openfoam-2.2.0 installation on cluster of Redhat 4.1.2-48
 

Hi！
I want to install OpenFoam on a machine with Redhat 4.1.2, but the Gcc version of Redhat is 4.1.2. an other Gcc version is installed in path: /public/source/gcc-source/gcc-4.7.1/gcc_install/, but i dont know how to use it.

i try to install gcc-4.6.2 in the thirdparty directory, but after installation, i type "gcc --version", it showed gcc-4.1.2.
How can i do in this situation?:confused::(

foamInstallationTest is shown as:

Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: ln0
OS: Linux version 2.6.18-194.el5
-------------------------------------------------------------------------------

Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /locallustre/home/caijiejin/OpenFOAM yes yes
$WM_PROJECT_USER_DIR ...e/caijiejin/OpenFOAM/caijiejin-2.2.0 no no
$WM_THIRD_PARTY_DIR .../caijiejin/OpenFOAM/ThirdParty-2.2.0 yes yes
-------------------------------------------------------------------------------

Checking the OpenFOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR ...me/caijiejin/OpenFOAM/OpenFOAM-2.2.0 yes yes yes
$FOAM_APPBIN ....2.0/platforms/linux64Gcc46DPOpt/bin no yes
$FOAM_SITE_APPBIN ....2.0/platforms/linux64Gcc46DPOpt/bin no no
$FOAM_USER_APPBIN ....2.0/platforms/linux64Gcc46DPOpt/bin no no
$WM_DIR ...jiejin/OpenFOAM/OpenFOAM-2.2.0/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 ....2.0/platforms/linux64Gcc46DPOpt/lib no yes
$FOAM_SITE_LIBBIN ....2.0/platforms/linux64Gcc46DPOpt/lib no no
$FOAM_USER_LIBBIN ....2.0/platforms/linux64Gcc46DPOpt/lib no no
$MPI_ARCH_PATH ...platforms/linux64Gcc46/openmpi-1.6.3 no yes
-------------------------------------------------------------------------------

Third party software
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
flex /usr/bin/flex
ERROR: gcc version is too old for this release of OpenFOAM
User version : 4.1.2
Minimum required: 4.3.2
gcc 4.1.2 /usr/bin/gcc
gzip 1.3.5 /bin/gzip
tar 1.15.1 /bin/tar
icoFoam
WARNING: Conflicting installations:
OpenFOAM settings : /locallustre/home/caijiejin/OpenFOAM/OpenFOAM-2.2.0/platforms/linux64Gcc46DPOpt/bin/icoFoam
current path :
CRITICAL ERROR
-------------------------------------------------------------------------------

Summary
-------------------------------------------------------------------------------
The system test has evoked 1 fatal error(s).
The foam installation contains 1 critical error(s).
Review the output for warning messages and consult
the installation guide for troubleshooting.
Done


anyone helps? Thank you!

Greetings Zeng,

I have not tried the following instructions with CentOS 4.x, but you can try them out and let me know if anything goes wrong: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4

You might not want to follow the instructions for installing certain packages from step #1, but the rest should be OK.

Best regards,
Bruno

thankful Bruno!

i successfully install openfoam-2.2.0 on cluster but no totally follow the tutorial you give. i checked the system again and found it is RedHat Enterprise Linux 5.5 x86_64, the command "module load openmpi-x86_64" can't be used on this cluster.
i follow the installation tutorial http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.2.0/CentOS_SL_RHEL#CentOS_6.4 step #5 to #7 to build the gcc-4.6.2, and then build the thirdparty and openfoam.

Best regards,
Zeng

Hello.
I have similar situation. But gcc version is OK.
What is wrong?

Greetings Avdeev,

According to the "make.log" file, the very first error is this:
Which means that something very strange has happened, because GCC 4.6.1 could only have been build with success if you had built MPFR properly as well.

I'm guessing you simply ran the makeGcc46 script without verifying which exact versions of software were defined in OpenFOAM's "settings.sh" file. If this is the case, then follow these steps:

1. Edit the file "$WM_PROJECT_DIR/etc/config/settings.sh".
2. Search for this block of code:
   
   Code:

   ---

           gcc_version=gcc-4.6.1
        gmp_version=gmp-5.0.4
        mpfr_version=mpfr-3.1.0
        mpc_version=mpc-0.9

   ---

3. Change the block to this:
   
   Code:

   ---

           gcc_version=gcc-4.6.1
        gmp_version=gmp-5.0.2
        mpfr_version=mpfr-3.0.1
        mpc_version=mpc-0.9

   ---

4. Save and close the file.
5. Start a new terminal.
6. Run Allwmake once again and it should build everything properly.

Best regards,
Bruno

Yes, Bruno, you right - I simply ran the makeGcc46.

But making changes in settings.sh has no effect. :(

Anyway, after that I tryed to follow (http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4) and everything working now.
Yes-yes, I would have to use this manual before asking here, but using external binUtils scare me a little - why it not included in thirdparty?

Thank you, Bruno!

Hello,

I had the same gcc version problem for installation of OpenFoam 2.2.0 in my cluster, which i solved through the instruction from weblink.

But I can not build the paraview and gives the following error-

ERROR: ParaView not found in /home/jzb292/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc45/paraview-3.12.0

I don't know what happened.

OpenFoam runs good.

Please help me out.

Thanks
Manjura

Greetings Manjura,

Run the following commands:
When it stops running, check the contents of the file "mkpv.log". If you do not understand why an error is showing up, please compress the file and attach it to your next post.
For example, you can compress the file with the following command:
Best regards,
Bruno

Thanks for reply.

I got the following message when i run- ./makeParaView -qmake $(which qmake-qt4) :

/usr/bin/which: no qmake-qt4 in (/home/jzb292/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/gperftools-svn/bin:/home/jzb292/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/paraview-3.12.0/bin:/home/jzb292/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/bin:/home/jzb292/OpenFOAM/jzb292-2.2.0/platforms/linux64GccDPOpt/bin:/home/jzb292/OpenFOAM/site/2.2.0/platforms/linux64GccDPOpt/bin:/home/jzb292/OpenFOAM/OpenFOAM-2.2.0/platforms/linux64GccDPOpt/bin:/home/jzb292/OpenFOAM/OpenFOAM-2.2.0/bin:/home/jzb292/OpenFOAM/OpenFOAM-2.2.0/wmake:/home/jzb292/projects/gnuplot/bin:/home/jzb292/projects/git/bin:/share/apps/python/2.7.3/bin:/share/apps/cuda/5.0/bin:/share/apps/openmpi/1.6/bin:/share/apps/texlive/2012/bin/x86_64-linux:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/share/apps/gcc/4.7.1/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/local/sbin/:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/jzb292/bin)
'-qmake' option requires an argument

usage: makeParaView [OPTION] [CMAKE-OPTION]
options:
-rebuild for repeated builds (-make -install) *use with caution*
-mesa with mesa (if not already enabled)
-mpi with mpi (if not already enabled)
-python with python (if not already enabled)
-cmake PATH with the cmake version corresponding to the cmake path given
-qmake PATH with the Qt version corresponding to the qmake path given
-qt with extra Qt gui support (if not already enabled)
-qt-VER with Qt version corresponding to
$WM_THIRD_PARTY_DIR/platforms/linux64Gcc/qt-VER/bin/qmake
-gcc force g++ instead of the value from $WM_CXX
-verbose verbose output in Makefiles
-version VER specify an alternative version (current value: 3.12.0)
-major VER specify an alternative major version for special builds
-mesa-include DIR
location of mesa headers (current value: /usr/include/GL)
-mesa-lib PATH path to mesa library (current value: /usr/lib64/libOSMesa.so)
-python-lib PATH path to python library (current value: none)
-help

The -no-FEATURE option can be disable these features (if not already disabled):
mesa mpi python qt

CMake options start with a capital letter and contain an '='.
For example,
makeParaView BUILD_TESTING=ON PARAVIEW_GENERATE_PROXY_DOCUMENTATION=OFF
to add tests and avoid building documentation

For finer control, the build stages can be selected or deselected individually:
-config -no-config
-make -no-make
-install -no-install


* Make and install paraview-3.12.0 located under
$WM_THIRD_PARTY_DIR/ParaView-3.12.0
-> $WM_THIRD_PARTY_DIR/platforms/linux64Gcc/paraview-3.12.0

Thanks for your help.

Manjra

Hi Manjura,

My guess is that you did not follow step #1 properly, because the absence of qmake-qt4 indicates that you do not have installed the package "qt-devel".

Best regards,
Bruno

I do not have the administrator access to install the 'Development tools'.

How can i perform step-1?

Thanks

Hi Manjura,

If you do not have administrative powers, then you either have to ask the administrator to install the packages or you can follow these instructions: http://openfoamwiki.net/index.php/In...HEL#CentOS_5.8 - It's for CentOS 5.8 and OpenFOAM 2.1.1, but you only need to follow from step #10.

Step #10 has the instructions for doing a custom build of Qt, then #11 indicates how to use this custom build of Qt for building ParaView.

Best regards,
Bruno

I've tryed to perform step #10 (http://openfoamwiki.net/index.php/In...HEL#CentOS_5.8)
but it finished with error
some googling shows, that I need install from sources
build-dep qt4-qmake
right?

Greetings Avdeev,

That error is familiar... If I remember correctly and by looking into your log file, I would say that you didn't do these two command lines properly:
Best regards,
Bruno

Bruno, yes, error was in g++.conf file. I've ran "sed ..." script more than one time and it was g++4444 instead of g++44. It's corrected.

But now another error:

mkqt.log.zip

Hi Avdeev,

:eek: a 21MB log file... I forgot how big Qt really is!

OK, the error you got was in fact:
Well this is very confusing... "g++44" would mean that you should be using Gcc 4.4, but the error message clearly is referring to Gcc 4.5.2.
OK, after reading the past posts, I've managed to figure out that you were following the instructions for CentOS 6.4.
But why are you building the custom Qt?


Anyway, it took me a while to deduce this, but I think these steps should fix the problem:

1. Once again, tdit the file "qt-everywhere-opensource-src-4.6.4/mkspecs/common/g++.conf" with a text editor.
2. Now, you should see that there are several occurrences of "gcc", "g++", "g++44" and "gcc44".
3. But since you have the custom built Gcc 4.5.2 from the instructions for CentOS 6.4, then you should remove all "44" from "g++44" and "gcc44". This way you will only have "gcc" and "g++", which will make sure that you are only using Gcc/G++ 4.5.2.
4. Save the file.
5. Try building Qt 4.6.4 once again!

Best regards,
Bruno

Hi Bruno,

I've already build OF on our x86_64 redhat linux cluster. But I got some problems when building paraview. Basically I just followed the instruction here
http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4
However I don't have the access to to administrator. So I just skip the 1st step. I used custom built Gcc 4.5.2 compiled OF. When I tried to build paraview, I think I need to do a custom build of both CMake 2.8 and Qt 4.6 or higher. There's no problem when I built CMake. But when I tried to build Qt following step 10 here http://openfoamwiki.net/index.php/In...HEL#CentOS_5.8
When I conducting ./getQt, the terminal showed me the following message:

Which means qt-everywhere-opensource-src-4.6.4.tar.gz cannot be extracted. Then, I went to download dir using file to check the file type of qt-everywhere-opensource-src-4.6.4.tar.gz. It showed me this:
Since the file type here is not correct I am wondering is the source address which is given in the instruction is not available? Or is there any other reason may lead to this error? Thanks

Anyone has the same problem?

This link doesn't work.
Maybe you can edit getQt to use this link instead? :
http://download.qt-project.org/archi...c-4.6.4.tar.gz

/Eysteinn

Thanks Eysteinn. This link works. I have built Qt 4.6.4.
However, when I conduct the 11 step here http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4

It shows me this:

[jaq526@takara PV3Readers]$ wmSET $FOAM_SETTINGS
Cannot open configuration file /home/jaq526/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc/openmpi-1.6.3/share/openmpi/mpicc-wrapper-data.txt
Error parsing data file mpicc: Not found

Is there any suggested solution for this problem?

Thanks
JYJ

Greetings to all!

I completely forgot to update the getQt script... I'll fix this later today.

@JYJ: OK, since you don't have root permissions, then I need to know something: in step #4, did you use the option "WM_MPLIB=SYSTEMOPENMPI"?
Because if you did, then you shouldn't have :(

By the way, try running this command:
What does it give you?

Best regards,
Bruno

Thanks Bruno,
I think that's the reason. Unfortunately, I did use the option "WM_MPLIB=SYSTEMOPENMPI".
The which mpirun gave me this:

/usr/lib64/openmpi/bin/mpirun

So, I think I need to modify the following section in $Home/OpenFoam/OpenFoam-2.2.0/etc/bashrc
-------------------------------------------------------------------------------------------------------------------------------
#- MPI implementation:
# WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI
# | GAMMA | MPI | QSMPI | SGIMPI
export WM_MPLIB=OPENMPI
--------------------------------------------------------------------------------------------------------------------------------
Is this the right reason of my problem? Do you have any idea on solving this?

Best regards,
JYJ

Hi JYJ,

Here's what you should do:

1. Edit the file "$HOME/.bashrc".
2. Find the line similar to this:
   
   Code:

   ---

   source $HOME/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc  WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45 WM_MPLIB=SYSTEMOPENMPI

   ---

3. Change it to this:
   
   Code:

   ---

   source $HOME/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc  WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45

   ---

   In essence, simply remove "WM_MPLIB=SYSTEMOPENMPI" from the end of that line.
4. Start a new terminal.
5. Now do the step #8 from here: http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4
6. Then you can do the second part of step #11 from here, namely the one that starts with "cd $FOAM_UTILITIES": http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4

Best regards,
Bruno

Hi Bruno,
I followed your suggestion and edited .bashrc. Now it is as the following: (jaq526 is the user's name)


# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
source $HOME/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc
# User specific aliases and functions
module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc
module load openmpi-x86_64
module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45
module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45

Then, I re-did the steps from step 8 of the instruction. But when I conducted ./Allwmake, it gave me this:
ERROR: ParaView not found in /home/jaq526/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc45/paraview-3.12.0

Now, I have no idea on this:(

:eek: OK, first of all, let's do some clean up on the "~/.bashrc" file. Change this:
To this:
Secondly, when you start a new terminal, does it give you any messages?

Bruno,

I modified the .bashrc. But there is not any message when I start a new terminal after I did the .bashrc modification. Now, the file is as follows
What do you think? Is that Ok now to complier OF again?

Don't worry, it's not meant to give any messages. The ones usually given are error or warning messages and we don't want to see those :).

I think so! Let's go by parts.
First take care of confirming if OpenFOAM is well built, by following the step #8. If possible, package the "make.log" file as explained in step #9, and attach the file to your next post, because I want to confirm if everything is OK on OpenFOAM's end.

Then for step #11, run makeParaView like this:
Then package the file "make.pv.log" and attach it as well, so I can confirm if everything is OK.

Hi Bruno,

I re-did the steps as you told me. The make.log and make.pv.log are packaged and attached here. But seems haven't solved the problem. The error "ERROR: ParaView not found in /home/jaq526/OpenFOAM/ThirdParty-2.2.0/platforms/linux64Gcc45/paraview-3.12.0" still exits when I conduct ./Allwmake. Please help to check the log file. Thank you.

Hi JYJ,

:eek: qmake-qt4 wasn't found, which is why it didn't even try to build ParaView.

Try running these two commands:
The first one shouldn't show anything and the second one might show something.
If the second one does show something, then you can run:
If not, then the custom build of Qt probably isn't built/installed... I don't know/remember if you've already done the steps #9 and #10 from here: http://openfoamwiki.net/index.php/In...HEL#CentOS_5.8 - if not, you should. Then do #11 as well.

Best regards,
Bruno

Yes, Bruno. You are right. qt-4 hasn't been built successfully. I tried to find out the problem today. I found this information in mkqt.log

Then, I found the file in /mkspecs/linux-g++-64/qmake.conf and the content is as follow:
But in our system, there isn't a dir named X11R6 under usr -_-|||

Here is the mkqt.log. You can see the error which I mentioned above.

Hi JYJ,

I know I've had this problem before... and it ended up in not having to do anything with the X11.

Check the contents of the file "qt-everywhere-opensource-src-4.6.4/mkspecs/common/g++.conf". The references to "gcc" and "g++" should indicate "gcc44" and "g++44" or whichever name your custom build of GCC is using, such as "gcc-4.5" and "g++-4.5".

Best regards,
Bruno

Bruno,
This problem has been solved. I really appreciate your help in the past days. Thanks.

Best regards,
Yijiu

$MPI_ARCH_PATH ...0/platforms/linux64Gcc/openmpi-1.6.3 no yes
 

Hello Everyone,

I have tried to install OpenFOAM on my personal Drive on my Cluster

OpenFOAM 2.1.0 worked but when running simulations some simulations are just stuck on iterations I have no clue as to why (Problem 1) and here is the test Log
Now I tried to Install OpenFOAM 2.2.0 on my Drive on the Cluster and the mpirun command to run my simulations in parallel is not working (Problem 2), can Some one tell me why this might be happening I tried installing twice the same problem is there

the only difference between OpenFOAM 2.1.0 and 2.2.0 log is that in 2.2.0
it is a no and this is critical !!!!

how to make this an yes

If you require anything else please do let me know.
Thanks for your time and Efforts,
Regards,
Hasan K.J