Maths Institute Install Guide

The Maths Institute already most of the packages listed in InstallGuides/DebianEtch installed, so begin by connecting to the Chaste repository as described in the DeveloperInstallGuide.

XSD

Although the Maths Institute system has XSD installed, it seems to be missing some required files, which can result in a build error message. Therefore install a full version of XSD in the directory /scratch/chaste by opening a terminal and typing the following.

bash
export base="/scratch/chaste"

cd $base

# For 32 bit:
wget http://codesynthesis.com/download/xsd/2.3/linux-gnu/i686/xsd-2.3.1-i686-linux-gnu.tar.bz2
tar -xjf xsd-2.3.1-i686-linux-gnu.tar.bz2

# For 64 bit you might need to do this instead:
#wget http://codesynthesis.com/download/xsd/2.3/linux-gnu/x86_64/xsd-2.3.1-x86_64-linux-gnu.tar.bz2
#tar -xjf xsd-2.3.1-x86_64-linux-gnu.tar.bz2

cd $base/src
wget http://www.apache.org/dist/xerces/c/2/sources/xerces-c-src_2_8_0.tar.gz
tar -zxf xerces-c-src_2_8_0.tar.gz
export XERCESCROOT=$base/src/xerces-c-src_2_8_0
cd $XERCESCROOT/src/xercesc/
./runConfigure -plinux -cgcc -xg++ -P$base
make
make install

Intel Compiler

If you need to install the Intel compiler, follow the DeveloperInstallGuide. Install it in the directory /scratch/chaste, since that's the intel_path that is in the maths.py configuration script.

PETSc and MPI

The Maths Institute has PETSc 2.3.2-p6 installed. In your hostconfig file, set petsc_2_3_path to /usr/lib/petsc/.

Download MPICH from ​ftp://ftp.mcs.anl.gov/pub/mpi/mpich.tar.gz , unpack and do

cd mpich-1.2.7p1
./configure --prefix=$base -with-comm=shared --with-device=ch_shmem --enable-sharedlib --disable-f77
make
cd examples/test/
make testing
cd ../..
make install
# You may now remove the mpich-1.2.7p1 folder if you wish.

Hdf5

Type the following:

export base="/scratch/chaste"
cd $base/src
wget ftp://ftp.hdfgroup.org/HDF5/prev-releases/hdf5-1.6.6/src/hdf5-1.6.6.tar.gz
tar -zxf hdf5-1.6.6.tar.gz
cd hdf5-1.6.6
export CC=mpicc 
./configure --enable-parallel --prefix=$base/hdf5
make
cd test
make check
cd ../testpar
make check
cd ..
make install

Install CVODE

As InstallCvode, but use --prefix=$base

Install parMETIS

As InstallParMetis, but do cd $base instead of cd $HOME. The Maths Institute doesn't have MPI installed, so there is no "mpi.h" in /usr/include. To tell parMETIS to look into where you installed MPI (see above), prior to doing make you should edit Makefile.in as follows: add -I/scratch/chaste/mpich-1.2.7p1/include to the line starting INCDIR and add -L/scratch/chaste/mpich-1.2.7p1/lib to the line starting LIBDIR.

Eclipse

Lastly, go to Window->Preferences->C/C++->Editor->Appearance and select "Insert spaces for tabs". This ensures nice tabbing.

(Also, see extra options in SetupEclipse)