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)

• InstallXmlTools

• InstallHdf5 (for file output)

• InstallParMetis (for mesh partitioning)

• InstallCodegen -- chaste_codegen itself is distributed via pypi, but you'll need to install its dependencies

• SetEnvironmentVariables

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.

• InstallSubversionJavahl

• InstallJava

• InstallGuides/EclipsePlugins

• SetupEclipse

Accessing the code

• ChasteGuides/AccessCodeRepository.

• 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