Summary

This is the main code of the project "Interacting Active Surfaces" and follows the ideas in the manuscript:

https://doi.org/10.1101/2022.03.21.484343

The code is written in C++, with the idea of storing cells in different partitions and parallelised with MPI and OpenMP. The library makes use of the Trilinos library for the management of linear algebra objects such as vectors and matrices.

The code is structured into different source subfolders ("Auxiliary", "BasisFunctions", "Cell", "Integration", "Solvers", "Tensor" and "Tissue"). The "Extern" folder contains external libraries used for some parts of the code. The folder "Tests" contains some tests that can be ignored. The folder "Tutorials" contains several subfolders that are meant to serve as a way to illustrate the usage of the library and they follow the examples in the manuscript.

Installation

To install ias, you will need to install the following packages first:

• OpenMPI: Tools for MPI including compiler. To install this package, you can either install it via a package manager, e.g. in Ubuntu:

sudo apt install libopenmpi-dev

or directly from the source code (https://www.open-mpi.org/software/ompi/v4.1/), e.g.

wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz
tar -zxvf openmpi-4.1.1.tar.gz
cd openmpi-4.1.1
./configure --prefix=MPI_PATH
make all
make install

where you have to change MPI_PATH to the path where you want OpenMPI to be installed.

• Trilinos: This package is used to handle linear algebra objects and solvers in a distributed memory fashion (MPI). To install this package, you can either install it via a package manager, e.g. in Ubuntu:

sudo apt install trilinos-all-dev

or directly from the source code (https://github.com/trilinos/trilinos). With git, follow these steps

git clone https://github.com/trilinos/Trilinos.git

will download the project in a new folder called "Trilinos". Inside that folder, create a build folder, configure and make:

cd Trilinos
mkdir build
cd build
cmake -DBUILD_SHARED_LIBS:BOOL=YES \
      -DTrilinos_ENABLE_Amesos2:BOOL=YES \
      -DTrilinos_ENABLE_AztecOO:BOOL=YES \
      -DTrilinos_ENABLE_Amesos:BOOL=YES \
      -DTrilinos_ENABLE_Belos:BOOL=YES \
      -DTrilinos_ENABLE_Epetra:BOOL=YES \
      -DTrilinos_ENABLE_Isorropia:BOOL=YES \
      -DTrilinos_ENABLE_OpenMP=ON \
      -DTrilinos_ENABLE_Fortran=YES \
      -DTPL_ENABLE_MPI:BOOL=YES \
      -DBUILD_SHARED_LIBS=ON \
      -DCMAKE_BUILD_TYPE=Release \
      -DTPL_ENABLE_Netcdf=OFF \
      -DTrilinos_ENABLE_PyTrilinos=OFF \
      -DTrilinos_ENABLE_STK:BOOL=OFF \
      -DCMAKE_C_FLAGS="-O3" \
      -DCMAKE_CXX_FLAGS="-O3" \
      -DCMAKE_FORTRAN_FLAGS="-O3" \
      -DCMAKE_C_COMPILER="MPI_PATH/bin/mpicc" \
      -DCMAKE_CXX_COMPILER="MPI_PATH/bin/mpicxx" \
      -DCMAKE_FORTRAN_COMPILER="MPI_PATH/bin/mpif90" \
      -DCMAKE_INSTALL_PREFIX=TRILINOS_PATH \
      ..
make install

where you have to change TRILINOS_PATH to the path where you want Trilinos to be installed and MPI_PATH to the path to where MPI was installed.

• VTK: This library is used for IO. Again you can directly install it with your package manager, e.g. in Ubuntu

sudo apt install vtk9

or you can install it from sources (https://vtk.org/download/), e.g.

wget https://www.vtk.org/files/release/9.0/VTK-9.0.1.tar.gz
tar -zxvf VTK-9.0.1
cd VTK-9.0.1
mkdir build
cd build
cmake -DBUILD_SHARED_LIBS:BOOL=YES \
      -DBUILD_SHARED_LIBS=ON \
      -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_C_COMPILER="MPI_PATH/bin/mpicc" \
      -DCMAKE_CXX_COMPILER="MPI_PATH/bin/mpicxx" \
      -DCMAKE_INSTALL_PREFIX=VTK_PATH \
      ..

where you have to change VTK_PATH to the path where you want VTK to be installed and MPI_PATH to the path to where MPI was installed (if you don't know it, try typing which mpicc, which should give you MPI_PATH/bin).

Once all previous packages all installed, then to install ias. First download the code if you don't have it already

git clone git@github.com:torressancheza/ias.git

Inside the ias folder,

mkdir build
cd build
cmake -DBUILD_SHARED_LIBS:BOOL=YES \
      -DTrilinos_DIR=TRILINOS_PATH/lib/cmake/Trilinos \
      -DVTK_DIR=VTK_PATH/lib/cmake/vtk-X \
      -DCMAKE_CXX_COMPILER=CXX \
      -DCMAKE_C_COMPILER=CC \
      -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_INSTALL_PREFIX=IAS_PATH \
      ..
make install

where IAS_PATHis the path where you want ias to be installed, TRILINOS_PATH is the path where Trilinos was installed, VTK_PATH the path where VTK was installed (note that in the same line X should match the Vtk version, e.g. 9.0), and MPI_PATH the path to where MPI was installed. If you are working on MacOS and want to use Xcode, you might want to add right after .., -G Xcode so that Xcode files are generated.

Usage

Authors

Alejandro Torres-Sánchez

Max Kerr Winter

Guillaume Salbreux

Licence

The code is provided under the MIT licence (see licence.txt).