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

# sh small.sh 6 # to create cx6_2048.dat and cx6_2048.2048.dat , etc.
# sh small.sh 7 # to run the small multisplit sims
# sh small.sh 4 # to create cx5.dat
if test "$1" = "" ; then
	exit 0
fi

if test "$2" = "" ; then
	MSOPT="8"
else
	MSOPT="$2"
fi

PHASE=$1

SIMDIR=/bglscratch/hines/nrntraub
RESULTDIR=small${PHASE}
BINDIR=/home/hines/bin
STD=stdout

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

echo wait for partition
date
PART=`waitforfree`
echo "$PART is free"
/bgl/bin/allocpart $PART


run() {
echo $*
(time mpirun -noallocate -partition $PART -np $1 -mode VN \
 -cwd $SIMDIR \
 -exe $SIMDIR/powerpc64/special \
 -env "BLG_CHKPT_ENABLED=0" -args "_init.hoc" \
 )>& $SIMDIR/$RESULTDIR/$STD.$2
}

phase() {
  nhost="$3"
  sed "
    /default_var.*wholecell_prefix/s/cxwhole/cxsmall_whole/
    /default_var.*multisplit_prefix/s/cx/$prefix/
    /default_var.*multisplit_nhost/s/256/$nhost/
    /default_var.*load_balance_phase/s/0/$1/
    /default_var.*msoptfactor/s/8/$MSOPT/
  " init.hoc > _init.hoc
  run $2 $3
}

if test "$PHASE" = 6 ; then
for i in 256 512 1024 2048 ; do
  nhost=$i
  prefix=cxsmall${MSOPT}_$nhost
  STD=stdout$MSOPT
  phase $PHASE 256 $nhost
  $NRNIV -c "{load_file(\"hoc/binfo.hoc\")}" -c "mymetis3(\"$prefix\",$nhost)" \
    >> $SIMDIR/$RESULTDIR/$STD.$i
done
fi

if test "$PHASE" = 7 ; then
for i in 256 512 1024 2048 ; do
rm -f out$i.dat
  nhost=$i
  prefix=cxsmall${MSOPT}_$nhost
  STD=stdout$MSOPT
  phase $PHASE $i $nhost
  sortspike out$i.dat $SIMDIR/$RESULTDIR/out${MSOPT}.$i
done
fi

if test "$PHASE" = 4 ; then
  i=256
  nhost=$i
  prefix=cxsmall_$nhost
  phase $PHASE 256 $nhost
  for nhost in 32 64 128 256 512 ; do
  $NRNIV -c "{load_file(\"hoc/binfo.hoc\")}" -c "mymetis2(\"cxsmall_whole\",$nhost)" \
    >> $SIMDIR/$RESULTDIR/stdout.$i
  done
fi

if test "$PHASE" = 5 ; then
for i in 32 64 128 256 ; do
  rm -f out$i.dat
  nhost=$i
  prefix=cxsmall_$nhost
  phase $PHASE $nhost $nhost
  sortspike out$i.dat $SIMDIR/$RESULTDIR/out.$i
done
fi

freepart $PART

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