OpenCL-backed neural simulations using the methods of the Neural Engineering Framework.
Project description
This project is an OpenCL-based simulator for brain models built using Nengo. It can be orders of magnitude faster than the reference simulator in nengo for large models.
Usage
To use the nengo_ocl project’s OpenCL simulator, build a nengo model as usual, but pass sim_ocl.Simulator when creating a simulator for your model:
import numpy as np import nengo # define the model model = nengo.Network() with model: stim = nengo.Node(np.sin) a = nengo.Ensemble(n_neurons=100, dimensions=1) b = nengo.Ensemble(n_neurons=100, dimensions=1) nengo.Connection(stim, a) nengo.Connection(a, b, function=lambda x: x**2, synapse=0.01) probe_a = nengo.Probe(a, synapse=0.01) probe_b = nengo.Probe(b, synapse=0.01) from nengo_ocl.sim_ocl import pyopencl as cl ctx = cl.create_some_context() # build the model sim = nengo_ocl.sim_ocl..Simulator(model, context=ctx) # run the model sim.run(10) # plot the results import matplotlib.pyplot as plt plt.plot(sim.trange(), sim.data[probe_a]) plt.plot(sim.trange(), sim.data[probe_b]) plt.show()
Dependencies and Installation
General: * Python 2.6 or better * One or more OpenCL implementations (test with e.g. PyOpenCl)
A working installation of OpenCL is the most difficult part of installing Nengo OCL. See below for more details on how to install OpenCL.
Python packages: * NumPy * nengo * networkx * mako * PyOpenCL
In the ideal case, all of the Python dependencies will be automatically installed when installing nengo_ocl with
pip install nengo_ocl
If that doesn’t work, then do a developer install to figure out what’s going wrong.
Developer Installation
First, pip install nengo. For best performance, make sure a fast version of Numpy is installed by following the instructions in the Nengo README. Currently, nengo_ocl is compatible with Nengo 2.0.x, supporting most features.
Once Nengo is installed, install the remaining dependencies:
pip install networkx mako pyopencl
This repository can then be installed with:
git clone https://github.com/nengo/nengo_ocl.git
cd nengo_ocl
python setup.py develop --user
If you’re using a virtualenv (recommended!) then you can omit the --user flag.
Installing OpenCL
How you install OpenCL is dependent on your hardware and operating system. A good resource for various cases is found in the PyOpenCL documentation:
Below are instructions that have worked for the Nengo OCL developers at one point in time.
Intel OCL on Debian/Ubuntu Linux
Intel provides an OpenCL driver for at least some of their multicore processors. Core-i7 and Xeon chips can be quite good for running Nengo simulations.
Details: http://software.intel.com/en-us/forums/topic/390630
Download Intel SDK for OpenCL for applications from Intel’s OpenCL website
Extract
tar zxvf intel_sdk_for_ocl_applications_2012_x64.tgz
Convert RPM files to .deb
sudo apt-get install -y rpm alien libnuma1 # Get conversion packages fakeroot alien --to-deb opencl-1.2-*.rpm # Convert all RPMs
Install .deb packages. They will be put in /opt/intel
sudo dpkg -i opencl-1.2-*.deb # Install all .debs
Add library to search path
sudo touch /etc/ld.so.conf.d/intelOpenCL.conf Put in the line: ``/opt/intel/opencl-1.2-3.0.67279/lib64``
Link the Intel ICD file
sudo ln /opt/intel/opencl-1.2-3.0.67279/etc/intel64.icd /etc/OpenCL/vendors/intel64.icd
Run ldconfig
sudo ldconfig
AMD OCL on Debian Unstable
On Debian unstable (sid) there are packages in non-free and contrib to install AMD’s OCL implementation easily. Actually, the easiest thing would be to apt-get install python-pyopencl. But if you’re using a virtual environment, you can sudo apt-get install opencl-headers libboost-python-dev amd-opencl-icd amd-libopencl1 and then pip install pyopencl.
Nvidia OCL on Debian/Ubuntu Linux
On Debian unstable (sid) there are packages for installing the Nvidia OpenCL implementation as well.
sudo apt-get install nvidia-opencl-common nvidia-libopencl1
Ensure that the Nvidia driver version matches the OpenCL library version. You can check the Nvidia driver version by running nvidia-smi in the command line. You can find the OpenCL library version by looking at the libnvidia-opencl.so.XXX.XX file in the /usr/lib/x86_64-linux-gnu/ folder.
Note! At the time of writing (Sept 2013) these drivers provide only OpenCL-1.1 rather than the more current OpenCL-1.2. Consequently, you may find that pyopencl’s default build creates a binary Python module (_cl.so) that cannot be loaded (i.e. import pyopencl fails in the Python interpreter). You can fix this one of two ways:
Use the generic libOpenCL.so driver-loading library from another provider (by e.g. following the Intel instructions above), and simply don’t try to use new 1.2 features on NVidia devices.
Follow PyOpenCL’s build instructions to compile an OpenCL-1.1 version of PyOpenCL.
It’s nice to have a CPU OpenCL driver, so we recommend option (1).
Release History
0.1.0 (June 8, 2015)
Initial release of Nengo OpenCL! Supports Nengo 2.0.x on Python 2.6+ and 3.3+.
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