Hi Mads,

first of all I like to thank you for your "cookbook".
Brilliant!
I'm working on a 64-bit ubuntu 9.04 version.
After three attempts of installation it seems that I'm pretty close to a successful installation.
At the moment I've got still two critcal errors. As a newbie I'm a little helpless.
It would be very kind if you could give me an advise.
Attached find below a excerpt of the "Checking Installation Script".

------------------------------------------------------
Checking installation - you should see NO criticals...
------------------------------------------------------
Executing /home/aurel/OpenFOAM/OpenFOAM-1.6.x/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: aurel-desktop
OS: Linux version 2.6.28-15-generic
-------------------------------------------------------------------------------


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/aurel/OpenFOAM yes yes
$WM_PROJECT_USER_DIR /home/aurel/OpenFOAM/aurel-1.6.x yes no
$WM_THIRD_PARTY_DIR /home/aurel/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/aurel/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 .../aurel/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 ...FOAM/aurel-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
-------------------------------------------------------------------------------
WARNING: gcc version does not match gcc supplied with this release of OpenFOAM
Supplied version: 4.3.3
User version :
Minimum required: 4.3.1

gcc
WARNING: Conflicting installations:
OpenFOAM settings : /home/aurel/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/bin/gcc
current path : /usr/bin/gcc
CRITICAL ERROR

gzip 1.3.12 /bin/gzip
tar 1.20 /bin/tar
icoFoam
WARNING: Conflicting installations:
OpenFOAM settings : /home/aurel/OpenFOAM/OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/icoFoam
current path :
CRITICAL ERROR

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


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

The foam installation contains 2 critical error(s).

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

done.

Regards

Aurel

Linux version and OF must be consistency
 

Hi, Aurel,
I also met the same problem above when I install OF. the problem is resulted probably by the version disagreement between OF and Linux.
Suggest you carefully check the downloaded OF version (32 or 64 bit) and your installed Linux version (32 or 64 bit).

Good luck!!

Michael, Min LI

Good morning Michael,

I'm working with Ubuntu 9.04 64-bit version and I used the 64-bit installation script of Mads. What did I wrong?

Regards

Aurel

I am glad you liked the script, although you are still facing some trouble. Let's get you pass that bump in the road.

I remember such error, and first thing that comes to my mind is that you may not have sourced the file
. ~/OpenFOAM/OpenFOAM-1.6.x/etc/bashrc
Secondly, is the following link created:
ln -s ~/OpenFOAM/ThirdParty-1.6 ~/OpenFOAM/ThirdParty-1.6.x
Third (I could go on here :-)), are you positive, that Allwmake is successful? Try to run it again, and it will update whatever file is not compiled.

Let me know how it works out while I try to remember what this error is caused by. Maybe someone else remembers?

/Mads

Hi Mads,

the above listed bash commands are exactly the same like in your installation script. I see no difference at all. (only that: in the installation script behind the "ln -s" command are two blanks! could this be responsible for the error?)
I'm pretty sure that the "Allwmake" worked successfully. Compiling time took at least 3 hours. But this is probably no indication for a complete installation.
Anyway, in the evening I will try your suggestions.

Best regards

Aurel







/Mads[/QUOTE]

They are the exact same commands :) but I have experienced that some times, when running the script by manually copying each line and inserting them into the command window, one tends to loose a line or a command is not recognised. It was just to make sure that didn't happen in your case.

The Allwmake can easily take more than 3 hours, depending on your hardware.

/Mads

Hi MadsR,

Couple of questions regarding your cookbook. The thing is, I'm total Linux newb :o(downloaded Ubuntu 9.04 couple of hours ago) and it looks like I'm doing something wrong. I started your scipt in terminal (did c/p since didn't know better) and it started to "do its thing". The procedure didn't last as long as you said (all in all 20-30 mins. max), didn't get any errors (think). The problem is, I don't know where to start openFoam, so I suspected the script wasn't finished (but then again, I didn't get the message I would kill the process). Obviously I'm doing something wrong. If you have time, could you please give me step-by-step procedure for complete linux newb.

Thanks.

Good morning Mads,

I did what you told me and it seems to work. There are still some "no's" in the checking installation script.
Is it neccessary that there are only "yes"?
Below find the checking installation print. What is your opinion? Does it look ok? Are there still some installation work neccessary?

Best regards

Aurel

Checking installation - you should see NO criticals...
------------------------------------------------------
Executing /home/aurel/OpenFOAM/OpenFOAM-1.6.x/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: aurel-desktop
OS: Linux version 2.6.28-15-generic
-------------------------------------------------------------------------------


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/aurel/OpenFOAM yes yes
$WM_PROJECT_USER_DIR /home/aurel/OpenFOAM/aurel-1.6.x yes no
$WM_THIRD_PARTY_DIR /home/aurel/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/aurel/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 .../aurel/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 ...FOAM/aurel-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 1.20 /bin/tar
icoFoam 1.6.x ...penFOAM-1.6.x/applications/bin/linux64GccDPOpt/icoFoam
-------------------------------------------------------------------------------


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

Critical systems ok.


done.

: command not foundine 48:
aurel@aurel-desktop:~$

Aurel: I have never seen ": command not foundine 48: " before. Apart from that, you should be fine. Does it work? :-)

Luka: what does c/p mean? :-) if it only took 30 minutes you either have a very fast computer or the script died somewhere. Try copying each line with the mouse and paste them into the command window, and see what happens at each command. This should work. Remember to be logged in as the user who are going to run OpenFOAM (that is not as root or anything else).

/Mads

Hi Mads,

are there any test cases available for running the program to see previously if the system is working?
Do have a guidance about that?
I know that on the OF homepage are informations given.
Before I'm able to start my own case I have to learn to work with OF.

Best regards

Aurel

Hi Mads

Thanks for the excelent script. Saved my butt in a tight spot... Worked perfectly! :)

The FORCE is still with you ;)

/Jan

Aurel: sure. The first thing you could try is just to type icoFoam. You will see either 1) command not found or 2) some output from OpenFOAM which states that it can't see any case to run. Secondly you should make a directory in your home folder and copy a simple cavity-test-case to it:

cd ~
mkdir myOpenFoamCases
cd myOpenFoamCases
cp -r ~/OpenFOAM/OpenFOAM-1.6.x/tutorials/incompressible/icoFoam/cavity .
cd cavity
blockMesh (generates a predefined mesh)
icoFoam (runs icofoam)

then use paraFoam to view the results.

Jan: Hi Jan! Happy to help you. Please keep me posted on your advances with OpenFOAM :-)

/Mads

Hi MadsR,

I followed your tips and it seems that every thing went fine (Base configuration ok.

Critical systems ok.). Thanks for the script. Rep point for you.

Hi Mads,

again thank you for your assistance.
1) icoFoam gave me an output.
2) I copied "cavity" in the directory /myOpenFoamCases
3) blockMesh gave following output

aurel@aurel-desktop:~/myOpenFoamCases/cavity$ blockMesh
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.6.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 1.6.x-99d4b831e6f2
Exec : blockMesh
Date : Oct 15 2009
Time : 21:10:24
Host : aurel-desktop
PID : 7486
Case : /home/aurel/myOpenFoamCases/cavity
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time


Creating block mesh from
"/home/aurel/myOpenFoamCases/cavity/constant/polyMesh/blockMeshDict"
Creating blockCorners
Creating curved edges
Creating blocks
Creating patches
Creating block mesh topology
Default patch type set to empty
Check block mesh 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 points with scale 0.1
Creating cells
Creating patches
Creating mesh from block mesh
Default patch type set to empty
Writing polyMesh

4) icoFoam gave following output for a lot time steps (the first time steps are listed below):

time step continuity errors : sum local = 9.45906e-09, global = -3.01342e-19, cumulative = 3.75172e-18
ExecutionTime = 0.13 s ClockTime = 0 s

Time = 0.275

Courant Number mean: 0.116922 max: 0.852131
DILUPBiCG: Solving for Ux, Initial residual = 2.29666e-06, Final residual = 2.29666e-06, No Iterations 0
DILUPBiCG: Solving for Uy, Initial residual = 4.82143e-06, Final residual = 4.82143e-06, No Iterations 0
DICPCG: Solving for p, Initial residual = 1.17435e-06, Final residual = 7.37825e-07, No Iterations 1
time step continuity errors : sum local = 8.44922e-09, global = 6.18731e-19, cumulative = 4.37045e-18
DICPCG: Solving for p, Initial residual = 1.03418e-06, Final residual = 6.73945e-07, No Iterations 1
time step continuity errors : sum local = 7.93654e-09, global = -1.09883e-18, cumulative = 3.27162e-18
ExecutionTime = 0.13 s ClockTime = 0 s

Time = 0.28

Courant Number mean: 0.116922 max: 0.852131
DILUPBiCG: Solving for Ux, Initial residual = 2.15919e-06, Final residual = 2.15919e-06, No Iterations 0
DILUPBiCG: Solving for Uy, Initial residual = 4.5588e-06, Final residual = 4.5588e-06, No Iterations 0
DICPCG: Solving for p, Initial residual = 8.87539e-07, Final residual = 8.87539e-07, No Iterations 0
time step continuity errors : sum local = 9.6874e-09, global = 3.59741e-19, cumulative = 3.63136e-18
DICPCG: Solving for p, Initial residual = 1.11354e-06, Final residual = 7.94958e-07, No Iterations 1
time step continuity errors : sum local = 8.94508e-09, global = -8.45544e-19, cumulative = 2.78582e-18
ExecutionTime = 0.13 s ClockTime = 0 s

.... and so on.5. paraFoam works, but I see no results!
Do you have an idea what did I wrong.

Best regards

Aurel

New to Openfoam
 

any tips??
gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
thx alot.

Hi, Mads.

I am installing on OF 1.6 on Ubuntu 9.04 64 bit using your 64 bit script. But I got some errors. Follow are some of them.

I think dado had similar problems. But he got them solved with the 64-bit script. Could you give me some advices?

Thanks.

Jin

Jin, looks like a problem with zlib. Manually execute sudo apt-get install zlib1g-dev and if that works try executing the script again. If not, post the error.

Hi Akidess, thanks for the reply. I tried to execute your script to update the zlib. But it shows my zlib is the newest version.

And I am wondering whether the error is related to the hardware configuration of my computer. This computer has 16 CPU cores. The type is Intel Xeon CPU W5590. The operation system is Ubuntu 9.04.

Here I attach the details of the first error about zlib. It may provide some information about error.

Thanks.

Jin

Jin, this is definitely a software problem. Do you have the file OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libz.so? If so, try

export LD_LIBRARY_PATH=$HOME/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/:${LD_LIBRARY_PATH}

and then recompile with ./Allwmake.

This seems to be a problem with how the system zlib library was compiled. The installation script might have to be changed to accommodate for this...

Akidess, I can not find the libz.so under the directory $HOME/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/. But there is a file libz.so.1.2.3.3 in /lib/. So I made a link $HOME/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libz.so directing to /lib/libz.so.1.2.3.3. It does work. I successfully compiled the libscotch.so.

But now I still have one error. It is caused by cmake. The error I got is as follows.

Quote:

make[3]: Leaving directory `/home/openfoam/OpenFOAM/OpenFOAM-1.6.x/applications/utilities/postProcessing/graphics/PV3FoamReader/vtkPV3Foam' + cd PV3FoamReader + mkdir -p Make/linux64GccDPOpt + cd Make/linux64GccDPOpt + cmake ../.. ./Allwmake: 1: cmake: not found + make make[3]: Entering directory `/home/openfoam/OpenFOAM/OpenFOAM-1.6.x/applications/utilities/postProcessing/graphics/PV3FoamReader/PV3FoamReader/Make/linux64GccDPOpt' make[3]: *** No targets specified and no makefile found. Stop. make[3]: Leaving directory `/home/openfoam/OpenFOAM/OpenFOAM-1.6.x/applications/utilities/postProcessing/graphics/PV3FoamReader/PV3FoamReader/Make/linux64GccDPOpt' make[2]: *** [PV3FoamReader] Error 2

This lead to a failure to compile the applications.

However, when I test the installation with foamInstallationTest

I got:



What should I do then?

Thanks.

Jin