Installation Guide¶
NERDSS¶
NERDSS (NonEquilibrium Reaction-Diffusion Self-assembly Simulator) requires a C++ compiler and the GNU Scientific Library (GSL). Once these prerequisites are installed, you can compile NERDSS from source.
0. Download the NERDSS source code from the official repository
git clone https://github.com/mjohn218/NERDSS.git
cd NERDSS
1. Install a C++ Compiler
macOS: Install XCode or Command Line Tools
Ubuntu: Install via apt, for example:
sudo apt-get install g++
2. Install GNU Scientific Library (GSL) (v2.5+)
macOS: Use Homebrew:
brew install gsl
Ubuntu: Use apt:
sudo apt-get install libgsl-dev
3. Compile NERDSS
Run
make clean
make serial
The executable nerdss will appear in the ./bin directory
For more details on using NERDSS, see its documentation.
Parallel NERDSS¶
To build NERDSS with MPI support, follow these steps:
1. Install a C++ Compiler with MPI support:
macOS: Install OpenMPI with Homebrew:
brew install open-mpi
Ubuntu: Install OpenMPI through apt:
sudo apt install openmpi-bin libopenmpi-dev
2. Install GNU Scientific Library (GSL) (v2.5+):
macOS: Use Homebrew:
brew install gsl
Ubuntu: Use apt:
sudo apt install libgsl-dev
3. Compile NERDSS with MPI support:
Checkout to the mpi branch:
git checkout mpi
Run:
make clean
make mpi
The executable nerdss_mpi will appear in the ./bin directory
4. Running Simulations
To start a parallel simulation, use the command:
mpirun -np 4 ./nerdss_mpi -f parms.inp
ionerdss¶
ionerdss can be installed directly from PyPI (recommend to conda environment):
0. Create a conda environment (optional but recommended)
Download and install Anaconda or Miniconda, then create a new conda environment for ionerdss:
conda create -n ionerdss python=3.9
conda activate ionerdss
1. Install ioNERDSS
pip install ioNERDSS
After installation, you can import ionerdss in Python or Jupyter Notebook:
import ionerdss as ion
ion.some_function()
For documentation on setting up models and analyzing simulator output, see the ionerdss tutorial.