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[OpenFOAM.org] openfoam-2.2.0 installation on cluster of Redhat 4.1.2-48

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Old   October 26, 2013, 12:08
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Yijiu Jiang
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Quote:
Originally Posted by wyldckat View Post
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:
Code:
which mpirun
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
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Old   October 26, 2013, 12:57
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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
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Old   October 26, 2013, 23:26
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Quote:
Originally Posted by wyldckat View Post
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
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Old   October 27, 2013, 03:14
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OK, first of all, let's do some clean up on the "~/.bashrc" file. Change this:
Code:
# 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
To this:
Code:
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific aliases and functions

module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45
Secondly, when you start a new terminal, does it give you any messages?
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Last edited by wyldckat; October 27, 2013 at 03:15. Reason: Fixed broken [CODE] marker
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Old   October 27, 2013, 08:46
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Quote:
Originally Posted by wyldckat View Post
OK, first of all, let's do some clean up on the "~/.bashrc" file. Change this:
Code:
# 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
To this:
Code:
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific aliases and functions

module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45
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
Code:
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific aliases and functions


module load openmpi-x86_64
source /home/jaq526/OpenFOAM/OpenFOAM-2.2.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc45
What do you think? Is that Ok now to complier OF again?
Last edited by wyldckat; October 27, 2013 at 14:38. Reason: Added [CODE][/CODE]
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Old   October 27, 2013, 14:45
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Quote:
Originally Posted by y_jiang View Post
But there is not any message when I start a new terminal after I did the .bashrc modification.
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 .

Quote:
Originally Posted by y_jiang View Post
What do you think? Is that Ok now to complier OF again?
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:
Code:
./makeParaView -qmake $(which qmake-qt4) > make.pv.log 2>&1
Then package the file "make.pv.log" and attach it as well, so I can confirm if everything is OK.
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Old   October 28, 2013, 10:39
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Quote:
Originally Posted by wyldckat View Post
Code:
./makeParaView -qmake $(which qmake-qt4) > make.pv.log 2>&1
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.
Attached Files
File Type: gz make.log.tar.gz (4.6 KB, 2 views)
File Type: gz make.pv.log.tar.gz (948 Bytes, 1 views)
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Old   October 28, 2013, 16:03
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Hi JYJ,

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

Try running these two commands:
Code:
which qmake-qt4
which qmake
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:
Code:
./makeParaView -qmake $(which qmake) > make.pv.log 2>&1
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
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Old   October 28, 2013, 22:15
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Quote:
Originally Posted by wyldckat View Post
Hi JYJ,

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



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

Code:
You might need to modify the include and library search paths by editing
 QMAKE_INCDIR_X11 and QMAKE_LIBDIR_X11 in /home/jaq526/OpenFOAM/ThirdParty-2.2.0/qt-everywhere-opensource-src-4.6.4/mkspecs/linux-g++-64.
Then, I found the file in /mkspecs/linux-g++-64/qmake.conf and the content is as follow:
Code:
MAKEFILE_GENERATOR    = UNIX
TEMPLATE                = app
CONFIG                  += qt warn_on release incremental link_prl
QT                      += core gui
QMAKE_INCREMENTAL_STYLE = sublib

QMAKE_CFLAGS            = -m64
QMAKE_LFLAGS            = -m64

include(../common/g++.conf)
include(../common/linux.conf)

QMAKE_LIBDIR_X11      = /usr/X11R6/lib64
QMAKE_LIBDIR_OPENGL   = /usr/X11R6/lib64


load(qt_config)
But in our system, there isn't a dir named X11R6 under usr -_-|||
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Old   October 28, 2013, 22:27
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Here is the mkqt.log. You can see the error which I mentioned above.
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File Type: gz mkqt.log.tar.gz (16.5 KB, 2 views)
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Old   October 29, 2013, 18:01
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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
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Old   October 30, 2013, 10:44
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Quote:
Originally Posted by wyldckat View Post
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
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Old   June 10, 2015, 12:53
Default $MPI_ARCH_PATH ...0/platforms/linux64Gcc/openmpi-1.6.3 no yes
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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
Code:
Executing /panfs/panasas01/aero/mk14466/OpenFOAM/OpenFOAM-2.1.0/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               newblue3
OS:                 Linux version 2.6.32-220.23.1.el6.x86_64
-------------------------------------------------------------------------------


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /panfs/panasas01/aero/mk14466/OpenFOAM   yes       yes
$WM_PROJECT_USER_DIR .../aero/mk14466/OpenFOAM/mk14466-2.1.0  no        no
$WM_THIRD_PARTY_DIR  ...ro/mk14466/OpenFOAM/ThirdParty-2.1.0  yes       yes
-------------------------------------------------------------------------------


Checking the OpenFOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR      ...aero/mk14466/OpenFOAM/OpenFOAM-2.1.0  yes  yes  yes

$FOAM_APPBIN         ...-2.1.0/platforms/linux64GccDPOpt/bin  yes  yes  yes
$FOAM_SITE_APPBIN    .../2.1.0/platforms/linux64GccDPOpt/bin  no        no
$FOAM_USER_APPBIN    ...-2.1.0/platforms/linux64GccDPOpt/bin  no        no
$WM_DIR              ...k14466/OpenFOAM/OpenFOAM-2.1.0/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         ...-2.1.0/platforms/linux64GccDPOpt/lib  yes  yes  yes
$FOAM_SITE_LIBBIN    .../2.1.0/platforms/linux64GccDPOpt/lib  no        no
$FOAM_USER_LIBBIN    ...-2.1.0/platforms/linux64GccDPOpt/lib  no        no
$MPI_ARCH_PATH       ...0/platforms/linux64Gcc/openmpi-1.5.3  yes  yes  yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
flex     2.5.35    /usr/bin/flex                                            
gcc      4.4.7     /usr/bin/gcc                                             
gzip     1.3.12    /bin/gzip                                                
tar      1.23      /bin/tar                                                 
icoFoam  2.1.0     ...M/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.
Critical systems ok.

Done
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

Code:
Executing /panfs/panasas01/aero/mk14466/OpenFOAM/OpenFOAM-2.2.0/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               newblue3
OS:                 Linux version 2.6.32-220.23.1.el6.x86_64
-------------------------------------------------------------------------------


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /panfs/panasas01/aero/mk14466/OpenFOAM   yes       yes
$WM_PROJECT_USER_DIR .../aero/mk14466/OpenFOAM/mk14466-2.2.0  no        no
$WM_THIRD_PARTY_DIR  ...ro/mk14466/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      ...aero/mk14466/OpenFOAM/OpenFOAM-2.2.0  yes  yes  yes

$FOAM_APPBIN         ...-2.2.0/platforms/linux64GccDPOpt/bin  yes  yes  yes
$FOAM_SITE_APPBIN    .../2.2.0/platforms/linux64GccDPOpt/bin  no        no
$FOAM_USER_APPBIN    ...-2.2.0/platforms/linux64GccDPOpt/bin  no        no
$WM_DIR              ...k14466/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         ...-2.2.0/platforms/linux64GccDPOpt/lib  yes  yes  yes
$FOAM_SITE_LIBBIN    .../2.2.0/platforms/linux64GccDPOpt/lib  no        no
$FOAM_USER_LIBBIN    ...-2.2.0/platforms/linux64GccDPOpt/lib  no        no
$MPI_ARCH_PATH       ...0/platforms/linux64Gcc/openmpi-1.6.3  no        yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
flex     2.5.35    /usr/bin/flex                                            
gcc      4.4.7     /usr/bin/gcc                                             
gzip     1.3.12    /bin/gzip                                                
tar      1.23      /bin/tar                                                 
icoFoam  2.2.0     ...M/OpenFOAM-2.2.0/platforms/linux64GccDPOpt/bin/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
Base configuration ok.
Critical systems ok.

Done
the only difference between OpenFOAM 2.1.0 and 2.2.0 log is that in 2.2.0
Code:
$MPI_ARCH_PATH       ...0/platforms/linux64Gcc/openmpi-1.6.3  no        yes
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
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