par-RSnet - a version of RSnet for parallel GENESIS

RSnet is a demonstration of a simple network, consisting of a grid of simplified neocortical regular spiking pyramidal cells, each one coupled with excitory synaptic connections to its four nearest neighbors. This might model the connections due to local association fibers in a cortical network.

The example RSnet simulation was designed to be easily modified to allow you to use other cell models, implement other patterns of connectivity, or to augment with a population of inhibitory interneurons and the several other types of connections in a cortical network. Details of running the simulation and understanding the scripts are in the "Creating large networks with GENESIS" section of the GENESIS Modeling Tutorial, Tutorials/genprog/net-tut.html.

The serial genesis version may be run from the networks/RSnet directory with the command "genesis RSnet.g".

par-RSnet.g is the main script of the parallel version, which was written as an example for the GENESIS Modeling Tutorial "Converting large network simulations to PGENESIS". It may be run in its default configuration from the networks/par-RSnet directory with the command

    pgenesis -nodes 4 par-RSnet.g

after installing MPI and PGENESIS. The Mini-tutorial "Using Parallel GENESIS on PCs with Multicore Processors" gives further details. This version of the script has been tested on a PC with a 2.4 GHz Intel Q6600 quad core processor, running GENESIS 2.3 and PGENESIS 2.3.1 under Fedora Linux. A typical execution time for a similarly configured version of RSnet.g was about 3.1 times longer than for par-RSnet.g. Because of the lack of inhibition, the network fires rapdily, generating many internode SPIKE messages. Thus, a speedup closer to the number of processor cores would likely be obtained in a network with more balanced inhibition and excitation.

This script has the default definitions:
int graphics = 1 // display control panel, graphs, optionally net view
int output = 1   // send simulation output to a file
int batch = 0    // if (batch) do a run with default params and quit
int netview = 0  // show network activity view (very slow, but pretty)

These may be changed to show the network view widget to visualize the propagation of network activity. This can be useful for understanding the behavior of the network, but is much slower, due to the large number of messages sent to the view from remote nodes.. If the batch flag is changed to 1 and graphics to 0, it produces the output file Vm.dat. This contains the Vm of each of the 1024 cells at 1001 time steps. It is large - about 11 MB, but can be compressed with bzip2 to about 12 KB.

Further details are given in the tutorial.


DPchans.g5643 bytesThu Mar 3 23:12:16 2005
par-RSnet.g20843 bytesWed Jun 10 15:52:59 2009
pgraphics.g8178 bytesWed Apr 2 22:48:58 2008
protodefs.g1351 bytesTue Mar 15 23:53:05 2005
README2826 bytesWed Jun 10 16:42:44 2009
RScell.p783 bytesTue Mar 15 22:46:22 2005

Dave Beeman
Wed Jun 10 16:41:07 MDT 2009