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];
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netmod
parscalebush
AMPA.mod *
arhRT03.mod *
cadecay.mod
cadRT03.mod
cah.mod
calRT03.mod
catRT03.mod *
GABAa.mod *
GABAb.mod *
intf.mod
k2RT03.mod *
kahpRT03.mod
kaRT03.mod *
kca.mod *
kcRT03.mod
kdr.mod
kdrp.mod
kdrRT03.mod *
kmRT03.mod *
misc.mod
myfit.mod
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
stats.mod
vecst.mod
batch.hoc
bg
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
geom.hoc
init.hoc
netcon.inc
network.hoc
nqsnet.hoc
nspike.dat
params.hoc
parnetwork.hoc
parnqsnet.hoc
perfrun.hoc
prebatch_.hoc
run.hoc
spkplt.hoc *
x_vs_nspike.hoc
                            
bg() {
	echo "bg $1 $2 $3"
	sed "
s/^ncell = 500$/ncell = $2/
s/^tstop = 500$/tstop = $3/
" < init.hoc > init_.hoc
#/^want_all_spikes/d
#/^pnm.gatherspikes/d
#/^spike2file/d
rm out.dat
bgrun $5 $4 $1 init_.hoc
mv temp.$1 temp$5$1.$2.$3
if test -f out.dat ; then
  sort -k 1n,1n -k 2n,2n out.dat > out$5$1.$2.$3
fi
}

if test "$1" != "" ; then
	bg $1 $2 $3 $4 $5
else

if false ; then

bg 500 50000 200 R100
bg 1000 50000 200 R100 VN
bg 250 50000 200 R100
#bg 125 50000 200 R1000

fi

if false ; then

bg 50 10000 200 R1000
bg 125 10000 200 R1000
bg 250 10000 200 R100
bg 500 10000 200 R100
bg 1000 10000 200 R101 VN
bg 1000 10000 200 R10
bg 2000 10000 200 R10 VN
bg 2000 10000 200 R0

bg 125 20000 200 R1003
bg 250 20000 200 R1000 VN
bg 500 20000 200 R101
bg 1000 20000 200 R101 VN
bg 1000 20000 200 R10
bg 2000 20000 200 R10 VN
bg 4000 20000 200 R0 VN

#bg 250 40000 200 R100 out of memory
bg 500 40000 200 R100
bg 1000 40000 200 R10
bg 2000 40000 200 R10 VN
bg 4000 40000 200 R0 VN

#bg 500 80000 200 R100 out of memory
bg 1000 80000 200 R10
bg 2000 80000 200 R10 VN
bg 4000 80000 200 R0 VN

bg 4000 160000 200 R0 VN out of memory

fi

if true ; then


bg 8000 40000 200 R_32 VN
bg 4000 40000 200 R_32

bg 8000 80000 200 R_32 VN
bg 4000 80000 200 R_32

bg 8000 160000 200 R_32 VN
bg 4000 160000 200 R_32

bg 4000 20000 200 R_32

fi


fi

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