Auryn simulator

Simulator for spiking neural networks with synaptic plasticity

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quick_start [2016/08/18 17:51] – [Running a first simulation] zenkequick_start [2017/09/29 10:57] (current) – [Running a first simulation] Fixes example code zenke
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 First, install cmake, git and some additional packages. Under Ubuntu or Debian simply  First, install cmake, git and some additional packages. Under Ubuntu or Debian simply 
 <code>sudo apt-get install cmake git build-essential libboost-all-dev</code> <code>sudo apt-get install cmake git build-essential libboost-all-dev</code>
-now download and compile Auryn with the following commands+on any other platform you will need to install a C++ compiler a few [[manual:required libraries|libraries]]  and the programs git and cmake. Now download and compile Auryn with the following commands
 <code> <code>
 git clone https://github.com/fzenke/auryn.git git clone https://github.com/fzenke/auryn.git
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 ./bootstrap.sh && make ./bootstrap.sh && make
 </code> </code>
-This will checkout the ''master'' branch and compile it in the subdirectory ''auryn/build/''. At this point cmake will complain about any missing [[manual:required libraries|libraries]].  The static library ''libauryn.a'' will be placed under ''build/release/src/''You can install it to your systems default directory or elsewhere using ''make install''. For more detailed instructions on where to download and how to compile go to [[manual:compileAuryn|howto compile Auryn]].+This will checkout the ''master'' branch and compile it in the subdirectory ''auryn/build/''. At this point cmake will complain about any missing [[manual:required libraries|libraries]].  The static library ''libauryn.a'' will be placed under ''build/release/src/''I usually leave it there and tell my compiler [[manual:CompileAndRunAurynSimulations|explicitly where to find it]], but you can also install it to your systems default directory using ''make install''. For more detailed instructions on where to download and how to compile go to [[manual:compileAuryn|howto compile Auryn]].
  
  
 ===== Running a first simulation ===== ===== Running a first simulation =====
  
-Now, let's run a first small Auryn simulation:+Now, let's run a first small Auryn simulation from the example directory
 <code> <code>
-cd examples +zenke@possum:~$ cd auryn/build/release/examples 
-./sim_poisson+zenke@possum:~/auryn/build/release/examples$ 
 +zenke@possum:~/auryn/build/release/examples$ ./sim_poisson  
 +[=========================] 100%      t=1.0s  f=5.2 Hz in SpikingGroup    
 +( 0) Freeing ...
 </code> </code>
-This will only take a few milliseconds and generate a bunch of Poisson spikes. If you have gnuplot installed (sudo apt-get install gnuplot) you can visualize them from the command line with+This will only take a few milliseconds and generate a bunch of Poisson spikes and store them in 'poisson.0.ras'. If you have gnuplot installed (sudo apt-get install gnuplot) you can visualize them from the command line with
 <code> <code>
 echo "plot 'poisson.0.ras' with dots lc rgb 'black'" | gnuplot -p echo "plot 'poisson.0.ras' with dots lc rgb 'black'" | gnuplot -p
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 For more details on this example go [[examples:sim_poisson|here]].  For more details on this example go [[examples:sim_poisson|here]]. 
  
-===== Running a second simulation =====+===== Running a network simulation =====
  
-Okay nice, let's do the same again for an actual network. Let's run a small version of Vogels Abbott balanced net.+Okay nice, let's do the same again for an actual network. Let's run a small balanced net, the [[examples:sim_coba_benchmark|Vogels Abbott benchmark]]  net.
 <code shell> <code shell>
 zenke@possum:~/auryn/build/release/examples$ ./sim_coba_benchmark --dir . zenke@possum:~/auryn/build/release/examples$ ./sim_coba_benchmark --dir .
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-===== Next steps ===== +====== Next steps ======
- +
-After you have [[manual:compileAuryn|compiled Auryn]], you will probably want to familiarize yourself with the simulator first using the supplied [[examples:start|examples]] provided under ''examples''. As a next step you might want to actually change things in these examples to learn how to use the simulator. To learn how to do that you can read [[manual:compileAndRunAurynSimulations|here]].+
  
-**Running in parallel with MPI.** +After you have [[manual:compileAuryn|compiled Auryn]], you will probably want to familiarize yourself with the simulator using the supplied [[tutorials:start]] and [[examples:start]]More on how to compile your own simulations [[manual:CompileAndRunAurynSimulations|here]].
-Auryn natively compiles against MPI and most of the time you will want to use in parallel to get good performance. Parallel execution is relatively simpleSee [[manual:parallel_execution|how it's done]].+
quick_start.1471542666.txt.gz · Last modified: 2016/08/18 17:51 by zenke