Installing Chaste without root permissions
I'm trying to install all the necessary items without having root permissions on the machine in question. It's going well so far, so I thought I'd better document what I've done before I forget it...
Note that my machine has a local build of gcc version 4.1.1, so this may introduce some differences for you.
Note also that these instructions assume you are using the bash shell. If your prompt ends in a dollar symbol, you're probably OK.
Top Tip: whenever you add anything to the .bashrc file then also type it in to the terminal (.bashrc is run on login)
Work out where to install
There probably isn't enough space on your network filestore, and that'll be a bit slow anyway, so much better if you can install everything on the local disk. I have a folder /home/scratch/jonc that I can write to, so I'm installing everything in there. Alter paths to suit your circumstances:
export base="/home/scratch/jonc"
Install Boost
Download version 1.33.1 from http://sourceforge.net/project/showfiles.php?group_id=7586&package_id=8041
Unpack somewhere sensible, configure, and install:
cd boost-1.34.0 ./configure --prefix=$base --with-libraries=serialization make install
Install XSD
I cheat for this by copying XSD itself from one of the Chaste machines. Installing Xerces is rather more complicated!
scp -r chaste@userpc44.comlab.ox.ac.uk:xsd-2.3.1-i686-linux-gnu/ $base/ 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 gmake gmake install
Install scons
Download the latest stable tarball from http://www.scons.org
Extract and cd into the folder. Run
python setup.py install --prefix=$base
You'll need to add $base/bin to your PATH. Perhaps add the following to your ~/.bashrc
export PATH=$base/bin:$PATH
At some point you'll need to add the folder $base/lib to LD_LIBRARY_PATH, so may as well add that to your ~/.bashrc now too:
export LD_LIBRARY_PATH=$base/lib
Install Java
Install J2SE (Update 6 at time of writing) from http://java.sun.com/j2se/1.5.0/download.jsp
Make sure to choose the "Linux self-extracting file" version.
Run the downloaded executable from within $base.
Now add the following to your ~/.bashrc
export PATH=$base/jdk1.6.0_10/bin:$PATH export JAVA_HOME=$base/jdk1.6.0_10
Install Subversion and JavaHL
JavaHL is used by subclipse, the Eclipse interface to subversion. It seems to be more reliable than the pure Java interface.
Download and unpack the latest subversion (1.3 when this was written) from http://subversion.tigris.org/
cd subversion-1.3.0 ./configure --with-ssl --enable-javahl --disable-mod-activation --prefix=$base make make install
During this process svn might request the install of apr and apr-utils, it gives you instructions on how to get them (using svn - pretty nifty) and gives instructions on how to carry on with the install.
Install Eclipse
Download the latest stable version from http://www.eclipse.org/ and unpack it in $base. I used 3.1.2.
You may want to add $base/eclipse to your PATH as well.
To clear cached subversion credentials when starting eclipse, try the following:
cd $base mv eclipse/eclipse eclipse/eclipse.exec
Then create a file $base/eclipse/eclipse with the contents:
#!/bin/bash /bin/rm -f ~/.subversion/auth/svn.simple/* /bin/rm -f $base/eclipse/configuration/org.eclipse.core.runtime/.keyring exec $base/eclipse/eclipse.exec
And make it executable:
chmod a+x eclipse/eclipse
Run eclipse and when prompted, set your workspace to $base/eclipse/workspace
Install Eclipse Plugins
Run eclipse and go to Help -> Software Updates -> Find and Install. Select "Search for new features to install". Click on "New Remote Site" a few times to add the following:
- CDT: http://download.eclipse.org/tools/cdt/releases/eclipse3.1
- subclipse: http://subclipse.tigris.org/update_1.0.x
- (optional) PyDev: http://pydev.sf.net/updates/
Then click Finish to search for updates. You probably want to install the latest versions of everything found under those sites.
Set Editor preferences
Go to Window->Preferences->C/C++->Editor and under the Appearance tab select "Insert spaces for tabs".
Set Pydev preferences
Go to Window->Preferences and expand the Pydev section. You'll want to change at least the 'Interpreter - Python' subsection to add a new interpreter /usr/bin/python.
Install Valgrind
Download the latest stable tarball (3.1.0 at time of writing) from http://valgrind.org/downloads/
Unpack and cd into the resulting directory. Then run
./configure --prefix=$base make make install
Install PETSc and MPI
Download MPICH from ftp://ftp.mcs.anl.gov/pub/mpi/mpich.tar.gz , unpack and do
cd mpich-1.2.7p1 ./configure --prefix=$base -with-comm=shared --with-device=ch_shmem --enable-sharedlib --disable-f77 make cd examples/test/ make testing cd ../.. make install # You may now remove the mpich-1.2.7p1 folder if you wish.
PETSc 2.3.1 seems to work without the workarounds needed for 2.2.1:
wget ftp://ftp.mcs.anl.gov/pub/petsc/petsc-2.3.1.tar.gz tar xvfz petsc-2.3.1.tar.gz rm petsc-2.3.1.tar.gz cd petsc-2.3.1-p19/ export PETSC_DIR=`pwd` ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=$base --with-x=false -PETSC_ARCH=linux-gnu --with-clanguage=cxx make all ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=$base --with-x=false --with-debugging=0 -PETSC_ARCH=linux-gnu-opt --with-clanguage=cxx make all
To avoid compiler warnings (which the Chaste build turns into errors) apply the patch available from InstallPetscAndMpi:
cd $base/include/mpi2c++ patch -p3 <../../mpi.patch
Actually, I think this is redundant now, as the build is configured to ignore warnings in 'system' libraries.
Install HDF5
As InstallHdf5, but use --prefix=$base
Install CVODE
As InstallCvode, but use --prefix=$base
Install parMETIS
As InstallParMetis, but do cd $base instead of cd $HOME