OpenFOAM and FOAM-extend on Your Own Laptop
Table of Contents
Installation and updating of Ubuntu
14.04 LTS in Virtual Box (under Windows 7, in this case):
Install OpenFOAM-2.4.x Debug version
(after the above, i.e. with OpenFOAM-2.4.x installed)
Install Emacs, ddd, Python, Numpy,
SciPy, Matplotlib, Gnuplot, PyFoam
Install FOAM-extend-3.1 (including
PyFoam, swak4Foam etc.)
The teaching is designed so
that you should follow the steps I do on a computer. It is highly recommended
that you install the software on your own laptop so that you are independent.
The Linux commands below are written for bash shell.
By following the
instructions below, you should be able to install Ubuntu 14.04 LTS,
OpenFOAM-2.4.x (one optimal and one debug version), FOAM-extend-3.1, PyFoam, Python packages, Gnuplot
etc., and later perhaps some additional useful things that we will use in the
course. We will pull the git source and compile from
scratch, since we will then get access to updates and bug fixes. OpenFOAM-2.4.0
can also be installed as a package, which is much faster, but gives less
control in my opinion (http://openfoam.com/download/ubuntu.php). Feel free to
try it out if you like – you can have both that version and the git versions installed at the same time!
Note that I am
(unfortunately) using Word to generate this web page, which means that Word
sometimes decides to change some characters to other characters that look the
same, but aren’t (e.g. – is not the same as - or -- and “ is not the same as
"). I think that I have fixed this everywhere, but you never know. That is
one reason for copy-pasting single rows rather than multiple rows, and check
that all went well. Another reason is that some lines will require you to press
a key at some point, such as the “sudo apt-get”
lines. Let me know if you run into problems, and I’ll help you.
This
section takes about 1.5 hour to complete.
Download Ubuntu 14.04 LTS
(note that you can get it for free by setting your contribution to zero):
http://www.ubuntu.com/download, get Ubuntu Desktop (in my case 64 bit), save iso-file
(Optional: burn iso to CD (if you do, make sure to
burn it as iso, to make the CD bootable!))
You can use VirtualBox to install Linux and OpenFOAM
in your current OS. It is recommended to use the official version downloadable
from the Sun web page, https://www.virtualbox.org/wiki/Downloads.
If you are installing VirtualBox in Ubuntu the
version that is installed through the package manager does not support all options
(e.g. the USB controllers), since that version omits some proprietary software.
If you already have Virtualbox
OSE installed from the Ubuntu repositories, uninstall it before installing the
.deb file from Oracle’s website. See also: http://openfoam.com/resources/windows.php.
After installing VirtualBox, start it and:
Create new virtual disk:
Click on New
Name: Ubuntu 14.04 LTS
Operating System: Linux
Version: Ubuntu (in my case: “(64 bit)”)
Base memory: 2048MB (25% of total on the machine in my case, minimum 2GB
required for 64-bit operating system)
Create a virtual hard drive now
VDI
Fixed size, 30GB (2GB is enough to just test one OpenFOAM
installation)
Settings can be changed later, using "settings"
Click on Create
Install Ubuntu on the
virtual disk:
Double-click on the virtual disk you just created
In the pop-up window, click on the icon “Choose a virtual optical disk file”,
and browse to the downloaded Ubuntu iso-file
Ubuntu should initialize in a window named “Ubuntu 14.04 LTS [Running] – Oracle
VM VirtualBox”.
At the top of the window there may be some information about “Auto capture
keyboard” and “mouse pointer integration”. Just click the x to hide the
comments.
Click on Install Ubuntu and choose your specific settings
I recommend that you tick: Download updates while installing, and Install this
third-party software
When it asks you if it should erase the whole disk, it refers to the virtual
disk you have just created in VirtualBox, and not
your Windows disk. NOTE: MAKE SURE THAT THE INSTALLATION PROCESS HAPPENS IN A
SEPARATE WINDOW, AS DESCRIBED ABOVE! YOU SHOULD BE ABLE TO READ THAT “This
computer currently has no detected operating systems. What would you like to
do?”. If it says that you already have an operating system, you are probably
trying to install Ubuntu directly on your computer and not through VirtualBox. If so, make sure that you do it through VirtualBox – otherwise you may risk to delete your old
operating system.
Restart when asked (just click on the button that pops up). You may need to
press Enter at some point.
To the left of your Ubuntu window, there should be an icon which says ‘Search
your computer and online resources’ when you move the pointer over it. Use it
to search for Software Updater, and use the Software Updater to install recent
updates to your Ubuntu installation. Restart again (just click on buttons).
I had some problems that
the desktop did not resize. This was solved by clicking on “Devices/Insert
Guest Addition CD image”, and restarting the virtual machine.
Occasionally, the Guest Addition may not be possible to mount and you get a
pop-up window asking you if you want to force unmounts. This may not work. In
Ubuntu, Open the Disks utility (click on “Search your computer and online
sources”, in the left bar of Ubuntu, and enter “disks”), Under CD/DVD: mount
the Guest Addition and then eject it. After that it should be possible to Insert
it again, as explained above.
It is also convenient to be able to cut-and-paste between windows and Ubuntu:
At the top of the VirtualBox window, do
Devices/Shared Clipboard/Bidirectional
There is a risk that the terminal windows will time-out during ssh to some other computer. To avoid this behavior, you can
do the following (you need to give your root password):
sudo echo "ServerAliveInterval
60" >> /etc/ssh/ssh_config
This
section takes about 6 hours to complete
Straight-forward according
to http://www.openfoam.org/download/git.php
(for 2.4.x, later in http://www.openfoam.org/archive/2.4.0/download/)
See also: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.4.0/Ubuntu
Open a
terminal window:
CTRL-ALT-T
type (copy-paste from homepage, line-by-line):
mkdir $HOME/OpenFOAM
cd $HOME/OpenFOAM
sudo su - #Makes you root user, so that you can run apt-get directly and without
entering password
apt-get install git-core #You may have to type Y at some
point(s) when doing these commands
apt-get install build-essential flex bison cmake zlib1g-dev libopenmpi-dev openmpi-bin gnuplot libreadline-dev libncurses-dev libxt-dev
apt-get install qt4-dev-tools libqt4-dev libqt4-opengl-dev freeglut3-dev libqtwebkit-dev
apt-get install libscotch-dev libcgal-dev
exit #Stop being root user
git
clone git://github.com/OpenFOAM/OpenFOAM-2.4.x.git
wget
http://downloads.sourceforge.net/project/foam/foam/2.4.0/ThirdParty-2.4.0.tgz
You may have to press Enter here, to get the prompt back.
tar xzf ThirdParty-2.4.0.tgz
rm ThirdParty-2.4.0.tgz
mv ThirdParty-2.4.0 ThirdParty-2.4.x
echo "alias OF24x='. $HOME/OpenFOAM/OpenFOAM-2.4.x/etc/bashrc'" >>
$HOME/.bashrc
Some
checks, before proceeding:
gcc --version
#Gives 4.8.4. Required: 4.5.0. Ok!
flex --version
#Gives 2.5.35. Seems to have worked ok!
Close the terminal window,
open a new one:
CTRL-ALT-T
and continue:
OF24x
foam
The following line takes about 3h. You can do CTRL-C and continue later,
by starting again from where you opened a new terminal window above
./Allwmake
./Allwmake>& log_Allwmake
#Second time is fast, just to easier check the log file for possible errors
(search for “rror”) - in my case none.
rm log_Allwmake
Compile ParaView-4.1.0
(takes 2.5h):
qmake --version #Gives Qt version 4.8.6. Required: 4.7.2 or newer. Ok!
cmake --version #Gives 2.8.12.2. Required:
2.8.8 or newer. Ok!
cd $WM_THIRD_PARTY_DIR
./makeParaView4
#This is what takes 2.5h
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
wmSET
./Allwclean
./Allwmake
Test the installation:
CTRL-ALT_T #To open
an new terminal window
OF24x
mkdir -p $FOAM_RUN
run
cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity .
cd cavity
blockMesh
icoFoam
paraFoam
This
section takes about 4h to complete.
Compile Debug version,
without recompiling ThirdParty:
echo "alias
OF24xDebug='. $HOME/OpenFOAM/OpenFOAM-2.4.x/etc/bashrc
WM_COMPILE_OPTION=Debug'" >> $HOME/.bashrc
Open new terminal window
CTRL-ALT_T
OF24xDebug
cd $WM_THIRD_PARTY_DIR/platforms
ln -s linux64GccDPOpt linux64GccDPDebug
foam
./Allwmake
#This takes 4 hours
./Allwmake>& log_Allwmake
#Second time is fast, just to easier check the log file for possible errors
(search for “rror”) - in my case none.
rm log_Allwmake
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers
Don’t do wmSET since it will not pick Debug
version – see alias wmSET! Instead:
OF24xDebug
./Allwclean
./Allwmake
Test the installation:
CTRL-ALT_T #To open
an new terminal window
OF24xDebug
mkdir -p $FOAM_RUN
run
rm -r cavity
cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity .
cd cavity
blockMesh
icoFoam
paraFoam
This takes 10min to complete.
We will do debugging with gdb and Emacs. Emacs needs to be installed:
sudo apt-get install emacs24
You can
also try ddd for debugging (not available at
Chalmers):
sudo apt-get install ddd
Python-related packages
sudo apt-get install python
python-dev python-matplotlib python-numpy python-scipy
Gnuplot
sudo apt-get install gnuplot
xmgrace
sudo apt-get install grace
For
OpenFOAM-2.4.x, the PyFoam package is not included
(which it is for FOAM-extend).
We will
follow the installation instructions for PyFoam at http://openfoamwiki.net/index.php/Contrib_PyFoam
There was a
problem installing version 0.6.5, so I switched back one version.
Condensed
installation instructions:
mkdir $HOME/OpenFOAM/linuxSrc
cd $HOME/OpenFOAM/linuxSrc
wget http://openfoamwiki.net/images/3/3b/PyFoam-0.6.4.tar.gz
tar xzf
PyFoam-0.6.4.tar.gz
rm
PyFoam-0.6.4.tar.gz
cd PyFoam-0.6.4
Install as
regular user (recommended):
python setup.py install --prefix=$HOME/OpenFOAM/PyFoam-0.6.4
echo "alias PF064='export PYTHONPATH=\$HOME/OpenFOAM/PyFoam/PyFoam-0.6.4/lib/python2.7/site-packages:\$PYTHONPATH;
export PATH=\$HOME/OpenFOAM/PyFoam-0.6.4/bin:\$PATH'"
>> $HOME/.bashrc
Open a new
window and type (<TAB> refers to the tab key):
PF064
pyFoam<TAB><TAB>
You will
see numerous pyFoam commands that can be used to help
you use OpenFOAM efficiently.
You should
also consider installing swak4foam: http://openfoamwiki.net/index.php/Contrib/swak4Foam
“A library that
combines the functionality of groovyBC and funkySetFields: it offers the user
the possibility to specify expressions involving the fields and evaluates them.
This library offers a number of utilities (for instance funkySetFields to
set fields using expression), boundary conditions (groovyBC to
specify arbitrary boundary conditions based on expressions) and function
objects that allow doing many things that would otherwise require programming.”
The
foam-extend (foam-extend.org)
fork has some features that are not in OpenFOAM-x.x.x,
such as the GGI interface. If you do not need those features, you do not have
to follow this section.
This
section takes about 5h or more – leave the computer over-night (where this
message is repeated).
For other
installation instructions, see also:
·
http://sourceforge.net/p/openfoam-extend/wiki/Home/
·
http://openfoamwiki.net/index.php/Installation/Linux/foam-extend-3.1
·
And
later the file $WM_PROJECT_DIR/doc/buildInstructions/Ubuntu/Ubuntu_14.04,
also located here:
https://sourceforge.net/p/openfoam-extend/foam-extend-3.1/ci/master/tree/doc/buildInstructions/Ubuntu/Ubuntu_14.04
The
compilation procedure is actually very simple, but I modify it slightly to use
more system installations. I have included some information that is commented,
if anyone would like to do other modifications.
Open new
terminal window and type (line-by-line, since you have to type your password on
the “sudo” lines)
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install git-core build-essential binutils-dev flex zlib1g-dev qt4-dev-tools libqt4-dev
sudo apt-get install libncurses5-dev libiberty-dev libxt-dev rpm mercurial graphviz openmpi-bin libopenmpi-dev cmake
mkdir $HOME/foam
cd $HOME/foam
git clone
git://git.code.sf.net/p/openfoam-extend/foam-extend-3.1 foam-extend-3.1
cd foam-extend-3.1
This part is where I do some changes
to the installation procedure, to use more system installed software in Ubuntu
14.04. You can skip this if you like. But then you will not have Paraview compiled, and you will waste some disk space on
software that may be installed in the system. Instead of compiling Paraview, you can also install it with “sudo
apt-get paraview”, but then you don’t get the
foam-extend-specific reader.
####################################################################
#
# Create a prefs.sh file
cp etc/prefs.sh-EXAMPLE
etc/prefs.sh
# Make the sourcing less chatty
sed
-i
s/"FOAM_VERBOSE=1"/"FOAM_VERBOSE="/g etc/prefs.sh
# Use openmpi 1.6.5 as supplied by Ubuntu
14.04
sed -i
s/"#export WM_MPLIB=SYSTEMOPENMPI"/"export
WM_MPLIB=SYSTEMOPENMPI"/g etc/prefs.sh
sed -i
s/"#export OPENMPI_DIR=path_to_system_installed_openmpi"/"export
OPENMPI_DIR=\/usr"/g etc/prefs.sh
sed -i
s/"#export OPENMPI_BIN_DIR=\$OPENMPI_DIR\/bin"/"export
OPENMPI_BIN_DIR=\$OPENMPI_DIR\/bin"/g etc/prefs.sh
# Use Qt 4.8.6 as provided by Ubuntu 14.04
(instead of 4.8.5, in ThirdParty)
sed -i
s/"#export QT_DIR=path_to_system_installed_qt"/"export
QT_DIR=\/usr"/g etc/prefs.sh
sed -i
s/"#export QT_BIN_DIR=\$QT_DIR\/bin"/"export
QT_BIN_DIR=\$QT_DIR\/bin"/g etc/prefs.sh
# Use cmake 2.8.12.2 as provided by Ubuntu
14.04 (instead of 2.8.12, in ThirdParty)
sed -i
s/"( rpm_make -p cmake"/"#(
rpm_make -p cmake"/g ThirdParty/AllMake.stage1
# Compile and install bison-2.7 from the ThirdParty
packages.
sed -i
0,/"#( rpm_make -p bison-2.7"/s//"( rpm_make -p bison-2.7"/ ThirdParty/AllMake.stage1
#
####################################################################
See the etc/prefs-sh-EXAMPLE file for more
examples, e.g.:
#Tell the compiler to use the
number of cores you have available (if you uncomment the line and change the
number 4 to what you have)
#echo "export WM_NCOMPPROCS=4" >>
etc/prefs.sh
#Use the system installation of paraview (if you uncomment the following lines and make
sure that you have Paraview installed in your system)
#sed -i
s/"#export PARAVIEW_SYSTEM=1"/"export PARAVIEW_SYSTEM=1"/g
etc/prefs.sh
#sed -i
s/"#export PARAVIEW_DIR=path_to_system_installed_paraview"/"export
PARAVIEW_DIR=\/usr "/g etc/prefs.sh
#sed -i
s/"#export PARAVIEW_BIN_DIR=\$PARAVIEW_DIR\/bin"/"export
PARAVIEW_BIN_DIR=\$PARAVIEW_DIR\/bin"/g etc/prefs.sh
#sed -i
-e 's=\.OpenFOAM=\.foam=' bin/paraFoam
####################################################################
Set up the foam-extend-3.1
environment:
echo "alias f31='.
\$HOME/foam/foam-extend-3.1/etc/bashrc'"
>> $HOME/.bashrc
Close the terminal window and open a new one (doing:
CTRL-ALT_T) and type:
f31
Compile (this takes 5h or more – leave the computer
over-night):
foam
./Allwmake.firstInstall #Wait 5h!
Again, to make sure that all went well (takes some minutes):
./Allwmake.firstInstall
>& log&
Look for errors in the log file. There should be none.
It should say "up to date" on each
application/library
Test the installation:
CTRL-ALT_T #To open
an new terminal window
f31
mkdir -p $FOAM_RUN
run
cp -r $FOAM_TUTORIALS/incompressible/icoFoam/cavity .
cd cavity
blockMesh
icoFoam
paraFoam
When running paraFoam you
may get some messages in the terminal window and in a pop-up-window. Just move
that pop-up-window out of sight and ignore the messages.