Chaste installation on Centos

There's a historical version of this installation guide too

These are the steps that I followed to install all the Chaste dependencies, run the test pack and build the executable.

Details of the machine are:

Host: compute-lung

Linux version 2.6.32-220.17.1.el6.x86_64 CentOS release 6.2 (Final)

Preliminary

Note: do not install Boost. This Centos comes with Boost 1.41.0 which is too buggy to use with Chaste

yum install scons subversion
yum install eclipse eclipse-cdt eclipse-subclipse subversion-javahl
yum install openmpi openmpi-devel
yum install  gcc-gfortran gcc-c++ valgrind valgrind-openmpi xerces-c-devel xsd zlib-devel
yum install python-lxml python-dateutil


#For rdflib
rpm -ivh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-7.noarch.rpm
yum install python-rdflib
yum install joe


#For Amara
# This is a bit too tricky but I basically used bits and pieces from the Fedora repos

#VTK and CVODE
yum install vtk-devel
rpm -i ftp://rpmfind.net/linux/fedora/linux/releases/17/Everything/x86_64/os/Packages/s/sundials-2.3.0-11.fc17.x86_64.rpm
rpm -i ftp://rpmfind.net/linux/fedora/linux/releases/17/Everything/x86_64/os/Packages/s/sundials-devel-2.3.0-11.fc17.x86_64.rpm

Boost (1.42)

#Install Boost-jam rpm: boost-jam-3.1.18-1.7.x86_64
wget http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz
tar xvfz boost_1_42_0.tar.gz 
cd boost_1_42_0
bjam "-sTOOLS=gcc" --prefix=$HOME/boost install

PETSc (version 3.1)

PETSc 3.1 takes care of downloading, compiling and installing blas, lapack, ((openmpi,)) hdf5, parmetis and hypre

### Really required!
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/

wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.0.0-p8.tar.gz
tar xzvf petsc-3.0.0-p8.tar.gz 
rm petsc-3.0.0-p8.tar.gz
cd petsc-3.0.0-p8/
export PETSC_DIR=`pwd`


export PETSC_ARCH=linux-gnu
./config/configure.py  --download-f-blas-lapack=yes --with-mpi-dir=/usr/lib64/openmpi --download-hdf5=yes --download-parmetis=yes --download-hypre=yes -with-x=false --with-clanguage=cxx
make all

export PETSC_ARCH=linux-gnu-opt
./config/configure.py  --download-f-blas-lapack=yes --with-mpi-dir=/usr/lib64/openmpi --download-hdf5=yes --download-parmetis=yes --download-hypre=yes -with-x=false --with-clanguage=cxx --with-debugging=0
make all