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
nrntraub
cells
hoc
mod
net
README
balcomp.hoc *
bgrunme
bgsmall.sh
bgsplit.sh
cell_templates.hoc *
clear.hoc *
finit.hoc *
fortmap.hoc *
gidcell.hoc
gidcell.ses *
init.hoc
manage_setup.hoc
metisbal.sh
mosinit_orig.hoc *
onecell.hoc
onecell.ses *
prcellstate.hoc *
prepare.sh
printcon.hoc *
spkplt.hoc *
vclampg.hoc *
vcompclamp.hoc *
vcompsim.hoc *
                            
#!/bin/sh


R=`waitforfree`
allocpart $R

if false ; then

bgnoalloc $R 1 -c "load_balance_phase=1" init.hoc
bgnoalloc $R 4 -c "load_balance_phase=2" init.hoc
bgnoalloc $R 4 -c "load_balance_phase=4" init.hoc
bgnoalloc $R 5 hoc/balcomp.hoc

NRNIV=/home/hines/neuron/nrnobj/powerpc64/bin/nrniv sh metisbal.sh \
	32 64 128 256 512 > metisbal.stdout

fi

if true ; then

for i in 32 64 128 256 ; do
	for phase in 0 3 5 ; do
		rm -f out$i.dat
		bgnoalloc VN $R $i -c "load_balance_phase=$phase" init.hoc
		sortspike out$i.dat out$i.$phase.dat
		cmp out.std.nogap out$i.$phase.dat
		mv temp.$i stdout.$i.$phase
	done
done

fi

freepart $R

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