Auryn simulator

Simulator for spiking neural networks with synaptic plasticity

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manual:compileauryn

Image illustration by Larry Ellmore for [[http://www.goodreads.com/book/show/878973.Pillars_of_Pentegarn|Pillars of pentegarn]], adapted by Alex Seeholzer, 2016

In most cases, compiling Auryn is hardly going to be that difficult, but there are a few things to keep in mind.

Getting and compiling Auryn

To compile and run Auryn download and unpack the source from GitHub. You can either download a release version or clone either the master branch or a more recent development version.

Requirements

Apart from a standard C++ build environment you will need the Boost libraries and a working MPI implementation. See required libraries for more details. To get the code, I recommend git and, finally, to build the binaries I recommend cmake. With these preliminaries met, you can proceed as follows.

Getting the source with git

First clone Auryn's repository

git clone https://github.com/fzenke/auryn.git

This will create a new directory ./auryn with the source code.

Getting the source as a zip archive or tar ball

Alternatively, if you cannot use git, you can download zips or tar archives of the latest releases from GitHub latest stable release.

To unpack a tgz compressed archive of a release using for instance tar:

tar -xzf auryn-XY.tar.gz

where XY is the respective version number.

Building Auryn from source

Once you have downloaded the sources, compile Auryn using cmake. For this to work you have to install cmake http://www.cmake.org (under Debian, Ubuntu, etc – sudo apt-get install cmake). To build Auryn using cmake simply run:

cd auryn/build/release
./bootstrap.sh && make

Instead of the bootstrap script you can also invoke cmake directly as follows

cmake ../../ -DCMAKE_BUILD_TYPE=Release && make

If you want to specify an install prefix add the option -DCMAKE_INSTALL_PREFIX:PATH=/path/you/want to cmake. The Built type option will make sure that the library is built with compiler flags that make use of hardware optimizations (i.e. -O3 -DNDEBUG -march=native -ffast-math).

Either way you will find the compiled library libauryn.a under ./src and several simulation examples under ./examples. By issuing make install, the libraries will be installed to your system default directories (include and lib). In Debian based systems that is most likely /usr/local/. However, you do not need to install the library under this path, but instead point the linker to directly when compiling your Auryn simulation.

Frustrated?? Newbies are welcome to ask questions in the support forum. Unfortunately you need to register because of the spam flood the forum got in the past. Using an academic e-mail address will speed up the registration process.

Running a test

If you compiled Auryn using the existing Makefile (the old way) you can test the setup by issuing from within the build/home directory (if you used cmake you will find the examples under build/examples)

make sim_poisson && ./sim_poisson

which will compile the example code sim_poisson and generate the following output

[=========================] 100%      t=1.0 s  f=45.3 Hz  
( 0) Freeing ...

This tells you that the simulations called sim_poisson has finished simulating one second of 1000 poisson processes. You find three new files poisson.* in the same directory

[...]
380 -rw-r--r-- 1 zenke lcn1 383240 Dec  9 15:13 sim_isp_big.o
688 -rwxr-xr-x 1 zenke lcn1 699695 Dec  9 15:13 sim_isp_big
 76 -rw-r--r-- 1 zenke lcn1  69702 Dec  9 15:43 poisson.0.ras
  0 -rw-r--r-- 1 zenke lcn1     36 Dec  9 15:43 poisson.0.prate
  4 -rw-r--r-- 1 zenke lcn1    809 Dec  9 15:43 poisson.0.log

These are the output files of the simulation. Their meaning is described in more detail in the examples section.

Generate Doxygen code documentation

Now might be a good time to also compile the doxygen docs.

Building your own simulations/programs

See the CompileAndRunAurynSimulations guide to see how you can conveniently link your own simulations against the Auryn library.

Building other versions

Auryn development version

Some of the newest features might only be available in the development version. If you want to compile the development version, simply clone and compile Auryn as follows:

git clone -b develop https://github.com/fzenke/auryn.git
cd auryn/build/release/
./bootstrap.sh && make

Building Auryn without MPI

Starting from v0.8 you can build Auryn without MPI if need be. To do so, open the file src/auryn/auryn_definitions.h and comment out the line:

#define AURYN_CODE_USE_MPI

This will disable any dependence on MPI in the source code. Then in the CMakeLists.txt file in the Auryn root directory find the line

FIND_PACKAGE(MPI REQUIRED)

and comment it out or remove the REQUIRED part. This should now allow you to build Auryn without MPI support. To that end, follow the instructions to build Auryn from above.

Building Auryn with debug symbols (reduces performance)

To create a debug run instead use:

cd build/debug
cmake ../../ -DCMAKE_BUILD_TYPE=Debug
make

or alternatively

cd build/debug
./bootstrap && make

This will turn off all optimizations and compile all binaries with the “-g” (at least for gcc that's the one).

People hacking the simulator code will probably want to enable the -Wall option. To do so modify the file CMakeLists.txt in the Auryn root and uncomment the line add_definitions(-Wall). Then compile the code in your build directory using

cmake ../../ -DCMAKE_BUILD_TYPE=Debug && make VERBOSE=1

to show compiler warnings.

Building older versions of Auryn (<v0.7.0)

See instructions here.

manual/compileauryn.txt · Last modified: 2018/02/28 18:52 by zenke