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];
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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

if test "$#" = 0 ; then
echo "sh bgrunme partition np phase nhost(for phase 4, 6)"
exit 0
fi

NRNIV=/home/hines/neuron/nrnobj/powerpc64/bin/nrniv

R=$1
np=$2
nhost=$np
PHASE=$3
shift
shift
shift

echo partition $R   np $np   phase $PHASE

run() {
  bgrun VN $R $np $*
}

phase() {
 p=$1
 shift
 run -c "load_balance_phase=$p" $*
 mv temp.$np stdout.$nhost.$p
}

# create mcomplex.dat
if test "$PHASE" = "1" ; then
phase 1 $PHASE init.hoc
fi

# whole cell load balance with specified prefix and nhost
if test "$PHASE" = "4" ; then
prefix=cxwhole
nhost=$1
sed "
/default_var.*wholecell_prefix/s/cxwhole/$prefix/
" init.hoc > _init.hoc
phase $PHASE _init.hoc
$NRNIV -c "{load_file(\"hoc/binfo.hoc\")}" -c "mymetis2(\"$prefix\",$nhost)" \
  >> stdout.$nhost.$PHASE
fi

#whole cell load balance run with specified prefix
if test "$PHASE" = "5" ; then
prefix=cxwhole
sed "
/default_var.*wholecell_prefix/s/cxwhole/$prefix/
" init.hoc > _init.hoc
phase $PHASE _init.hoc
sortspike out$nhost.dat out$nhost.$PHASE
rm out$nhost.dat
fi

# base round robin run
if test "$PHASE" = "0" ; then
phase $PHASE init.hoc
sortspike out$nhost.dat out$nhost.$PHASE
rm out$nhost.dat
fi

# multisplit load balance with specified prefix and nhost
if test "$PHASE" = "6" ; then
nhost="$1"
prefix=cx_$nhost
sed "
/default_var.*multisplit_prefix/s/cx/$prefix/
/default_var.*multisplit_nhost/s/256/$nhost/
" init.hoc > _init.hoc
phase $PHASE _init.hoc
$NRNIV -c "{load_file(\"hoc/binfo.hoc\")}" -c "mymetis3(\"$prefix\",$nhost)" \
  >> stdout.$nhost.$PHASE
fi


# multisplit load balance run
if test "$PHASE" = "7" ; then
prefix=cx_$nhost
sed "
/default_var.*multisplit_prefix/s/cx/$prefix/
" init.hoc > _init.hoc
phase $PHASE _init.hoc
sortspike out$nhost.dat out$nhost.$PHASE
rm out$nhost.dat
fi




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