Auryn simulator

Simulator for spiking neural networks with synaptic plasticity

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manual:aube [2016/06/16 19:01]
zenke created
manual:aube [2017/04/18 18:21]
zenke [Auryn Binary Extract (aube)]
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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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 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.txt · Last modified: 2017/04/18 18:22 by zenke