIRD_PARTY_DIR/makeGcc, so it will build to the fullest CPU power of your working machine (although not a POSIX friendly action, by what I've read);
  2. for the 32bit version, change the variable WM_ARCH_OPTION via patch (as I did) or via sed or something like that, from 64 to 32, so it will build to the proper folder paths. Because by what I interpreted from your script, it will use the folder paths of the 64 bit version as targets, while under the 32bit version.
And that's it! Sorry to drop in on this thread, but it seemed the best place for informing you, as well as others that might drop by here!

------------------------------------

By the way, Just read the last post...
Quote:
FoamInstallationTest indicates just the one critical error, that being the compiler conflict.
Edit ~/OpenFOAM/OpenFOAM-1.6/etc/settings.sh, and change the variable setting from compilerInstall=OpenFOAM to compilerInstall=System (around line 98). Launch a new terminal and run foamInstallationTest again. This should fix the critical issue associated with gcc. NOTE: Ubuntu 9.04 uses gcc-4.3.3, which just happens to be the version that comes with OpenFOAM's ThirdParty package... but the build isn't identical.. I think!

As for OpenMPI, the problem is that this cookbook script implicitly uses the pre-built version of OpenMPI that comes with one of the packages. If you want to rebuilt OpenMPI, do:
Code:
cd $WM_THIRD_PARTY_DIR/openmpi-1.3.3
make distclean
rm -rf platforms/$WM_OPTIONS
cd $WM_PROJECT_DIR
rm -rf $FOAM_LIBBIN
rm -rf $FOAM_APPBIN
./Allwmake
This should take out the prebuilt OpenMPI, remove the built OpenFOAM binaries, and then force rebuilding the whole thing. Don't worry, it should need a complete rebuilt, since it will just need to relink every library and application against the new OpenMPI build!

Hopes this solves the issues!

Best regards,
Bruno
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Old   November 21, 2009, 19:56
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  #118
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I solved the problem with blockMesh not being able to write files. It was a permissions promblem, since the script was run with sudo and hence the OpenFOAM installation owned by root. Daa.

Philip
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Old   November 23, 2009, 18:47
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  #119
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Hi. I followed your instruction book. Can someone take a quick look at this and tell me if its ok?

Code:
Executing /home/xye/OpenFOAM/OpenFOAM-1.6.x/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               xye-desktop
OS:                 Linux version 2.6.31-15-generic
-------------------------------------------------------------------------------


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/xye/OpenFOAM                       yes       yes
$WM_PROJECT_USER_DIR /home/xye/OpenFOAM/xye-1.6.x             yes       no
$WM_THIRD_PARTY_DIR  /home/xye/OpenFOAM/ThirdParty-1.6.x      yes       yes
-------------------------------------------------------------------------------


Checking the OpenFOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR      /home/xye/OpenFOAM/OpenFOAM-1.6.x        yes  yes  yes

$FOAM_APPBIN         ...6.x/applications/bin/linux64GccDPOpt  yes  yes  yes
$FOAM_SITE_APPBIN    ...nFOAM/site/1.6.x/bin/linux64GccDPOpt  no        no
$FOAM_USER_APPBIN    ...6.x/applications/bin/linux64GccDPOpt  yes  yes  no
$WM_DIR              /home/xye/OpenFOAM/OpenFOAM-1.6.x/wmake  yes  yes  yes
-------------------------------------------------------------------------------


Checking the OpenFOAM env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN         ...M/OpenFOAM-1.6.x/lib/linux64GccDPOpt  yes  yes  yes
$FOAM_SITE_LIBBIN    ...nFOAM/site/1.6.x/lib/linux64GccDPOpt  no        no
$FOAM_USER_LIBBIN    ...enFOAM/xye-1.6.x/lib/linux64GccDPOpt  no        no
$MPI_ARCH_PATH       ...nmpi-1.3.3/platforms/linux64GccDPOpt  yes  yes  yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
gcc      4.3.3     ...M/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/bin/gcc
gzip     1.3.12    /bin/gzip                                                
tar      1.22      /bin/tar                                                 
icoFoam  1.6.x     ...penFOAM-1.6.x/applications/bin/linux64GccDPOpt/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.

Critical systems ok.


done.
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Old   November 23, 2009, 20:49
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Quote:
Originally Posted by Xye View Post
Hi. I followed your instruction book. Can someone take a quick look at this and tell me if its ok?

[/CODE]
It's ok, no errors.
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