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
pardentategyrus
readme.html *
bgka.mod *
CaBK.mod *
ccanl.mod *
Gfluct2.mod *
gskch.mod *
hyperde3.mod *
ichan2.mod *
LcaMig.mod *
nca.mod *
tca.mod *
DG500_M7.hoc *
dgnetactivity.jpg *
dgnettraces.jpg *
init.hoc
initorig.hoc *
M2I10sp.txt
modstat *
mosinit.hoc *
parRI10sp.hoc
perfrun.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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