Installation Guide for Nektar++ on HPC

Installing Dependencies

Boost, BLAS, LAPACK and Scotch are mandatory libraries required by Nektar++ along with GCC and CMAKE. You can check if these are already available on your HPC or system using module avail [library]. If they are available you can load them using module load [library/version]. Otherwise, follow the steps to install them on your system.

Create a folder nektar-depend where all the dependencies will be downloaded, extracted and built. This keeps the home directory clean. All the libraries and Nektar++ will be installed in $HOME/local.

mkdir nektar-depend && cd nektar-depend

Boost

• Download the source code and extract it

wget https://archives.boost.io/release/1.88.0/source/boost_1_88_0.tar.gz
tar -xvzf boost_1_88_0.tar.gz
cd boost_1_88_0

• Configure the installation

./bootstrap.sh --prefix=$HOME/local

• Install the code

.b2 install

• Export the path to installation directory. You can add to the .bashrc for ease of access in future.

export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
export CPATH=$HOME/local/include:$CPATH
export LIBRARY_PATH=$HOME/local/lib:$LIBRARY_PATH
export PATH=$HOME/local/bin:$PATH

BLAS and LAPACK

The OpenBLAS library provides support for both BLAS and LAPACK, so there is no need to install LAPACK separately.

• Download the source code and extract it

wget https://github.com/OpenMathLib/OpenBLAS/releases/download/v0.3.28/OpenBLAS-0.3.28.tar.gz
tar -xvzf OpenBLAS-0.3.28.tar.gz
cd OpenBLAS-0.3.28

• Install the code

make -j4
make install PREFIX=$HOME/local

Scotch

• Download the source code and extract it

wget https://gitlab.inria.fr/scotch/scotch/-/archive/v7.0.7/scotch-v7.0.7.tar.gz
tar -xvzf scotch-v7.0.7.tar.gz
cd scotch-v7.0.7

• Create a build directory

mkdir build && cd build

• Configure the installation

cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/local -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC"

• Install the code

make -j4 prefix=$HOME/local
make install

ARPACK

ARPACK is the collection of Arnoldi methods used for Linear Stability analysis. If you are planning to use Nektar++ for linear stability analysis, then this library is a mandatory one. It depends on the BLAS and LAPACK library, so make sure you have installed it and the path to binaries are added.

Note

This library is mandatory for Linear Stability Solver of Nektar++. Make sure to enable the NEKTAR_USE_ARPACK option during configuration of Nektar++ installer.

• Download and extract the source code

wget https://github.com/opencollab/arpack-ng/archive/refs/tags/3.9.1.tar.gz
tar -xvzf 3.9.1.tar.gz
cd arpack-ng-3.9.1

• Create a build directory

mkdir build && cd build

• Configure the installation

cmake -DEXAMPLES=ON -DMPI=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX:PATH=$HOME/local ..

• Install the code

make
make install

OpenCascade (OCCT)

OpenCascade library is required for mesh generation and optimization in Nektar++. The steps below are used to compile the OCCT library from source.

Note

This library is NOT required for conversion of mesh to Nektar++ format. You may skip this step if you have disabled the NEKTAR_USE_MESHGEN option.

• Install the dependencies of OCCT library

sudo apt update && sudo apt install -y \
    build-essential cmake git \
    freeglut3-dev libx11-dev libxext-dev \
    libxt-dev libgl1-mesa-dev libglu1-mesa-dev \
    libfreetype6-dev libtbb-dev \
    libxmu-dev libxi-dev \
    libpng-dev libglfw3-dev \
    libeigen3-dev libfontconfig1-dev

• Download and extract the source code

wget https://github.com/Open-Cascade-SAS/OCCT/archive/refs/tags/V7_9_1.tar.gz
tar -xvzf V7_9_1.tar.gz && cd OCCT-7_9_1

• Create a build directory

mkdir build && cd build

• Configure the build using cmake.

cmake .. \
  -DCMAKE_INSTALL_PREFIX=$HOME/local
  -DBUILD_MODULE_Draw=OFF \
  -DBUILD_MODULE_ApplicationFramework=ON -DBUILD_MODULE_DataExchange=ON \
  -DBUILD_MODULE_ModelingData=ON -DBUILD_MODULE_ModelingAlgorithms=ON \
  -DBUILD_MODULE_Visualization=ON -DCMAKE_BUILD_TYPE=Release

• Install the library

make -j4 install

Installing Nektar++

Download and extact the source code

wget https://www.nektar.info/src/nektar%2B%2B-5.8.0.tar.gz && tar -xvzf nektar++-5.8.0.tar.gz

Create the build directory

cd nektar-v5.8.0 && mkdir -p build && cd build

Configure the installation

• Initialize the configuration (It enforces the location of dependency binaries, if the GUI version is not able to find them.)

cmake .. \
  -DCMAKE_PREFIX_PATH=$HOME/local \
  -DCMAKE_LIBRARY_PATH=$HOME/local/lib:$HOME/local/lib64 \
  -DCMAKE_INCLUDE_PATH=$HOME/local/include \
  -DCMAKE_INSTALL_PREFIX=$HOME/local/nektar \
  -DCMAKE_C_COMPILER=gcc \
  -DCMAKE_CXX_COMPILER=g++ \
  -DCMAKE_CXX_STANDARD=17 \
  -DCMAKE_CXX_FLAGS="-std=c++17" \
  -DMPI_C_COMPILER=mpicc \
  -DMPI_CXX_COMPILER=mpicxx \
  -DNEKTAR_USE_MPI=ON

• Modify the configuration by running ccmake ../
  • Press c to start the configuration.
  • Select the components of Nektar++ (prefixed with NEKTAR_BUILD_) you would like to build. Disabling solvers which you do not require will speed up the build process.
  • Select the optional libraries you would like to use (prefixed with NEKTAR_USE_) for additional functionality. Check the list of configuration options can be accessed here.
  • Press c to continue the configuration.
  • Press g to generate the make files.

Compile the code

make -j4 install

Add to path

After completion of installation, add the bin and lib64 folders present in the default installation folder nektar-v5.8.0/build/dist to PATH.

export PATH=$PATH:$HOME/local/nektar/bin
export LD_LIBRARY_PATH=$HOME/local/nektar/lib64:$LD_LIBRARY_PATH