stux2000 / neurokernel

Neurokernel Project

Package Description

Neurokernel is a Python framework for developing models of the fruit fly brain and executing them on multiple NVIDIA GPUs.

Prerequisites

Neurokernel requires Python 2.7, at least one NVIDIA GPU, NVIDIA's GPU drivers, and CUDA 5.0 or later. To check what GPUs are in your system, you can use the inxi command available on most Linux distributions:

inxi -G

You can verify that the drivers are loaded as follows:

lsmod | grep nvidia

If no drivers are present, you may have to manually load them by running something like:

modprobe nvidia

as root.

Quick Start

Make sure you have pip installed (preferably in a virtualenv); once you do, install the following dependencies in the specified order (replace pip with the path to the copy of pip in your virtualenv):

pip install numpy
pip install cython
pip install numexpr
pip install tables
pip install pycuda

If installation of PyCUDA fails because some of the CUDA development files or libraries are not found, you may need to specify where they are explicitly. For example, if CUDA is installed in /usr/local/cuda/, try installing PyCUDA as follows:

CUDA_ROOT=/usr/local/cuda/ CFLAGS=-I${CUDA_ROOT}/include \
LDFLAGS=-L${CUDA_ROOT}/lib64 pip install pycuda

Replace ${CUDA_ROOT}/lib with ${CUDA_ROOT}/lib64 if your system is running 64-bit Linux. If you continue to encounter installation problems, see the PyCUDA Wiki for more information.

You will also need to have ffmpeg or libav installed to generate some of the demo visualizations.

Run the following to install the remaining Python package dependencies listed in setup.py and the latest Neurokernel code:

git clone https://github.com/neurokernel/neurokernel.git
pip install -e git+./neurokernel#egg=neurokernel

You can also install the code directly as follows:

cd neurokernel/
python setup.py install

or (if you want to tinker with the code without having to repeatedly reinstall it):

cd neurokernel/
python setup.py develop

Building the Documentation

To build the HTML documentation, you will need to install

• sphinx 1.2 or later.
• sphinx_rtd_theme 0.1.6 or later.

Once these are installed, run the following:

cd neurokernel/docs
make html

Supported Platforms

Neurokernel has been tested and installed on Linux. It may run on other platforms too; if you encounter problems, submit a bug report on GitHub.

More Information

More information about Neurokernel can be obtained from the project website at https://neurokernel.github.io.

Neurokernel's documentation is available at http://neurokernel.rtfd.org.

Authors & Acknowledgements

See the included AUTHORS file for more information.

License

This software is licensed under the BSD License. See the included LICENSE file for more information.