Auryn simulator

Simulator for spiking neural networks with synaptic plasticity

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manual:aube [2016/06/16 17:01] – created zenkemanual:aube [2017/04/18 16:22] (current) – [Extracting spikes from a single spk file.] zenke
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 ====== Auryn Binary Extract (aube) ====== ====== Auryn Binary Extract (aube) ======
  
-This command line tool extracts spike information from [[spk|binary spike raster files]] and converts them in the more digestible [[ras]] format. Binary files provide a significant simulation speed advantage over the old [[ras]] file format and allow random access to spike information. ''aube'' is capable of efficiently merging multiple [[spk]] files and export select temporal ranges from it to the more digestible [[ras]] format. It can be efficiently incorporated into Linux command-line and pipe based work flow and works flawlessly with [[gnuplot]]. The tool included with Auryn releases (ver. >0.6.1) and can be found in the ''tools'' directory. +This command line tool extracts spike information from [[spk|binary spike raster files]] and converts them in the more digestible [[ras]] format. Binary files provide a significant simulation speed advantage over the old [[ras]] file format, take less disk space and allow random access to temporal chunks of spike information. ''aube'' is capable of efficiently merging the multiple [[spk]] files generated by parallel simulations and exports only select temporal ranges from it. It can be efficiently incorporated into Linux command-line and pipe based work flow and works flawlessly with [[gnuplot]]. The tool included with Auryn releases (ver. >0.6.1) and can be found in the ''tools'' directory. For users doing their analysis in Python, the [[python tools]] offer an alternative to decoding spk files. These tools allow to directly import binary spiking data into Python without the detour via aube.
- +
 ===== Compiling/Installing aube ===== ===== Compiling/Installing aube =====
 ''aube'' is [[manual:compileauryn|compiled]] automatically with the rest of Auryn and located in the tools directory. It can be installed to your systems default install location (e.g. ''/usr/local/bin'') with the help of ''make install''. Otherwise you will have to ensure yourself that ''aube'' is in the PATH for the following examples to work. ''aube'' is [[manual:compileauryn|compiled]] automatically with the rest of Auryn and located in the tools directory. It can be installed to your systems default install location (e.g. ''/usr/local/bin'') with the help of ''make install''. Otherwise you will have to ensure yourself that ''aube'' is in the PATH for the following examples to work.
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 ===== Usage examples ===== ===== Usage examples =====
  
-To see how this works let's consider an example. Let's first generate some spiking output using the Vogels Abbott benchmark network witch conductance-based synapses (see [[examples:start]]).+To see how this works let's consider an example. Let's first generate some spiking output using the Vogels Abbott benchmark network with conductance-based synapses (see [[examples:start]]).
 To that end, we use example program ''examples/sim_coba_binmon.cpp'' which will be compiled with Auryn. You find it in your build directory under examples. In this directory, to run the code, just call: To that end, we use example program ''examples/sim_coba_binmon.cpp'' which will be compiled with Auryn. You find it in your build directory under examples. In this directory, to run the code, just call:
 <code> <code>
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 aube --input /tmp/coba.0.e.spk aube --input /tmp/coba.0.e.spk
 </code> </code>
 +or, alternatively, in short
 +<code>
 +aube -i /tmp/coba.0.e.spk
 +</code>
 +
  
 If you want to write the output to a file instead you can call: If you want to write the output to a file instead you can call:
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 mpirun -n 2 sim_coba_binmon --dir /tmp mpirun -n 2 sim_coba_binmon --dir /tmp
 </code> </code>
-This will run the same simulation using two parallel processes. Because each process writes only the spikes of the neurons it simulates (neurons are distributed across processes), you end up with multiple files ''/tmp/coba.*.e.spk''. After the simulation, however, you would like to merge these spikes to analyze all spikes. +This will run the Vogels Abbott benchmark using two parallel processes. Because each process writes only the spikes of the neurons it simulates (neurons are distributed across processes), you end up with multiple files ''/tmp/coba.*.e.spk''. After the simulation, however, you would like to merge these spikes to analyze all spikes. 
  
 Just call aube on all the input files: Just call aube on all the input files:
manual/aube.1466096468.txt.gz · Last modified: 2016/06/16 17:01 by zenke