Parallel network simulations with NEURON (Migliore et al 2006)

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Accession:64229
The NEURON simulation environment has been extended to support parallel network simulations. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
Reference:
1 . Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
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];
/
netmod
parbulbNet
parbush
pardentategyrus
parscalebush
perf1
README
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("Davison et. al. (> 1 minute setup)", "parbulb_launch()")
xbutton("Bush et. al.", "parbush_launch()")
xpanel()
b_.intercept(0)
b_.map("Figure 4 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 parbulb_launch() { localobj s
	s = new String()
	s.s = "Davison et. al. model"
	if (mkdll_("parbulbNet", s.s)) {
		load_file("par_batch1.hoc")
		setup_(s.s)
	}
}

proc parbush_launch() { localobj s
	s = new String()
	s.s = "Bush et. al. model"
	if (mkdll_("parbush", s.s)) {
		load_file("batch_.hoc")
		setup_(s.s)
	}
}

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