Chaste Dependency Modules

Utility scripts for installing Chaste dependencies as Environment Modules.

Usage

1. Install Environment Modules

Environment Modules enables switching between software versions by reconfiguring the shell environment.

Installation on Ubuntu:

apt-get install environment-modules
source /etc/profile.d/modules.sh

See Installing Modules on Unix for more details.

2. Prepare modulefiles location

Modulefiles are recipes for configuring the shell environment to access specific software versions. Environment Modules uses modulefiles from locations on MODULEPATH.

MODULES_DIR=${HOME}/modules
mkdir -p ${MODULES_DIR}/modulefiles
module use ${MODULES_DIR}/modulefiles
echo "module use ${MODULES_DIR}/modulefiles" >> ${HOME}/.bashrc

The command module use directory prepends directory to MODULEPATH.

3. Install Chaste dependencies

./install_xsd.sh --version=4.0.0 --modules-dir=${MODULES_DIR}
./install_xercesc.sh --version=3.2.1 --modules-dir=${MODULES_DIR}
./install_sundials.sh --version=5.8.0 --modules-dir=${MODULES_DIR}
./install_boost.sh --version=1.69.0 --modules-dir=${MODULES_DIR}
./install_vtk.sh --version=9.0.0 --modules-dir=${MODULES_DIR}
./install_petsc_hdf5.sh --petsc-version=3.12.4 --hdf5-version=1.10.4 \
    --petsc-arch=linux-gnu --modules-dir=${MODULES_DIR}

The utility scripts follow this directory structure:

<modules-dir>
|-- modulefiles
|-- opt
`-- src

Builds are done from src.

Software versions are installed to opt.

Modulefiles are placed under modulefiles.

4. Load installed dependencies

module load xsd/4.0.0
module load xercesc/3.2.1
module load sundials/5.8.0
module load boost/1.69.0
module load vtk/9.0.0
module load petsc_hdf5/3.12.4_1.10.4/linux-gnu

5. Build Chaste

See the Chaste Guides for detailed instructions on building Chaste.

Useful commands

module use directory enables using modulefiles located in directory.

module load modulefile loads modulefile into the environment.

module unload modulefile unloads modulefile from the environment.

module switch [modulefile1] modulefile2 switches version to modulefile2.

module list lists all currently loaded modulefiles.

module purge unloads all currently loaded modulefiles.

module avail lists all installed modulefiles.

module avail string searches for modulefiles that contain string.

module show modulefile prints the environment changes prescribed by modulefile.

See the module command help for more details.