Cell splitting in neural networks extends strong scaling (Hines et al. 2008)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:97917
Neuron tree topology equations can be split into two subtrees and solved on different processors with no change in accuracy, stability, or computational effort; communication costs involve only sending and receiving two double precision values by each subtree at each time step. Application of the cell splitting method to two published network models exhibits good runtime scaling on twice as many processors as could be effectively used with whole-cell balancing.
Reference:
1 . Hines M, Eichner H, Schuermann F (2008) Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors J Comput Neurosci 25(1):203-210 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Generic;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
/
splitcell
pardentategyrus
readme.html *
bgka.mod *
CaBK.mod *
ccanl.mod *
Gfluct2.mod *
gskch.mod *
hyperde3.mod *
ichan2.mod *
LcaMig.mod *
nca.mod *
tca.mod *
bg.sh
DG500_M7.hoc *
dgnetactivity.jpg *
dgnettraces.jpg *
init.hoc
initorig.hoc *
modstat *
mosinit_orig.hoc *
out.std
parRI10sp.hoc
RI10sp.hoc
test1.sh *
time *
                            
TITLE l-calcium channel
: l-type calcium channel


UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)
	(molar) = (1/liter)
	(mM) = (millimolar)
	FARADAY = 96520 (coul)
	R = 8.3134 (joule/degC)
	KTOMV = .0853 (mV/degC)
}

PARAMETER {
	v (mV)
	celsius 	(degC)
	glcabar		 (mho/cm2)
	ki=.001 (mM)
	cai (mM)
	cao (mM)
        tfa=1
}


NEURON {
	SUFFIX lca
	USEION lca READ elca WRITE ilca VALENCE 2
	USEION ca READ cai, cao VALENCE 2 
        RANGE glcabar, cai, ilca, elca
        GLOBAL minf,matu
}

STATE {
	m
}

ASSIGNED {
	ilca (mA/cm2)
        glca (mho/cm2)
        minf
        matu   (ms)
	elca (mV)   

}

INITIAL {
	rate(v)
	m = minf
	VERBATIM
	cai=_ion_cai;
	ENDVERBATIM
}

BREAKPOINT {
	SOLVE state METHOD cnexp
	glca = glcabar*m*m*h2(cai)
	ilca = glca*ghk(v,cai,cao)

}

FUNCTION h2(cai(mM)) {
	h2 = ki/(ki+cai)
}


FUNCTION ghk(v(mV), ci(mM), co(mM)) (mV) {
        LOCAL nu,f

        f = KTF(celsius)/2
        nu = v/f
        ghk=-f*(1. - (ci/co)*exp(nu))*efun(nu)
}

FUNCTION KTF(celsius (DegC)) (mV) {
        KTF = ((25./293.15)*(celsius + 273.15))
}


FUNCTION efun(z) {
	if (fabs(z) < 1e-4) {
		efun = 1 - z/2
	}else{
		efun = z/(exp(z) - 1)
	}
}

FUNCTION alp(v(mV)) (1/ms) {
	TABLE FROM -150 TO 150 WITH 200
	alp = 15.69*(-1.0*v+81.5)/(exp((-1.0*v+81.5)/10.0)-1.0)
}

FUNCTION bet(v(mV)) (1/ms) {
	TABLE FROM -150 TO 150 WITH 200
	bet = 0.29*exp(-v/10.86)
}

DERIVATIVE state {  
        rate(v)
        m' = (minf - m)/matu
}

PROCEDURE rate(v (mV)) { :callable from hoc
        LOCAL a
        a = alp(v)
        matu = 1/(tfa*(a + bet(v)))
        minf = tfa*a*matu
}
 



Loading data, please wait...