PyNN on SpiNNaker Developer Install Guide

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Contents

Ubuntu Linux Requirements

  1. Install Python
    sudo apt-get install python2.7
  2. Install numpy
    sudo apt-get install python-numpy
  3. Install scipy
    sudo apt-get install python-scipy
  4. Install lxml
    sudo apt-get install python-lxml
  5. Install pip
    sudo apt-get install python-pip
  6. Optional: Install matplotlib (often used in PyNN scripts for plotting graphs)
    sudo apt-get install python-matplotlib

Continue to the Git Clone to install the remaining requirements.

Fedora Linux Requirements

  1. Install Python
    sudo dnf install python
  2. Install numpy
    sudo dnf install numpy
  3. Install scipy
    sudo dnf install scipy
  4. Install lxml
    sudo dnf install python-lxml
  5. Install pip
    sudo dnf install python-pip
  6. Optional: Install matplotlib (often used in PyNN scripts for plotting graphs)
    sudo dnf install python-matplotlib

Continue to the Git Clone to install the remaining requirements.

Mac OS X Requirements

  1. Download and install MacPorts
  2. Install python
    sudo port install python27
    sudo port select --set python python27
  3. Install numpy
    sudo port install py27-numpy
  4. Install scipy
    sudo port install py27-scipy
  5. Install lxml
    sudo port install py27-lxml
  6. Install pip
    sudo port install py27-pip
    sudo port select --set pip pip27
  7. Optional: Install matplotlib (often used in PyNN scripts for plotting graphs)
    sudo port install py27-matplotlib

Continue to the Git Clone to install the remaining requirements.

32-bit Windows Requirements

  1. Download and install Python
  2. Download and install numpy
  3. Download and install scipy
  4. Download and install lxml
  5. Download and install setuptools and [pip] (https://github.com/SpiNNakerManchester/github.SpiNNakerManchester.io/releases/download/v1.0-win32/pip-1.5.6.win32-py2.7.exe)
  6. Optional: Download and install matplotlib (often used in PyNN scripts for plotting graphs)
    1. Download and install dateutil, pyparsing, six and matplotlib

Continue to edit your PATH, before installing the remaining requirements.

64-bit Windows Requirements

  1. Download and install Python
  2. Download and install numpy
  3. Download and install scipy
  4. Download and install lxml
  5. Download and install setuptools and [pip] (https://github.com/SpiNNakerManchester/github.SpiNNakerManchester.io/releases/download/v1.0-win64/pip-1.5.6.win-amd64-py2.7.exe)
  6. Optional: Download and install matplotlib (often used in PyNN scripts for plotting graphs)
    1. Download and install dateutil, pyparsing, six and matplotlib

Continue to edit your PATH, before installing the remaining requirements.

Windows Path Settings

  1. Edit your PATH environment variable to include the Python27, Python27\Scripts and (if installed) gtk\bin directories.
    1. Go to “Control Panel”
    2. Go to “System” (may be under “System and Security”)
    3. Select “Advanced System Settings”
    4. Select “Environment Variables”
    5. Select the “Path” in the “System Variables” box at the bottom
    6. Click on “Edit”
    7. Add the new directory by putting it before the existing string, followed by a single semi-colon; if you installed the dependencies to the default/recommended locations, prepend Path with:
      C:\Python27;C:\Python27\Scripts;

Continue to the Git Clone to install the remaining requirements.

Git Cloning Requirements

Central gitClone

You now need to clone the github resposorities for all the software stack. This requires you to run the following commands in a terminal, in the folder of your choice where the software will be installed.

git clone https://github.com/SpiNNakerManchester/sPyNNaker.git
cd sPyNNaker
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExtraModelsPlugin.git
cd sPyNNakerExtraModelsPlugin
sudo python setup.py develop --no-deps 
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNFrontEndCommon.git
cd SpiNNFrontEndCommon
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/PACMAN.git
cd PACMAN
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMan.git
cd SpiNNMan
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExternalDevicesPlugin.git
cd sPyNNakerExternalDevicesPlugin
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/DataSpecification.git
cd DataSpecification
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMachine.git
cd SpiNNMachine
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNakerGraphFrontEnd.git
cd SpiNNakerGraphFrontEnd
sudo python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/spinnaker_tools.git
git clone https://github.com/SpiNNakerManchester/spinn_common.git
git clone https://github.com/SpiNNakerManchester/ybug.git
git clone https://github.com/SpiNNakerManchester/Visualiser.git
git clone https://github.com/SpiNNakerManchester/PyNNExamples.git
sudo pip install enum34
sudo pip install six
sudo pip install pyNN==0.7.5

Continue to the C Compiler Install to install the remaining c compiler dependency

User-Only gitclone

You now need to clone the github resposorities for all the software stack. This requires you to run the following commands in a terminal, in the folder of your choice where the software will be installed.

git clone https://github.com/SpiNNakerManchester/sPyNNaker.git
cd sPyNNaker
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExtraModelsPlugin.git
cd sPyNNakerExtraModelsPlugin
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNFrontEndCommon.git
cd SpiNNFrontEndCommon
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/PACMAN.git
cd PACMAN
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMan.git
cd SpiNNMan
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExternalDevicesPlugin.git
cd sPyNNakerExternalDevicesPlugin
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/DataSpecification.git
cd DataSpecification
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMachine.git
cd SpiNNMachine
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNakerGraphFrontEnd.git
cd SpiNNakerGraphFrontEnd
python setup.py develop --no-deps --user
cd ..
git clone https://github.com/SpiNNakerManchester/spinnaker_tools.git
git clone https://github.com/SpiNNakerManchester/spinn_common.git
git clone https://github.com/SpiNNakerManchester/ybug.git
git clone https://github.com/SpiNNakerManchester/Visualiser.git
git clone https://github.com/SpiNNakerManchester/PyNNExamples.git
pip install enum34 --user
pip install six --user
pip install pyNN==0.7.5 --user

Continue to the C Compiler Install to install the remaining c compiler dependency

Virtualenv git clone

These instructions will install the required packages only in a virtualenv. Like the user-only installation, this can help when you don’t have root access or are on a shared machine. Additionally, it will help when you have several packages with conflicting dependencies, or those that occupy the same namespace (such as pyNN.spiNNaker if you have an older version of the toolchain).

If you already have installed sPyNNaker previously (and the optional sPyNNakerExtraDevicesPlugin and/or sPyNNakerExtraModelsPlugin), you will need to uninstall it:

  1. Activate your virtualenv, <name>
    source <name>/bin/activate
  2. Uninstall the existing tools
    pip uninstall pyNN-SpiNNaker
    pip uninstall sPyNNaker
    pip uninstall sPyNNakerExternalDevicesPlugin
    pip uninstall sPyNNakerExtraModelsPlugin

The installation of virtualenv and the linking to the external libraries is platform dependent.

Ubuntu Virtualenv Installation

  1. Install virtualenv
    sudo pip install virtualenv
  2. Create a virtualenv; <name> in the following can be replaced by the name of your choice
    virtualenv <name>
  3. Activate the virtualenv
    source <name>/bin/activate
  4. Link numpy to the virtualenv
    ln -s /usr/lib/python2.7/dist-packages/numpy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  5. Link scipy to the virtualenv
    ln -s /usr/lib/python2.7/dist-packages/scipy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  6. Link lxml to the virtualenv
    ln -s /usr/lib/python2.7/dist-packages/lxml* $VIRTUAL_ENV/lib/python2.7/site-packages/
  7. Optional: link matplotlib to the virtualenv and install dependencies (only if you chose to install matplotlib)
    pip install python-dateutil
    pip install pyparsing
    pip install six
    ln -s /usr/lib/pymodules/python2.7/matplotlib $VIRTUAL_ENV/lib/python2.7/site-packages/
    ln -s /usr/lib/pymodules/python2.7/pylab.py $VIRTUAL_ENV/lib/python2.7/site-packages/
  8. go to Virtual git clone to compelte the cloning of the git reposorities

You can now configure your environment.

32-bit Fedora Virtualenv Installation

  1. Install virtualenv
    sudo pip install virtualenv
  2. Create a virtualenv; <name> in the following can be replaced by the name of your choice
    virtualenv <name>
  3. Activate the virtualenv
    source <name>/bin/activate
  4. Link numpy to the virtualenv
    ln -s /usr/lib/python2.7/site-packages/numpy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  5. Link scipy to the virtualenv
    ln -s /usr/lib/python2.7/site-packages/scipy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  6. Link lxml to the virtualenv
    ln -s /usr/lib/python2.7/site-packages/lxml* $VIRTUAL_ENV/lib/python2.7/site-packages/
  7. Optional: link matplotlib to the virtualenv and install dependencies (only if you chose to install matplotlib)
    pip install python-dateutil
    pip install pyparsing
    pip install six
    ln -s /usr/lib/python2.7/site-packages/matplotlib $VIRTUAL_ENV/lib/python2.7/site-packages/
    ln -s /usr/lib/python2.7/site-packages/pylab.py $VIRTUAL_ENV/lib/python2.7/site-packages/
  8. go to Virtual git clone to compelte the cloning of the git reposorities

You can now configure your environment.

64-bit Fedora Virtualenv Installation

  1. Install virtualenv
    sudo pip install virtualenv
  2. Create a virtualenv; <name> in the following can be replaced by the name of your choice
    virtualenv <name>
  3. Activate the virtualenv
    source <name>/bin/activate
  4. Link numpy to the virtualenv
    ln -s /usr/lib64/python2.7/site-packages/numpy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  5. Link scipy to the virtualenv
    ln -s /usr/lib64/python2.7/site-packages/scipy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  6. Link lxml to the virtualenv
    ln -s /usr/lib64/python2.7/site-packages/lxml* $VIRTUAL_ENV/lib/python2.7/site-packages/
  7. Optional: link matplotlib to the virtualenv and install dependencies (only if you chose to install matplotlib)
    pip install python-dateutil
    pip install pyparsing
    pip install six
    ln -s /usr/lib64/python2.7/site-packages/matplotlib $VIRTUAL_ENV/lib/python2.7/site-packages/
    ln -s /usr/lib64/python2.7/site-packages/pylab.py $VIRTUAL_ENV/lib/python2.7/site-packages/
  8. go to Virtual git clone to compelte the cloning of the git reposorities

You can now configure your environment.

Mac OS X Virtualenv Installation

  1. Install virtualenv
    sudo pip install virtualenv
  2. Create a virtualenv; <name> in the following can be replaced by the name of your choice
    virtualenv <name>
  3. Activate the virtualenv
    source <name>/bin/activate
  4. Link numpy to the virtualenv
    ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  5. Link scipy to the virtualenv
    ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy* $VIRTUAL_ENV/lib/python2.7/site-packages/
  6. Link lxml to the virtualenv
    ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml* $VIRTUAL_ENV/lib/python2.7/site-packages/
  7. Optional: link matplotlib to the virtualenv and install dependencies (only if you chose to install matplotlib)
    pip install python-dateutil
    pip install pyparsing
    pip install six
    ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib $VIRTUAL_ENV/lib/python2.7/site-packages/
    ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pylab.py $VIRTUAL_ENV/lib/python2.7/site-packages/
  8. go to Virtual git clone to compelte the cloning of the git reposorities

You can now configure your environment.

Windows Virtualenv Installation

  1. Open a console as administrator and cd to your home directory
    cd %HOMEPATH%
  2. Install virtualenv
    pip install virtualenv
  3. Create a virtualenv; <name> in the following can be replaced by the name of your choice
    virtualenv <name>
  4. Activate the virtualenv
    <name>\Scripts\activate.bat
  5. Link numpy to the virtualenv
    mklink /D %VIRTUAL_ENV%\Lib\site-packages\numpy C:\Python27\Lib\site-packages\numpy
    mklink %VIRTUAL_ENV%\Lib\site-packages\numpy-1.9.1-py2.7.egg-info C:\Python27\site-packages\numpy-1.9.1-py2.7.egg-info
  6. Link scipy to the virtualenv
    mklink /D %VIRTUAL_ENV%\Lib\site-packages\scipy C:\Python27\Lib\site-packages\scipy
    mklink %VIRTUAL_ENV%\Lib\site-packages\scipy-0.14.1rc1-py2.7.egg-info C:\Python27\site-packages\scipy-0.14.1rc1-py2.7.egg-info
  7. Link lxml to the virtualenv
    mklink /D %VIRTUAL_ENV%\Lib\site-packages\lxml C:\Python27\Lib\site-packages\lxml
    mklink /D %VIRTUAL_ENV%\Lib\site-packages\lxml-3.4.1-py2.7.egg-info C:\Python27\site-packages\lxml-3.4.1-py2.7.egg-info
  8. Optional: link matplotlib to the virtualenv and install dependencies (only if you chose to install matplotlib)
    pip install python-dateutil
    pip install pyparsing
    pip install six
    mklink /D %VIRTUAL_ENV%\Lib\site-packages\matplotlib C:\Python27\Lib\site-packages\matplotlib
    mklink %VIRTUAL_ENV%\Lib\site-packages\pylab.py C:\Python27\Lib\site-packages\pylab.py
  9. Optional: To make matplotlib work within a virtualenv, create the following environment variables:
    TCL_LIBRARY: C:\Python27\tcl\tcl8.5
    TK_LIBRARY: C:\Python27\tcl\tk8.5
  10. go to virtual git clone to compelte the cloning of the git reposorities

You can now configure your environment.

Virtual git clone

You now need to clone the github resposorities for all the software stack. This requires you to run the following commands in a terminal, in the folder of your choice where the software will be installed.

git clone https://github.com/SpiNNakerManchester/sPyNNaker.git
cd sPyNNaker
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExtraModelsPlugin.git
cd sPyNNakerExtraModelsPlugin
python setup.py develop --no-deps 
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNFrontEndCommon.git
cd SpiNNFrontEndCommon
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/PACMAN.git
cd PACMAN
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMan.git
cd SpiNNMan
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/sPyNNakerExternalDevicesPlugin.git
cd sPyNNakerExternalDevicesPlugin
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/DataSpecification.git
cd DataSpecification
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNMachine.git
cd SpiNNMachine
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/SpiNNakerGraphFrontEnd.git
cd SpiNNakerGraphFrontEnd
python setup.py develop --no-deps
cd ..
git clone https://github.com/SpiNNakerManchester/spinnaker_tools.git
git clone https://github.com/SpiNNakerManchester/spinn_common.git
git clone https://github.com/SpiNNakerManchester/ybug.git
git clone https://github.com/SpiNNakerManchester/Visualiser.git
git clone https://github.com/SpiNNakerManchester/PyNNExamples.git
pip install enum34
pip install six
pip install pyNN==0.7.5

Continue to the C Compiler Install to install the remaining c compiler dependency

C Development Environment

  1. Primarily, you will need to install a C compiler that is compatible with SpiNNaker. At present, we recommend using gcc for this. Instructions for installing this on your system are below, depending on which platform you are using, as well as instructions for installing Perl, which is used by the development tools to modify the generated binaries to run on SpiNNaker:

Development Dependencies for 64-bit Ubuntu

  1. Install 32-bit libc
    sudo apt-get install libc6-i386
  2. Install perl and dependencies
    sudo apt-get install perl perl-tk libterm-readline-gnu-perl
  3. Follow the instructions for the Linux C Compiler

Development Dependencies for 64-bit Fedora

  1. Install 32-bit libc
    sudo dnf install glibc.i686
  2. Install perl and dependencies
    sudo dnf install perl perl-Tk perl-Term-ReadLine-Gnu
  3. Follow the instructions for the Linux C Compiler

Development Dependencies for 32-bit Ubuntu

  1. Install perl and dependencies
    sudo apt-get install perl perl-tk libterm-readline-gnu-perl
  2. Follow the instructions for the Linux C Compiler

Development Dependencies for 32-bit Fedora

  1. Install perl and dependencies
    sudo dnf install perl perl-Tk perl-Term-ReadLine-Gnu
  2. Follow the instructions for the Linux C Compiler

Linux C Compiler

  1. Download CodeSourcery GCC ARM EABI Compiler
  2. Extract the downloaded archive to the location of your choice
  3. Add the “bin” directory within the installed location to the PATH enviroment variable in .profile in your home directory e.g. append the following:
    export PATH=$PATH:<install-location>/bin
    where <install-location> is the place where you extracted the file.

Development Dependencies for Mac OS X

  1. Install the arm-none-eabi toolchain
    sudo port install arm-none-eabi-gcc
  2. Install perl and dependencies
    sudo port install perl5 p5-tk p5-term-readline-gnu
  3. Optional: Install Xcode and all its development tools from here NOTE: take into account your Mac version.

Development Dependencies for Windows

  1. Download the prepackaged MinGW Environment
  2. Extract the downloaded archive to the location of your choice
  3. Create a shortcut to MinGW/msys/1.0/msys.bat and add it to your start menu

You can now use the msys.bat to start up an environment from in which you can compile C code for SpiNNaker.

SpiNNakerTools Installation

  1. Create an environment variable SPINN_DIRS that points at the location of the cloned https://github.com/SpiNNakerManchester/spinnaker_tools.git (note that in Windows, this should be the MinGW Posix path e.g. if you have extracted the archive to C:\SpiNNaker-Tools\, you should set the environment variable to /c/SpiNNaker-Tools).
  2. Run make in the root directory of the extracted archive.

spinn_common Library Installation

The spinn_common library will be installed into the SpiNNaker Tools installation directory, as set up above.

  1. In the directory of the cloned https://github.com/SpiNNakerManchester/spinn_common.git, run make.
  2. Run make install.

SpiNNFrontEndCommon Library Installation

The SpiNNFrontEndCommon library will be installed into the SpiNNaker Tools installation directory, as set up above.

  1. In the c_common directory of the cloned https://github.com/SpiNNakerManchester/SpiNNFrontEndCommon.git, run make.
  2. Run make install.

YBug Installation

If you want to avoid having to run “source setup” in the ybug folder every time you log in or start a new terminal:

  1. Add the cloned ybug folder to your PATH environment variable
  2. Add the cloned ybug folder to your PERL5LIB environment variable (or create this environment variable if it is not already set; note that in Windows, this should be the MinGW Posix path e.g. if you have extracted the archive to C:\ybug\, you should set the environment variable to /c/ybug)
  3. If you are going to boot your board using ybug, create a new environment variable YBUG_PATH and set this to the boot subdirectory of the extracted ybug folder.

To run ybug:

  1. If you haven’t added the environment variables detailed above, go into the directory where you extracted the archive and run:
    source setup
  2. Run:
    ybug <ip-or-host>
    where <ip-or-host> is the ip address or hostname of your SpiNNaker board.

  3. Type help to get further usage instructions.

  4. Continue to the Compile Binaries to compelte the installation by compiling the binaries of the c code used by the tool chain.

Compile Binaries

To compile the c code used by the tool chain, run the following instructions from the base folder where all the software is installed:

cd spinnaker_tools
source setup
cd ..
cd spinn_common
make clean
make 
make install
cd ..
cd SpiNNMan/c_models/reinjector/
make 
cd ../../..
cd SpiNNFrontEndCommon/c_common/front_end_common_lib/
make install-clean
cd ..
make clean
make 
make install
cd ../..
cd sPyNNaker/neural_modelling/
make clean
make 
source setup
cd ../../SpiNNakerGraphFrontEnd/examples/
make clean
make

Continue to configure your environment.

Configuration

When SpyNNaker is first called, if a configuration file is not found, it will create one in your home directory and exit. It is possible to ask SpyNNaker to do this before you run your first simulation as follows:
python -c "import pyNN.spiNNaker"

Note that if you have previously installed a version of the spiNNaker software, you may already have a file called “.pacman.cfg” in your home directory. In this case, SpyNNaker will attempt to use this file for its paramters. If you don’t have this file, a new file called “.spynnaker.cfg” will be created in your home directory. You must edit this file to ensure that SpyNNaker can access your SpiNNaker machine. Upon opening this file, the part to alter will look like the following:
[Machine]
machineName = None
version = None

Within the file, you should set machineName to the IP address or hostname of your SpiNNaker machine, and version to the version of your SpiNNaker board; this will almost certainly be “3” for a 4-chip board or “5” on a 48-chip board.

The default ipaddress for a spinn-3 board is 192.168.240.253 and the default ipaddress for a spinn-5 board is 192.168.240.1

Network Configuration

Go to your network settings and set up your network adapter with the following settings:
1. ipaddress = 192.168.240.254 2. submask = 255.255.255.0 3. default gateway = 0.0.0.0

Running some examples

  1. Download the examples from here (zip) or here (tar.gz)
  2. Extract the archive
  3. Go to the “examples” folder
  4. Run:
    python va_benchmark.py
  5. You will see the system go through a series of processes from partitioning, to placement, to routing and finally to loading and running.
  6. Once the example has finished, you should see a graph, that will look something like this:
    VABenchmarkSpikes If you get the output above, you have successfully installed your system.

Troubleshooting

  1. If you experience the error:

**UnicodeDecodeError: 'ascii' codec can't decode byte 0xb0 in position 1: ordinal not in range(128)**

Then to solve it, edit C:\Python27\Lib\mimetypes.py and add these codes:

if sys.getdefaultencoding() != 'gbk':  
    reload(sys)
    sys.setdefaultencoding('gbk')

before the following line:

default_encoding = sys.getdefaultencoding()