install SWAN on RPM-based Linux distributions

prerequisites

The following packages must be installed first:

  • gfortran

  • cmake

  • ninja

  • perl

  • git

These packages can be installed using the default package manager dnf.

First, update the system

sudo dnf -y update

Next, run the following command to install GCC (GNU Compiler Collection) on the system

sudo dnf -y install gcc

and then gfortran

sudo dnf -y install gcc-gfortran

To install cmake, enter

sudo dnf -y install cmake

Finally, install ninja by running the following command

sudo dnf -y install ninja-build

Warning

On AlmaLinux OS 9 and Rocky Linux 9, this command must be preceded by the two commands below:

sudo dnf -y install dnf-plugins-core
sudo dnf config-manager --set-enabled crb

Note that both AlmaLinux 8 and Rocky 8 install an older version of Ninja, namely 1.8.2, while CMake requires 1.10+ in order to build fortran. So if possible, please upgrade to a higher OS version.

On Oracle Linux 9 ninja should be installed as follows:

sudo dnf --enablerepo=ol9_codeready_builder install ninja-build

Before installing perl, check if it is already present on your Linux distribution, by typing

perl -v

If perl is not installed, the shell reports that this command is not found. In that case, install the perl interpreter as follows

sudo dnf -y install perl

The same for git. Either verify the installation by typing git version or install it by running sudo dnf -y install git.

verify installations

Verify the required installations by checking their versions, as follows

gfortran --version

cmake --version

ninja --version

perl --version

git --version

If no error is reported, then the installation was successful.

Important

  • The CMake version must be at least 3.20 or newer.

  • The ninja version should be at least 1.10.

  • The perl version is 5 or higher.

installation SWAN

Once the prerequisites are taken care of, installing SWAN on your machine is a four-step process.

  1. download SWAN

git clone https://gitlab.tudelft.nl/citg/wavemodels/swan.git && cd swan

Paste this into a shell terminal.

  1. configure SWAN

make config

  1. build SWAN

make

  1. install SWAN

make install

SWAN is installed at folder $HOME/wavemodels/swan by default. To run SWAN, you need to make sure that the /bin folder in this directory is added to your system’s PATH. Open the terminal and enter

export PATH=$PATH:$HOME/wavemodels/swan/bin

You can check the new value of PATH by echoing it: echo $PATH. However, to set this permanently, you need to add it to your ~/.bashrc, as follows

echo export PATH=$PATH:$HOME/wavemodels/swan/bin >> ~/.bashrc
source ~/.bashrc

options for configuring SWAN

If desired, the build can be configured by passing one or more options below to make config.

fc=<compiler>

the Fortran90 compiler to use [default is determined by CMake]

mpi=on

enable build of SWAN with MPI [off by default]

metis=on

enable build of SWAN with Metis [off by default]

prefix=<folder>

set the installation folder [$HOME/wavemodels/swan by default]

For example, the following command

make config fc=gfortran prefix=/usr/local/swan

will configure SWAN to be built using gfortran and then install it at /usr/local/swan.

building with MPI support

The SWAN source code also supports memory-distributed parallelism for high performance computing applications. A message passing approach is employed based on the Message Passing Interface (MPI) standard that enables communication between independent processors.

Popular implementations are Open MPI and MPICH. The first one is typically offered by the package managers of Linux and macOS and can be combined with GCC such as gfortran.

Before installing Open MPI, make sure that your system is up to date and that GCC has been installed, see prerequisites.

To install Open MPI on a RPM-based Linux, run

sudo dnf -y install openmpi openmpi-devel

To verify whether the installation was successful, run the following command

ompi_info --version

or

mpirun --version

Warning

To use the compiler mpifort and runner mpirun on AlmaLinux, Rocky Linux and Fedora, you’ll need to set up the environment path. Insert the following commands

echo source /etc/profile.d/modules.sh >> ~/.bashrc
echo module load mpi/openmpi-$(arch) >> ~/.bashrc
source ~/.bashrc

Once Open MPI is operational, we proceed to build SWAN. First, we configure SWAN to be built with support for Open MPI, as follows

make config fc=mpifort mpi=on

The actual building is done by typing

make

Finally, to install SWAN, run the following command

make install

SWAN is now ready for high performance computing.

building with Metis support

SWAN can be compiled with support for Metis to partition an unstructured mesh so that simulations can be carried out on distributed-memory machines. For this, an MPI implementation is still required, click here for details.

The actual mesh partitioning implemented in SWAN is the multilevel k-way method as explained in the Metis manual.

For a proper building, the Metis software package must be installed first on your machine.

On a RPM-based Linux (e.g., Fedora):

sudo dnf -y install metis-devel

or, if that does not work (e.g., on Rocky Linux 8), enable the development repository:

sudo dnf -y --enablerepo=devel install metis-devel

However, on AlmaLinux 9+ and Rocky 9+ the development packages are moved to the CRB (CodeReady Builder) repo. In this case, run the following commands:

sudo dnf config-manager --set-enabled crb
sudo dnf makecache
sudo dnf -y install epel-release
sudo dnf -y install metis-devel

On Oracle Linux 9 Metis should be installed as follows:

sudo dnf -y install epel-release metis-devel

After Metis has been installed we continue with the build of SWAN. First, configure SWAN:

make config fc=mpifort mpi=on metis=on

Next, build SWAN:

make

And finally, install SWAN:

make install

clean up

To remove all files installed by make install, type the following command

make uninstall

If you want to remove the build directory and all files that have been created after running make or make build, then run

make clobber