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
net
durand.hoc *
groucho.hoc
groucho_gapbld.hoc *
groucho_gapbld_mix.hoc *
network_specification_interface.hoc
serial_or_par_wrapper.hoc *
synaptic_compmap_construct.hoc *
synaptic_map_construct.hoc *
                            
// groucho_gapbld_mix.hoc
/*
****************************this is one big comment ************************
! 15 Nov. 2003, variation of groucho_gapbld.f to allow for gj
! between 2 cell populations, eg suppyrRS and suppyrFRB, or
! tuftRS and tuftIB.  Structure of gjtable as before, with col. 1
! giving cell of 1st type and col. 3 giving coupled cell of 2nd type.

      SUBROUTINE GROUCHO_gapbld_mix (thisno, numcells1, numcells2,
     & numgj, gjtable, allowedcomps, num_allowedcomps, display)
c       Construct a gap-junction network for groucho.f
$1 thisno double
$2 numcells1 = number of cells in 1st population.
$3 numcells2 = number of cells in 2nd population.
$4 numgj = total number of gj to be formed between these populations.
// this is the output: gjtable = table of gj's: each row is a gj.  
   Entries are: cell A, compartment on cell A; cell B, compartment on cell B
$o5 allowedcomps = a list of compartments where gj allowed to form
$6 num_allowedcomps = number of compartments in a cell on which a gj 
$7 display
c    might form.
! IT IS ASSUMED THAT ALLOWEDCOMPS AND NUM_ALLOWEDCOMPS SAME FOR
! THE 2 POPULATIONS.
c display is an integer flag.  If display = 1, print gjtable

        INTEGER thisno, numcells1, numcells2, numgj, gjtable(numgj,4),
     &    num_allowedcomps, allowedcomps(num_allowedcomps)
        INTEGER i,j,k,l,m,n,o,p, ictr /0/
c ictr keeps track of how many gj have been "built"
        INTEGER display

        double precision seed, x1(1), x2(1), y(2)
****************************this is one big comment ************************
*/
objref gjtable,x1, x2, y1
obfunc groucho_gapbld_mix() { // see note above for arguments:
	thisno  = $1
	numcells1 = $2
	numcells2 = $3
	numgj = $4
	allowedcomps = $o5
	num_allowedcomps = $6
	display = $7
//	print "Arrived at groucho_gapbld_mix with display = ",display

	seed = new Vector()
	seed.append(137.e0)
	objref gjtable
	gjtable = new Matrix(numgj+1, 4+1) // FORTRAN-like indicies start at 1

	ictr = 0

// 2
	while (ictr < numgj) {
		k = 1
	    not_unique = 1
	    while (not_unique) {
		x1 = durand (seed, k, x1) // durand returns vec c-style indicies
		x2 = durand (seed, k, x2)
// c This defines a candidate cell pair
                k = 2
		y = durand (seed, k, y)
// c This defines a candidate pair of compartments

		i = int ( x1.x[0] * numcells1 ) + 1
		j = int ( x2.x[0] * numcells2 ) + 1

// c Is the ORDERED cell pair (i,j) in the list so far?
// superfluous but true           if (ictr.eq.0) goto 1

		not_unique = 0
		for eL = 1, ictr {
		  if ((gjtable.x(eL,1) == i) && (gjtable.x(eL,3) == j)) {not_unique = 1}
		}
		if (one_tenth_ncell) {
			not_unique = 0
		}
	    } // loop replaces  if (p.eq.1) goto 2

// c Proceed with construction
// 1
	    ictr = ictr + 1
	    m = int ( y.x[0] * num_allowedcomps ) + 1
	    n = int ( y.x[1] * num_allowedcomps ) + 1

	    gjtable.x[ictr][1] = i
	    gjtable.x[ictr][3] = j
	    gjtable.x[ictr][2] = allowedcomps.x[m]
	    gjtable.x[ictr][4] = allowedcomps.x[n]

	} // loop replacing if (ictr.lt.numgj) goto 2

// c Possibly print out gjtable when done.
//	print "at end of groucho_gapbld_mix display = ",display,", thisno = ",thisno
	if ((display == 1) && (thisno == 0)) {
		print " MIX GJTABLE"
		for i = 1, numgj {
	          printf("%6d, %6d %6d %6d \n",gjtable.x(i,1), gjtable.x(i,2), \
                                       gjtable.x(i,3), gjtable.x(i,4))
		}
	}
//	print "successfully printed or not"
	return gjtable
}

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