Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011)

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Accession:137845
Tests several spike exchange methods on a Blue Gene/P supercomputer on up to 64K cores.
Reference:
1 . Hines M, Kumar S, Schürmann F (2011) Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Front Comput Neurosci 5:49 [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];
begintime = startsw()
setuptime = begintime
{load_file("param.hoc")}
_tstop = tstop
{load_file("nrngui.hoc")}
tstop = _tstop

{load_file("netparmpi.hoc")}
objref pnm, pc

ncell = 2^ncellpow

objref pattern_stim, pattern_time, pattern_gid
proc pattern() {
	clipboard_retrieve($s1)
	pattern_time = hoc_obj_[1]
	pattern_gid = hoc_obj_
printf("pattern %d\n", pattern_time.size)
	pattern_stim = new PatternStim()
	pattern_stim.play(pattern_time, pattern_gid)
}
pnm = new ParallelNetManager(ncell)
pc = pnm.pc
{pc.timeout(1)}
fake_nhost = 0
fake_id = 0
if (fake_nhost) {
	pnm.nhost = fake_nhost
	pnm.myid = fake_id
	pattern("out.64k.spk")
}

objref gidvec
{load_file("randist.hoc")}
iterator pcitr() {local i1, i2, x
    if (giddist == 0) { // round robin (card dealing)
	i1 = 0
	for (i2=pnm.myid; i2 < ncell; i2 += pnm.nhost) {
		$&1 = i1
		$&2 = i2
		iterator_statement
		i1 += 1
	}
    }else if (giddist == 1){ // contiguous
	x = pnm.myid*(ncell/pnm.nhost)
	for i1 = 0, ncell/pnm.nhost-1 {
		i2 = i1 + x
		$&1 = i1
		$&2 = i2
		iterator_statement
	}
    }else{ //acording to gidvec
	for i1 = 0, gidvec.size-1 {
		$&1 = i1
		$&2 = gidvec.x[i1]
		iterator_statement
	}
    }
}

{load_file("perfrun.hoc")}
{load_file("spike2file.hoc")}

proc spikemode() {local u2i, cbuf
	cbuf = $1
	binqueue = 1
	selfqueue = $2
	bgpdma = $3
	u2i = use2interval
	if (u2i == -1) {
		if (bgpdma > 0) { u2i = 1 } else {u2i = 0}
	}
	if (pc.id == 0) {printf("compress_bufsize=%d binqueue=%d selfqueue=%d bgpdma=%d\n", cbuf, binqueue, selfqueue, bgpdma)}
	pc.spike_compress(cbuf, cbuf != 0, bgpdma + 4*u2i + 8*use2phase)
	cvode.queue_mode(binqueue, selfqueue)
}

{load_file("net.hoc")}

proc mkmodel() {local tt
	tt = startsw()
	ncellpow = $1
	ncon = $2
	ncell = 2^ncellpow
	mknet()
	if (n_xcell) {
		mk_extra_cells(n_xcell)
	}
	set_burst(burstsizepow, burstfactor)
	pnm.spikevec.resize(20000)
	want_all_spikes()
	mkmodel_time = startsw() - tt
	if (pc.id == 0) { printf("mkmodel_time %g\n", mkmodel_time)}
}

objref ncbintst
if (0 && pc.gid_exists(5)) {
	ncbintst = pc.gid_connect(10, pc.gid2obj(5))
	ncbintst.delay = 10
}

//{cvode_local(1)}
setuptime = startsw() - setuptime
if (pnm.myid == 0) {print "SetupTime: ", setuptime}
// mkmodel(ncellpow, ncon)

proc beforerun() {
	if (pnm.myid == 0) {
		printf("seq = %d\n", seq)
		printf("ncell = %d ncon = %d tstop = %g\n", ncell, ncon, tstop)
	}
	pnm.spikevec.resize(0)
	pnm.idvec.resize(0)
	init_run_random(run_random_low_offset_)
}

proc methodrun() {local tt, n, nmax
	tt = startsw()
	beforerun()
	bgpdma = $1
	if (bgpdma == 0) {
		spikemode(compress_bufsize,1, 0)
	}else{
		spikemode(0,1, bgpdma)
	}
	mkhist(100)
	setup_method_time = startsw() - tt

	prun()
	afterrun(tt)
}

proc afterrun() {local tt, n, nmax
	if (pnm.myid == 0) {print "RunTime: ", runtime}

	print_total_spikes()
	if (spkfile == 1) {
		spike2file()
	}
	if (bgpdma > 0) {
		n = pnm.pc.send_time(12)
		nmax = pnm.pc.allreduce(n, 2)
		if (pnm.myid == 0) {
			printf("max multisend ranks on rank 0 is %d\n", n)
			printf("max multisend ranks on all ranks is %d\n", nmax)
		}
	}
	methodrun_time = startsw() - $1
	elapsed_time = startsw() - begintime
	p_tperf()
	if (pnm.myid == 0) {
		print "method info ", pnm.pc.send_time(8)
		print "methodrun time: ", methodrun_time
		printf("elapsed_time = %g\n", elapsed_time)
		printf("real elapsed = %g\n", startsw() - begintime)
	}
}

proc another() {local tt
	tt = startsw()
	beforerun()
	set_maxstep_time = 0
	prun1()
	afterrun(tt)
}

proc doseries() {local i, m
	// 1 Allgather, 2 ISend, 3 DMA, 4 DMA+replay
	i = $1
	while(i) {
		m = i%10
		i = int(i/10)
		methodrun(m-1)
	}
}
//doseries(series)

proc finish() {
	pnm.pc.runworker()
	pnm.pc.done()
	printf("total time = %g\n", startsw() - begintime)
	quit()
}

if (done) {
	finish()
}

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