On Ubuntu, the following commands can be used to build all of the prerequisites. Keep in mind conflicts might occur depending on the state of your system. First run
sudo apt-get install g++-11 gcc-11 gfortran-11 libblas-dev liblapack-dev m4 gcovr python-pip
sudo pip install ford
Make sure that the correct CMake version is installed (there are possible conflicts with newer versions). For example, to install CMake 3.18.0:
wget https://github.com/Kitware/CMake/releases/download/v3.18.0/cmake-3.18.0.tar.gz
tar -zvxf cmake-3.18.0.tar.gz
cd ./cmake-3.18.0
./bootstrap -- -DCMAKE_USE_OPENSSL=OFF
make
make install
Then, to install a fresh build of MPI:
wget -O mpich.tar.gz https://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz
tar xfz mpich.tar.gz
mkdir mpich-install
cd ./mpich-3.4.2
./configure CC=gcc-11 CXX=g++-11 FC=gfortran-11 --prefix=/home/mpich-install FFLAGS=-fallow-argument-mismatch --with-device=ch3
make
make install
To install a compatible version of PETSc (make sure to set correct paths!):
git clone -b release-3.17 https://gitlab.com/petsc/petsc.git petsc
cd petsc
./configure --with-mpi-dir=/path/to/mpich-install --download-hypre=1 --download-fblaslapack=1 --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
make PETSC_DIR=/home/petsc PETSC_ARCH=arch-linux-c-opt all check
To install pFUnit (make sure to set paths):
git clone -b v4.2.2 https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
cd pFUnit
mkdir build
cd build
cmake .. -DSKIP_OPENMP=yes -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11 -DCMAKE_INSTALL_PREFIX=/path/to/installs/pFUnit
make install
The json-fortran library version used by ReMKiT1D can be installed using:
git clone -b 8.2.5 https://github.com/jacobwilliams/json-fortran.git
cd json-fortran
mkdir build
cd build
cmake .. -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11 -DCMAKE_INSTALL_PREFIX=/path/to/installs/json-fortran
make install
Install the hdf5 library:
git clone -b hdf5-1_13_0 https://github.com/HDFGroup/hdf5.git
cd hdf5
mkdir build
cd build
cmake .. -DCMAKE_Fortran_COMPILER=gfortran-11 -DCMAKE_C_COMPILER=gcc-11 -DCMAKE_CXX_COMPILER=g++-11 -DHDF5_BUILD_FORTRAN=ON -DCMAKE_INSTALL_PREFIX=/path/to/installs/hdf5
make install
et the environmental variables
export PFUNIT_DIR=/home/installs/pFUnit
export PETSC_DIR=/home/petsc
export PETSC_ARCH=arch-linux-c-opt
export PATH=$PATH:/home/installs/petsc
export PATH=$PATH:/home/installs/hdf5
export PATH=$PATH:/home/installs/json-fortran/jsonfortran-gnu-8.2.5
export PATH=$PATH:/home/mpich-install/bin:$PATH
export LD_LIBRARY_PATH=/home/mpich-install/lib:$LD_LIBRARY_PATH
NOTE: Some of the above paths might have to be set differently depending on your system setup and you might have to define the ones you need after the corresponding installation. Another option is to export the paths before the start of the installation process.
mkdir build
cd build
cmake ..
For test coverage enabled run with -DCMAKE_BUILD_TYPE=TESTING
make
make test
make docs
make gcovr
A Dockerfile is included in the repository that sets up an image with all ReMKiT1D prerequisites.
To build the image with docker run the following command in the docker folder of the repository
docker build --tag remkit1d:latest .
Note that ReMKiT1D needs to be copied into the docker image. This can be done either by mounting the local repository folder or using the docker cp command.
The docker cp approach can be done by running
docker run -it --name [CONTAINER_NAME] remkit1d
where [CONTAINER_NAME] should be replaced by the name you wish to give the container for use with the docker cp command. Then, in another terminal, run
docker cp /path/to/ReMKiT1D_repo [CONTAINER_NAME]:/home/
which will copy the ReMKiT1D repository folder into the docker container. After this is done follow the above ReMKiT1D build instructions within the docker image.