neurokernel

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.. -- rst --

.. image:: https://raw.githubusercontent.com/neurokernel/neurokernel/master/docs/source/_static/logo.png :alt: Neurokernel

Package Description

Project Website <https://neurokernel.github.io>_ | GitHub Repository <https://github.com/neurokernel/neurokernel>_ | Online Documentation <https://neurokernel.readthedocs.io>_ | Mailing List <https://lists.columbia.edu/mailman/listinfo/neurokernel-dev>_ | Forum <http://neurokernel.67426.x6.nabble.com/>_

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

.. image:: http://prime4commit.com/projects/98.svg :target: http://prime4commit.com/projects/98 :alt: Support the project

Prerequisites

Neurokernel requires

• Linux (other operating systems may work, but have not been tested);
• Python;
• at least one NVIDIA GPU with Fermi <http://www.nvidia.com/content/pdf/fermi_white_papers/nvidia_fermi_compute_architecture_whitepaper.pdf>_ architecture or later;
• NVIDIA's GPU drivers <http://www.nvidia.com/content/drivers/>_;
• CUDA <http://www.nvidia.com/object/cuda_home_new.html>_ 5.0 or later;
• OpenMPI <http://www.open-mpi.org>_ 1.8.4 or later compiled with CUDA support.

To check what GPUs are in your system, you can use the inxi <https://code.google.com/p/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.

Although some Linux distributions do include CUDA in their stock package repositories, you are encouraged to use those distributed by NVIDIA because they often are more up-to-date and include more recent releases of the GPU drivers. See this page <https://developer.nvidia.com/cuda-downloads>_ for download information.

If you install Neurokernel in a virtualenv environment, you will need to install OpenMPI. See this page <https://www.open-mpi.org/faq/?category=building#easy-build>_ for OpenMPI installation information. Note that OpenMPI 1.8 |openmpi_no_windows|_.

.. _openmpi_no_windows: https://www.open-mpi.org/software/ompi/v1.6/ms-windows.php .. |openmpi_no_windows| replace:: cannot run on Windows

Some of Neurokernel's demos require either ffmpeg <http://www.fmpeg.org>_ or libav <http://libav.org>_ installed to generate visualizations (see Examples_).

Installation

Conda ^^^^^ The easiest way to get neurokernel is to install it in a conda environment: ::

conda create -n nk python=3.7 c-compiler compilers cxx-compiler openmpi -c conda-forge -y conda activate nk python -m pip install neurokernel

Make sure to enable CUDA support in the installed OpenMPI by setting: ::

export OMPI_MCA_opal_cuda_support=true

Examples

Introductory examples of how to use Neurokernel to build and integrate models of different parts of the fly brain are available in the Neurodriver <https://github.com/neurokernel/neurodriver>_ package. To install it run the following: ::

git clone https://github.com/neurokernel/neurodriver cd ~/neurodriver python setup.py develop

Other models built using Neurokernel are available on GitHub <https://github.com/neurokernel/>_.

Building the Documentation

To build Neurokernel's HTML documentation locally, you will need to install

• mock <http://www.voidspace.org.uk/python/mock/>_ 1.0 or later.
• sphinx <http://sphinx-doc.org>_ 1.3 or later.
• sphinx_rtd_theme <https://github.com/snide/sphinx_rtd_theme>_ 0.1.6 or later.

Once these are installed, run the following: ::

cd ~/neurokernel/docs make html

Authors & Acknowledgements

See the included AUTHORS_ file for more information.

.. _AUTHORS: AUTHORS.rst

License

This software is licensed under the BSD License <http://www.opensource.org/licenses/bsd-license.php>. See the included LICENSE file for more information.

.. _LICENSE: LICENSE.rst

Notes

The Neurokernel Project is independent of the NeuroKernel Operating System developed by NeuroDNA Computer <http://www.neurokernel.com>_.