Developer Install Guide
The easiest ways to install Chaste are
- On Ubuntu - use the Ubuntu .deb package
- Other Linux systems - try following the minimal instructions on InstallGuide
- Non-Linux/Unix systems - install a virtual machine (e.g. using VirtualBox) running Ubuntu Linux, and install the Chaste package
Then see the section on checking out the code (below), and optional or optimised-code-related dependencies.
If you encounter any problems, or have an unusual setup, the following material may be useful.
InstallGuides/DependencyVersions lists the different versions of the dependencies that we test, know to work, think will work, won't work etc.
The main instructions on this page assume you are setting up a machine identical to the core Chaste development machines. We also have guides for a variety of other situations that the Chaste team or users have tried, listed at InstallGuides. Note that these may not be up-to-date, so some familiarity with installing software on Linux-like systems may be required.
NB: When creating new install guides, please name the page like 'InstallGuides/GuideName', so that it gets included in the public portion of the wiki.
Mandatory for running Chaste
All users of the source code, whether on a desktop, server or HPC, should ensure all of the below items are present.
- Install an operating system. The core developer machines currently use Ubuntu 10.04 (see InstallGuides/DeveloperUbuntuReinstall?). If you do choose Ubuntu then follow Ubuntu .deb package. The below instructions should work for other flavours of Linux. Previous installs were:
- InstallFedoraCore -- not needed on the Fedora Core 6 install
- InstallingFromRedHatFedoraCoreSixDvd
- InstallIntelCompiler -- technically not needed to run Chaste but used for the best performance
- InstallPetscAndMpi and/or InstallPetscAndMpiForProductionBuild (which requires InstallIntelCompiler).
- InstallBoost -- not needed on the new (Ubuntu / Fedora Core 6) installs
- InstallScons (our build framework)
- InstallHdf5 (for file output)
- InstallParMetis (for mesh partitioning)
- InstallCodegen -- chaste_codegen itself is distributed via pypi, but you'll need to install its dependencies
Highly recommended optional libraries
- InstallCvode -- (fast and accurate ODE solver for cell_based and single-cell-cardiac simulations)
For development machines
We use the following for development machines, but these can be skipped for servers and HPC installations that use a command-line interface to Chaste.
Accessing the code
- CheckoutUserProject -- if you already have or want to create a user project.
Optional (not needed to run the code)
- Testing
- InstallValgrind -- only needed for memory testing, not needed on the new (Ubuntu / Fedora Core 6) installs
- InstallGooglePerformanceTools -- for profiling using Google's tools
- InstallTextTest -- for running acceptance tests of the Chaste executable
- Visualization
- InstallParaview -- VTK visualizer
- InstallVtkStatic -- special instructions for making with static libraries
- InstallMeshalyzer -- for visualising cardiac simulations
- InstallInventor -- for visualisation in 3D (of cell_based simulations)
- InstallMplayer -- movie player
- Optional/experimental additions
- InstallAdaptivityLibrary -- for running adaptive meshing simulations (sequentially)
- Installing HYPRE/MUMPS with PETSc 3 -- installing the AMG preconditioner HYPRE or the direct solver MUMPS
Historical items, no longer needed
- InstallTetgenAndTetview -- now included in Chaste source.
- InstallTriangle -- now included in Chaste source.
- InstallNdiff -- used to be used for comparing results files to a tolerance
- InstallMetis -- superseded by parMETIS.
- InstallingDealii -- not needed unless you wish to use the dealii project