Code repository for the IOSSIM project

IOSSIM is the software/project aiming the whole brain simulation of the insect olfactory neuronal circit that include from the sensory processing to genelations of behavior patterns. IOSSIM is a part of ISLiM(Next generation integrated simulation of living matter1.

IOSSIM software stack


Bombyx Neuron Database 

The database that concrets the morphology and phisiological responses of single neurons in silkmoth, bombyx mori. More than 1600 data(2012/4) of neurons is registered and a part of it are opened to the public.


KNEWRiTE is our software for segmentation of single neuron morphology. it is based on Qt and executable under windows and linux enviroment. detailed explanations of this software is described in (ikeno et. al. 2012).
sorce codes is here. (using mercurial)


Neuroregister is a plugin software for Fiji. it helps mapping of swc files on stadndard brain coodinate system. sorce codes is here. (using mercurial)


We ported and optimized simulation environment "NEURON" on K computer to simulate a insect brain as multi-compartment Hodgkin-Huxley type model. To use SIMD units of SPARC64VIIIfx (CPU of K computer), we exchanged the order of the compartment loop and the ion channel loop and apply sector caches. These tuning improved single core performance 340 MFLOPS/core to 1560 MFLOPS/core (about 10% efficiency).Spike exchange method of “NEURON” (MPI_Allgather) demands large amount of time in case of 10,000 cores or more and simple asynchronous point-to-point method (MPI_Isend) is not effective either, because of a large number of function calls and long distance of interconnect pathway. To tackle these problems, we adopted MPI/OpenMP hybrid parallelization to reduce interconnect communications and we developed a program to optimize location of neurons on calculation nodes in the 3D torus network. As a these results, we obtained 187 TFLOPS with 196,608 CPU cores. Current situation is described in this poster. This software is licensed by GPL.

sorce 2012/09

How to intall NEURON_K+

for 12/06 version
1 Uncompress NEURON_K+.
> tar xvzf neuron_kplus_release[version].tar.gz
> mv neuron_kplus_release[version].tar.gz neuron_kplus
2. Download original NEURON source codes and move.
> wget http://www.neuron.yale.edu/ftp/neuron/versions/v7.2/nrn-7.2.tar.gz
> tar xvzf nrn-7.2.tar.gz
> mv nrn-7.2 neuron_kplus/nrn
3. Apply the patch to the NEURON.
> cd neuron_kplus
> patch -p0 < neuron_kplus_release[version].diff
4. Make MOD file compiler.
> cd nrn
> ../config_sh/config_mod_[machine].sh
> make
> make install

5. Make NEURON.
> ../config_sh/config_nrn_[machine].sh
> make
> make install

for 12/10 version
1 expanding sources
>tar xvf nrnkp121005.tar.gz

2 compile mod translator
>. config_mod_k.sh
>make install
you can find nocmodl ln root/nrnkp121001/x86_64/bin

3 compile the others
>. config_nrn_k.sh
> make
> make install
you can find nrniv and the others in nrnkp121001/sparc64/bin.

+++to compile mod files

1 generating special
1a)copy nocmodl which is the translator using GCC from mod to c GCC
From /$HOME/k+/nrn/sparc64/bin
>cp ../../x86_64/bin/nocmodl . 

1b)prepar mod files
in any folder do
>tar –xvf mod.tar.gz

1c)compile mod
from mod folder do

mod/sparc64/Special shoud be created.

2 execute jobs


In the appropriate directory do
>tar xvf hocjobs.tar.gz
2b)editing script file
>cd hocjobs
change the path in nkjob.sh
2c) execution
>pjsub nkjob.sh

updating of the site
Copyright (cc) 2005-2013 RIKEN BSI Neuroinformatics Japan Center. Some rights reserved.