Jonathan's installation on his new laptop

NB: This is outdated - the Ubuntu package is now the recommended approach.

Just recording my own notes for now. I can tidy it up if it would be helpful for others.

Ubuntu packages

sudo aptitude install scons subversion
sudo aptitude install joe xemacs21-gnome-nomule

In synaptic:

MPI

I've been getting odd errors trying to use Ubuntu's MPI, even after making sure it used the mpich version: 

sudo /usr/sbin/update-alternatives --set mpi /usr/lib/mpich-shmem/include

So I've installed the patched MPI from InstallPetscAndMpi, using 

./configure --prefix=$HOME/src/mpi --with-comm=shared --with-device=ch_shmem --disable-f77 --enable-sharedlib && make && make install

(I may experiment with the --disable-cxx --without-mpe flags.)

However, this still gives errors when compiling with shared libraries. I've now figured out that I can use Ubuntu's MPI without problems, provided I don't try to build shared Chaste libraries, so it looks like the root cause of the errors is the same.

PETSc

wget ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-2.3.3-p15.tar.gz
tar -zxf petsc-lite-2.3.3-p15.tar.gz
cd petsc-2.3.3-p15
export PETSC_DIR=`pwd`
./config/configure.py --with-mpi --with-x=false -PETSC_ARCH=linux-gnu --with-clanguage=cxx
make all
./config/configure.py --with-mpi --with-x=false -PETSC_ARCH=linux-gnu-opt --with-clanguage=cxx --with-debugging=0
make all

Note: if using your own MPI install, specify --with-mpi-dir=/path/to/mpich instead of --with-mpi.

XSD

Unfortunately, whilst Intrepid does have a package for this (xsdcxx) it's a different version from that used by Chaste. 

wget http://codesynthesis.com/download/xsd/2.3/linux-gnu/x86_64/xsd-2.3.1-x86_64-linux-gnu.tar.bz2
tar -jxf xsd-2.3.1-x86_64-linux-gnu.tar.bz2
# Ensure the xsd command is on your path, or add it to your hostconfig tools
ln -s /home/jonc/src/xsd-2.3.1-x86_64-linux-gnu/bin/xsd ~/bin/xsd

Other software & settings