Installing (or reinstalling) with Ubuntu

NB: this page is obseleted by the InstallGuides/UbuntuPackage.

If necessary, save the home area somewhere temporarily

# scp -r -C /home/ chaste@userpc58:home_userpc44
# rsync -avz /home/ chaste@userpc58:home_userpc44
[root@userpc59 ~]# rsync -avz /home/ chaste@chaste-bob:home_userpc59
[root@userpc60 ~]# rsync -avz /home/ chaste@chaste-bob:home_userpc60

Install from CD (Ubuntu 8.04 LTS i386 or x86_64). I thought about putting /home on a separate partition to facilitate future re-installs, but decided that this was more effort than the potential benefit warranted.
Put in network setting for fixed IP
Create bob Unprivileged user (on userpc44) with random password
- Copy bob's .ssh/authorized_keys2 from the server and check that svn@chaste.comlab is able to log in with no password
- Copy bob's home area
```
bob@chaste-bob:~$  rsync -avz /home/bob/ bob@userpc44
```
Changes to software repositories (via System->Administration->Software Sources)
- Add 3rd party software

Add Medibuntu (for acroread)

 echo "deb http://packages.medibuntu.org/ hardy free non-free" | sudo tee -a /etc/apt/sources.list
 wget -q http://packages.medibuntu.org/medibuntu-key.gpg -O- | sudo apt-key add - && sudo apt-get update

Things to possibly install

sudo aptitude install xorg-driver-fglrx #For ATI graphics card
# Then do System->Administration->Hardware Drivers

Things to install

sudo aptitude -y install acroread #PDFs
sudo aptitude -y install openssh-server xauth      #Logging in and x-forwarding
sudo aptitude -y install eclipse-cdt               #Eclipse and C++ IDE
sudo aptitude -y install subversion scons          #Subversion and Scons
sudo aptitude install joe                          #Simple editor "jmacs"
sudo aptitude -y install libsvn-javahl             #javahl for subclipse
sudo aptitude -y install sun-java5-jdk             #Decent Java for using javahl
sudo aptitude install libmozillainterfaces-java    #For Eclipse's lightweight integrated browser
sudo aptitude install g++                          #Gnu C++ compiler - needs to be there before build MPI
sudo aptitude -y install g++-4.1                   #For Intel compiler back-compatibility
sudo aptitude -y install libboost-serialization-dev  libxerces27-dev # For libraries and headers
sudo aptitude install ia32-libs                    #So we can run 32-bit binaries (like tetgen/triangle)
sudo aptitude install screen                       #Helpful for running long command-line stuff over ssh
sudo aptitude -y install lapack3-dev atlas3-base-dev # Lapack and blas
sudo aptitude -y install libgoogle-perftools-dev graphviz # Google profiler
sudo aptitude install gdb                          #Debugger
sudo aptitude install gawk                         #For mpi/sbin/cleanipcs
sudo aptitude install valgrind                     #For memcheck
sudo aptitude -y install meld terminator           #Graphical diff and split-screen terminal
sudo aptitude install xtightvncviewer              #Useful for logging into remote machines
sudo aptitude install libstdc++5                   #Needed for tetgen runtime
sudo aptitude install libgmp3c2                    #Needed for ndiff runtime
sudo aptitude -y install emacs gnuplot octave3.0   #Useful tools
sudo aptitude install libglu1-mesa-dev libfltk1.1-dev libpng12-dev #Needed to recompile meshalyzer
sudo aptitude install mencoder mplayer             #mplayer movie player
sudo aptitude install lib32g2c0                    #for tetview to run on a 64bit machine
sudo aptitude -y install gfortran                  #Fortran compiler for use with libraries linked to Imperial adaptivity library

Edit /etc/hostname to userpcxx.comlab.ox.ac.uk (for Scons and Intel checks)
Things like icc don't like /bin/sh -> dash, they prefer bash
```
sudo dpkg-reconfigure dash
```

Copying things back (not to the home area, but somewhere where they can be read)

chaste@userpc44:~$ rsync -avz chaste@userpc58:home_userpc44 old_home_areas
chaste@userpc59:~$ rsync -avz chaste@chaste-bob:home_userpc59 old_home_areas
chaste@userpc60:~$ rsync -avz chaste@chaste-bob:home_userpc60 old_home_areas

Note: if you are using the cell_based visualiser (written in java) and it doesn't compile, compiles with warnings or doesn't run, it may be because the Sun java compiler is not installed or not being used. See #752.
```
sudo aptitude install sun-java5-jdk
sudo update-java-alternatives -s java-1.5.0-sun
```

* For PyCml (see InstallPyCml)

sudo aptitude install python-dev
sudo aptitude install expat libexpat1-dev
sudo aptitude -y install python-setuptools
sudo easy_install "Amara==1.2.0.2"
sudo aptitude -y install python-librdf