Finding Chaste Dependencies

Running the Chaste configure step

cmake /path/to/Chaste

should find all Chaste dependencies automatically. This should certainly be the case on supported Ubuntu versions, and if you have followed the Install Guides.

This is a troubleshooting page with information for manually setting hints for dependency locations if they are not found automatically, or if you wish to use specific dependency versions when you have multiple versions installed.

Specifying a Compiler#

You can specify a C++ and C compiler by setting the CXX and CC environment variables. eg.

CXX=icpc CC=icc cmake /path/to/source

or

CXX=clang++ CC=clang cmake /path/to/source

Specifying PETSc#

You can specify a PETSc folder and Arch by setting the PETSC_DIR and PETSC_ARCH environment variables. eg.

PETSC_DIR=/path/to/petsc PETSC_ARCH=linux-intel cmake /path/to/source

OR setting the PETSC_DIR and PETSC_ARCH CMake variables. eg.

cmake -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=linux-intel /path/to/source

Once CMake has successfully found and tested the PETSc setup, this find/test setup will not be run on subsequent calls to cmake unless either the PETSC_DIR or PETSC_ARCH CMake variables are changed, or the PETSC_CURRENT variable is set to NO. e.g.

cmake -DPETSC_CURRENT=NO .

Specifying SUNDIALS#

You can specify a SUNDIALS folder by setting the SUNDIALS_ROOT environment variables.

Specifying HDF5#

You can specify a HDF5 folder by setting the HDF5_ROOT environment variables.

Specifying VTK#

You can specify a VTK directory by using the VTK_DIR CMake variable (note: NOT an environment variable). eg.

cmake -DVTK_DIR=/path/to/vtk /path/to/source

Specifying Boost#

You can specify a Boost directory by using the BOOST_ROOT CMake variable (note: NOT an environment variable).

Shell configuration#

You can, of course, configure your machine to set these environment variables automatically in every session. In bash, for example, you can do this by adding export VARIABLE=VALUE to your ~/.bashrc.

For instance, you may like to use clang and a specific PETSc install, so could add the following:

export CXX=clang++
export CC=clang

export PETSC_DIR=/path/to/favourite/petsc
export PETSC_ARCH=linux-gnu