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

 Download zip file 
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 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
nrntraub
hoc
balcomp.hoc *
binfo.hoc *
defvar.hoc *
karkar.hoc
lbcreate.hoc *
loadbal.hoc *
mscreate.hoc
msdiv.hoc *
parlib.hoc
parlib2.hoc
traubcon.hoc *
traubcon_net.hoc *
                            
{load_file("stdlib.hoc")}
proc default_var() {localobj s, pc
	s = new String()
	if (name_declared($s1) == 0) {
		if (argtype(2) == 2) {
			sprint(s.s, "~strdef %s", $s1)
			execute(s.s)
			sprint(s.s, "%s = \"%s\"", $s1, $s2)
		}else{
			hoc_ac_ = $2
			sprint(s.s, "%s = hoc_ac_", $s1)
		}
		execute(s.s)
	}
	pc = new ParallelContext()
	if (pc.id == 0) {
		sprint(s.s, "print \"%s  \", %s", $s1, $s1)
		execute(s.s)
	}
}


// BlueGene has an occasional system error with respect to
// incessantly changing directories with load_file
// following should work as long as nothing loaded twice
// and only used for files relative to the project
strdef curdir
curdir = "./"
proc localloadfile() {localobj dir, f, sf, oldcd, path
//	load_file($s1)
//	return

	oldcd = new String()
	oldcd.s = curdir

	sf = new StringFunctions()
	dir = new String()
	path = new String()
	f = new String()
	i = sf.head($s1, "/[^/]*$", dir.s)
	f.s = $s1
	if (i == -1) {
		dir.s = ""
	}else{
		sprint(dir.s, "%s/", dir.s)
		sf.right(f.s, i+1)
	}
	sprint(curdir, "%s%s", curdir, dir.s)
	sprint(path.s, "%s%s", curdir, f.s)
//printf("loading %s\n", path.s)
	xopen(path.s)
	curdir = oldcd.s
}

Loading data, please wait...