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 M, Eichner H, Schuermann F (2008) Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors J Comput Neurosci 25(1):203-210 [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
pardentategyrus
readme.html *
bgka.mod *
CaBK.mod *
ccanl.mod *
Gfluct2.mod *
gskch.mod *
hyperde3.mod *
ichan2.mod *
LcaMig.mod *
nca.mod *
tca.mod *
bg.sh
DG500_M7.hoc *
dgnetactivity.jpg *
dgnettraces.jpg *
init.hoc
initorig.hoc *
modstat *
mosinit_orig.hoc *
out.std
parRI10sp.hoc
RI10sp.hoc
test1.sh *
time *
                            
reproducible original after using mcellran4
setuptime=282.2
runtime=397.53

setuptime=283.25
runtime=393.73
real    11m22.686s
user    10m46.208s
sys     0m0.763s

after upgrading
setuptime=296.64
runtime=398.06

setuptime=292.35
runtime=399.24
real    11m38.260s
user    10m58.870s
sys     0m0.904s


after transforming. (also upgraded gcc)

1 host (NeuronDev)
setuptime=7.6000001
runtime=411.04

 time mpirun -nolocal -machinefile $HOME/mpi64 -np 12 $HOME/neuron/mpi-gcc3.2.3/x86_64/bin
nrniv init.hoc >& out12
setuptime=0.12999988
runtime=28.56
real    0m31.648s
user    0m0.389s
sys     0m0.324s

time mpirun -nolocal -machinefile $HOME/mpi64 -np 1 $HOME/neuron/mpi-gcc3.2.3/x86_64/bin
nrniv init.hoc >& out1
setuptime=0.25
runtime=330.85
real    5m33.093s
user    0m0.256s
sys     0m0.086s


time mpirun -nolocal -machinefile $HOME/mpi32 -np 24 $HOME/neuron/mpi-gcc2.96/i686/bin
nrniv init.hoc >& out24
setuptime=0.27999997
runtime=30.42
real    5m14.682s
user    0m0.471s
sys     0m0.650s

 time mpirun -nolocal -machinefile $HOME/mpi32 -np 1 $HOME/neuron/mpi-gcc2.96/i686/bin
nrniv init.hoc >& out1.i686
setuptime=0.46000004
runtime=607.08
real    10m9.389s
user    0m0.287s
sys     0m0.137s


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