Linux

PyPI Package

If you use Bohrium through Python, we strongly recommend to install Bohrium through pypi, which will include BLAS, LAPACK, OpenCV, and OpenCL support:

pip install --user bohrium

Note

On linux, Bohrium requires gcc in $PATH. E.g. on Ubuntu install the build-essential package: sudo apt install build-essential.

Ubuntu

On Ubuntu you can use apt-get:

sudo add-apt-repository ppa:bohrium/nightly
sudo apt-get update
sudo apt-get install bohrium
# Optionals
sudo apt-get install bohrium-opencl # GPU support
sudo apt-get install bohrium-visualizer # data visualizing
sudo apt-get install bohrium3 # Python3 support

Anaconda

To use Anaconda, simply install the Bohrium PyPI package in an environment:

# Activate the environment where you want to install Bohrium:
source activate my_env
# Install Bohrium using pip
pip install bohrium

Note

Bohrium requires gcc in $PATH. E.g. on Ubuntu install the build-essential package: sudo apt install build-essential.

Install From Source Package

Visit Bohrium on github.com and download the latest release: https://github.com/bh107/bohrium/releases/latest. Then build and install Bohrium as described in the following subsections.

You need to install all packages required to build NumPy:

sudo apt-get build-dep python-numpy

And some additional packages:

sudo apt-get install python-numpy python-dev swig cmake unzip cython libhwloc-dev libboost-filesystem-dev libboost-serialization-dev libboost-regex-dev zlib1g-dev libsigsegv-dev

And for python v3 support:

sudo apt-get install python3-dev python3-numpy python3-dev cython3

Packages for visualization:

sudo apt-get install freeglut3 freeglut3-dev libxmu-dev libxi-dev

Build and install:

wget https://github.com/bh107/bohrium/archive/master.zip
unzip master.zip
cd bohrium-master
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=<path to install directory>
make
make install

Note

The default install directory is ~/.local

Note

To compile to a custom Python (with valgrind debug support for example), set -DPYTHON_EXECUTABLE=<custom python binary>.

Finally, you need to set the LD_LIBRARY_PATH environment variables and if you didn’t install Bohrium in $HOME/.local/lib your need to set PYTHONPATH as well.

The LD_LIBRARY_PATH should include the path to the installation directory:

export LD_LIBRARY_PATH="<install dir>:$LD_LIBRARY_PATH"

The PYTHONPATH should include the path to the newly installed Bohrium Python module:

export PYTHONPATH="<install dir>/lib/python<python version>/site-packages:$PYTHONPATH"

Check Your Installation

Check installation by printing the current runtime stack:

python -m bohrium --info