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

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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 ML, Eichner H, Schürmann F (2008) Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors. J Comput Neurosci 25:203-10 [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
common
nrntraub
pardentategyrus
README
mkdll.result
mkdll.sh
mosinit.hoc
                            
load_file("nrngui.hoc")
load_file("stdlib.hoc")

mosinit=1
objref b_
b_ = new VBox()
b_.intercept(1)
b_.save("")
xpanel("")
xbutton("Santhakumar et. al.", "parden_launch()")
xbutton("Traub et. al.", "traub_launch()")
xpanel()
b_.intercept(0)
b_.map("Figure 3 Launch model", 100, 200, 200, 200)

objref mesg_box_
strdef mesg_string_
mesg_string_ = "Select a model to load mod files and setup. This will take a few seconds."
mesg_box_ = new VBox()
mesg_box_.intercept(1)
mesg_box_.save("")
xpanel("")
xvarlabel(mesg_string_)
xpanel()
mesg_box_.intercept(0)
doNotify()

proc parden_launch() { localobj s
	s = new String()
	s.s = "Santhakumar et. al. model"
	if (mkdll_("pardentategyrus", "", s.s)) {
		load_file("init.hoc")
		setup_(s.s)
	}
}

proc traub_launch() { localobj s
	s = new String()
	s.s = "Traub et. al. model"
	if (mkdll_("nrntraub", "mod", s.s)) {
		load_file("init.hoc")
		setup_(s.s)
	}
}

func mkdll_() { localobj s, f
	b_.unmap()
	doNotify()
	mesg_($s3, ": building dynamically loadable library")
	s = new String()
	sprint(s.s, "sh mkdll.sh %s \"%s\" %d", $s1, $s2, unix_mac_pc())
	system(s.s, s.s)
	f = new File()
	if (f.ropen("mkdll.result")) {
		if (f.gets(s.s) > 1) {
			hoc_sf_.left(s.s, hoc_sf_.len(s.s) - 1)
			mesg_("Loading ", s.s)
			nrn_load_dll(s.s)
			chdir($s1)
			sprint(s.s, "Setting up %s in %s", $s3, $s1)
			mesg_(s.s, " (may take some time)")
			return 1
		}
	}
	mesg_($s3, ": dll build failed. Exit and handle manually")
	return 0
}

proc setup_() { localobj s
	s = new String()
	sprint(s.s, " setup time is %g sec", setuptime)
	mesg_($s1, s.s)
}

proc mesg_() {
	if (!mesg_box_.ismapped()) {
		mesg_box_.map("Progress Message", 100, 200, 600, 50)
		doNotify()
	}
	sprint(mesg_string_, "%s %s", $s1, $s2)
	doNotify()
}

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