build.md

Build the library

The prerequisites can be installed with a couple of commands on linux systems.

• MPI, Most of our testing is done with openmpi but mpich should also work.
• build tools: CMake, python3
• compilers: fortran
• libraries: HDF5, FFTW3, LAPACK
• documentation (optional): Doxygen
• visualisation : gnuplot, paraview, VisIt

Install dependencies on Ubuntu

sudo apt-get install cmake git
sudo apt-get install libopenmpi-dev openmpi-bin libhdf5-openmpi-dev
sudo apt-get install  libfftw3-dev liblapack-dev libopenblas-dev
sudo apt-get install doxygen texlive graphviz

Install dependencies on Fedora

sudo dnf install git-all
sudo dnf install cmake python3
sudo dnf install gcc-gfortran
sudo dnf install hdf5-openmpi-devel openmpi-devel fftw-devel openblas-devel
sudo dnf install doxygen texlive-latex graphviz

Don't forget to load the mpi module

module load mpi/openmpi-x86_64

mpich on Fedora is not supported.

Install dependencies on MACOSX

The easiest way is to use Homebrew

brew install git cmake gfortran open-mpi
brew install hdf5-mpi openmpi fftw openblas
brew install doxygen graphviz

Download the sources

git clone https://github.com/selalib/selalib
cd selalib

Build the library

mkdir build
cd  build
cmake ..
make 

Check your installation

ctest --output-on-failure

To open an issue, follow this url: https://github.com/selalib/selalib/issues/new

Run a similation

In simulations directory, you will find examples to use the library, every program should have a README file with instructions.

Use as external library

If selalib is already installed on your server or if you just want to build and run a simulation. Copy files in one of the simulations directory and use the Makefile below:

SIM_NAME = bsl_dk_3d1v_polar
NML_FILE = dksim4d_polar_input.nml
SLL_DIR ?= /opt/selalib
FC = h5pfc    # hdf5 wrapper for mpif90
FFLAGS = -w -ffree-line-length-none -fall-intrinsics -O3 -fPIC -march=native -I${SLL_DIR}/include/selalib
FLIBS = -L${SLL_DIR}/lib -lselalib -lfftw3 -ldfftpack

${SIM_NAME}: sll_m_sim_${SIM_NAME}.o ${SIM_NAME}.o
	${FC} ${FFLAGS} -o ${SIM_NAME} $^ -I${SLL_DIR}/include/selalib ${FLIBS}

run: ${SIM_NAME}
	mpirun -np 8 $^ ${NML_FILE}

clean:
	rm -f *.o ${SIM_NAME} *.mod

selalib:
	git clone https://github.com/selalib/selalib.git

sll_build: selalib
	mkdir -p $@
	cd $@
	cmake ../selalib -DCMAKE_INSTALL_PREFIX=${SLL_DIR} \
 	       -DBUILD_TESTING=OFF -DBUILD_SIMULATIONS=OFF
	make install

.SUFFIXES: $(SUFFIXES) .F90

.F90.o:
	$(FC) $(FFLAGS) -c $<

.mod.o:
	$(FC) $(FFLAGS) -c $*.F90

Download, build and install the library with:

make sll_build

Run your simulation :

make run