Neurokernel is a Python framework for developing models of the fruit fly brain and executing them on multiple NVIDIA GPUs.
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.
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
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
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 about Neurokernel can be obtained from the project website at https://neurokernel.github.io.
Neurokernel's documentation is available at http://neurokernel.rtfd.org.
See the included AUTHORS file for more information.
This software is licensed under the BSD License. See the included LICENSE file for more information.