How to Install

See also

Go through this page to install libyt that is fault-tolerant to Python code, supports interactive Python prompt, supports reloading script, and supports Jupyter Notebook access.

To turn off some of the features, go to Details.

libyt

Requirements:

CMake (>=3.15)

A software build system.

pkg-config

Generally, Linux and macOS already have pkg-config installed. It is a helper tool for finding libraries and compiling applications.

Compiler (It should support c++14)

  • CXX: Path to g++ compiler.

  • CC: Path to gcc compiler.

Python (>=3.7)

The Python environment we want to use when doing in situ analysis. If we compile it from source, use --enable-shared when configuring.

  • PYTHON_PATH: Python installation prefix, the path contains folders include, lib etc.

  • numpy and other Python Dependencies

OpenMPI or MPICH

MPI used for compiling simulations and for compiling libyt should be the same.

  • MPI_PATH: MPI installation prefix, the path contains folders include, lib etc.

Readline

Readline library is already installed on Linux and macOS generally. If not, we can get through system package manager or compile from source ourselves. If we compile it from source, use --with-curses when configuring.

  • READLINE_PATH: readline installation prefix. Provide the path if it is not in system search path.

Follow the steps to install libyt that is fault-tolerant to Python code, and supports interactive Python prompt, reloading script, and Jupyter Notebook access:

  1. Shallow clone libyt and enter the folder:

    git clone --depth 1 https://github.com/yt-project/libyt "libyt"
cd libyt

  2. [Optional] Set gcc and g++ compiler:

    export CC=<path-to-gcc>
export CXX=<path-to-g++>

  3. Generate build files in build folder:

    • Serial Mode (using GCC):

      rm -rf build
cmake -S . -B build -DSERIAL_MODE=ON \
                    -DINTERACTIVE_MODE=ON \
                    -DJUPYTER_KERNEL=ON \
                    -DPYTHON_PATH=<your-python-prefix>

    • Parallel Mode (using MPI):

      rm -rf build
cmake -S . -B build -DINTERACTIVE_MODE=ON \
                    -DJUPYTER_KERNEL=ON \
                    -DPYTHON_PATH=<your-python-prefix> \
                    -DMPI_PATH=<your-mpi-prefix>

  4. Build project and install libyt:

    cmake --build build 
cmake --install build --prefix <libyt-install-prefix>

  5. libyt is now installed at <libyt-install-prefix> folder.

Python Dependencies

  • Option indicates under what circumstances will we need this package.

Python package

pip

Required version

Notes

Option

NumPy

numpy

<2.0

The fundamental package for scientific computing with Python.

Always

yt

yt

The core analytic tool.

Always

yt_libyt

yt-libyt

yt frontend for libyt.

Always

mpi4py

mpi4py

Python bindings for the Message Passing Interface (MPI) standard.
Make sure mpi4py used in Python and MPI used in simulation are matched. (Check how to install mpi4py here.)

-DSERIAL_MODE=OFF

jedi

jedi

Support auto-completion in Jupyter Notebook and JupyterLab. (We will have this if IPython is already installed.)

-DJUPYTER_KERNEL=ON

jupyter-client

jupyter-client

>=8.0.0

Jupyter Client.

-DJUPYTER_KERNEL=ON

jupyter_libyt

jupyter-libyt

Jupyter kernel provisioner for libyt.

-DJUPYTER_KERNEL=ON

Note

jupyter-client and jupyter_libyt are used for launching Jupyter Notebook and JupyterLab. Make sure the Python environment used for launching the notebook have them installed.

The Python used in in situ analysis which is also for compiling libyt and the Python used for launching Jupyter Notebook/JupyterLab might be different. For example, when running libyt in HPC cluster, the Python environment is different from the one starting Jupyter Notebook on your local laptop. (See Jupyter Notebook Access)

FAQs