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COMPILE.md

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Compile dependencies

These are instructions to compiling dependencies on your computer. Most of these will be available through regular software repositories (e.g. pip, apt, dnf, homebrew) but these may be outdated. We recommend compiling from the source you encounter compatibility issues.

MPI

Download the latest stable openmpi/mpich release and extract it anywhere. Navigate inside the extracted folder from the terminal and run the following commands:

./configure --enable-shared --prefix=/path/to/install-dir
make all
make install
make check

Now export the path

export MPI_DIR=/path/to/install-dir
export LD_LIBRARY_PATH=$MPI_DIR/lib:$LD_LIBRARY_PATH
export PATH=$MPI_DIR/bin:$PATH

HDF5

It is imperitive that you have the parallel version of HDF5. Obtain the latest version of HDF5 and extract it anywhere. You must link your installed MPI path as follows:

CC=$MPI_DIR/bin/mpicc FC=$MPI_DIR/bin/mpifort ./configure --enable-shared --enable-parallel --enable-fortran --prefix=/path/to/install-dir
make all
make install
make check

Now export the path

export HDF5_DIR=/path/to/install-dir
export LD_LIBRARY_PATH=$HDF5_DIR/lib:$LD_LIBRARY_PATH
export PATH=$HDF5_DIR/bin:$PATH

PETSc

Download the latest version of PETSc and extract it anywhere. PETSc can download and compile a number of useful external packages automatically during the configure stage.

./configure MPI-DIR=$MPI_DIR --with-mpi-dir=$MPI_DIR --with-hdf5-dir=$HDF5_DIR --with-shared-libraries --download-fblaslapack --download-scalapack --download-triangle --download-mumps --download-chaco --download-ctetgen --download-hypre --prefix=/path/to/install-dir

Follow the make instructions from the command line once configuration is complete. This will install PETSc and run some tests to ensure it is functioning properly. Now export the path:

export PETSC_DIR=/path/to/install-dir
export LD_LIBRARY_PATH=$PETSC_DIR/lib:$LD_LIBRARY_PATH
export PATH=$PETSC_DIR/bin:$PATH

Install Python bindings

We recommend doing this using pip,

[sudo] apt-get install pip

or equivalent on other operating systems. pip can be instructed to install to your home directory with the --user flag, e.g. pip install --user numpy. You can also upgrade an existing package by passing the --upgrade flag.

mpi4py

CC=$MPI_DIR/bin/mpicc MPICC=$MPI_DIR/bin/mpicc MPI_DIR=$MPI_DIR pip install mpi4py

h5py

CC=$MPI_DIR/bin/mpicc HDF5_DIR=$HDF5_DIR HDF5_MPI="on" pip install h5py

petsc4py

PETSC_DIR=$PETSC_DIR PETSC_ARCH=$PETSC_ARCH pip install petsc4py