def cx(env):
rank = int(env.pc.id())
lb = h.LoadBalance()
if os.path.isfile("mcomplex.dat"):
lb.read_mcomplex()
cxvec = h.Vector(len(env.gidlist))
for i, gid in enumerate(env.gidlist):
cxvec.x[i] = lb.cell_complexity(env.pc.gid2cell(gid))
env.cxvec = cxvec
return cxvec
def cx(env):
"""
Estimates cell complexity. Uses the LoadBalance class.
:param env: an instance of the `dentate.Env` class.
"""
rank = int(env.pc.id())
lb = h.LoadBalance()
if os.path.isfile("mcomplex.dat"):
lb.read_mcomplex()
cxvec = np.zeros((len(env.gidset), ))
for i, gid in enumerate(env.gidset):
cxvec[i] = lb.cell_complexity(env.pc.gid2cell(gid))
env.cxvec = cxvec
return cxvec
def lpt_bal(env):
rank = int(env.pc.id())
nhosts = int(env.pc.nhost())
cxvec = env.cxvec
gidvec = env.gidlist
# gather gidvec, cxvec to rank 0
src = [None] * nhosts
src[0] = zip(cxvec.to_python(), gidvec)
dest = env.pc.py_alltoall(src)
del src
if rank == 0:
lb = h.LoadBalance()
allpairs = sum(dest, [])
del dest
parts = lpt.lpt(allpairs, nhosts)
lpt.statistics(parts)
part_rank = 0
with open('parts.%d' % nhosts, 'w') as fp:
for part in parts:
for x in part[1]:
fp.write('%d %d\n' % (x[1], part_rank))
part_rank = part_rank + 1
from neuron import h
h.load_file("loadbal.hoc")
try:
lb = h.LoadBalance()
except AttributeError:
pass
def get_cell(env, gid, population):
"""
:param env:
:param gid:
:param population:
:return:
"""
h.load_file("nrngui.hoc")
h.load_file("loadbal.hoc")
h('objref fi_status, fi_checksimtime, pc, nclist, nc, nil')
h('strdef datasetPath')
h('numCells = 0')
h('totalNumCells = 0')
h('max_walltime_hrs = 0')
h('mkcellstime = 0')
h('mkstimtime = 0')
h('connectcellstime = 0')
h('connectgjstime = 0')
h('results_write_time = 0')
h.nclist = h.List()
datasetPath = os.path.join(env.datasetPrefix, env.datasetName)
h.datasetPath = datasetPath
## new ParallelContext object
# h.pc = h.ParallelContext()
# env.pc = h.pc
rank = int(env.pc.id())
nhosts = int(env.pc.nhost())
## polymorphic value template
h.load_file("./templates/Value.hoc")
## randomstream template
h.load_file("./templates/ranstream.hoc")
## stimulus cell template
h.load_file("./templates/StimCell.hoc")
h.xopen("./lib.hoc")
h.dt = env.dt
h.tstop = env.tstop
if env.optldbal or env.optlptbal:
lb = h.LoadBalance()
if not os.path.isfile("mcomplex.dat"):
lb.ExperimentalMechComplex()
if (env.pc.id() == 0):
mkspikeout(env, env.spikeoutPath)
env.pc.barrier()
h.startsw()
mkcells(env)
env.mkcellstime = h.stopsw()
env.pc.barrier()
if (env.pc.id() == 0):
print "*** Cells created in %g seconds" % env.mkcellstime
print "*** Rank %i created %i cells" % (env.pc.id(), len(env.cells))
h.startsw()
mkstim(env)
env.mkstimtime = h.stopsw()
if (env.pc.id() == 0):
print "*** Stimuli created in %g seconds" % env.mkstimtime
env.pc.barrier()
h.startsw()
connectcells(env)
env.connectcellstime = h.stopsw()
env.pc.barrier()
if (env.pc.id() == 0):
print "*** Connections created in %g seconds" % env.connectcellstime
print "*** Rank %i created %i connections" % (env.pc.id(), int(h.nclist.count()))
h.startsw()
# connectgjs(env)
env.connectgjstime = h.stopsw()
if (env.pc.id() == 0):
print "*** Gap junctions created in %g seconds" % env.connectgjstime
env.pc.setup_transfer()
env.pc.set_maxstep(10.0)
h.max_walltime_hrs = env.max_walltime_hrs
h.mkcellstime = env.mkcellstime
h.mkstimtime = env.mkstimtime
h.connectcellstime = env.connectcellstime
h.connectgjstime = env.connectgjstime
h.results_write_time = env.results_write_time
h.fi_checksimtime = h.FInitializeHandler("checksimtime(pc)")
if (env.pc.id() == 0):
print "dt = %g" % h.dt
print "tstop = %g" % h.tstop
h.fi_status = h.FInitializeHandler("simstatus()")
h.v_init = env.v_init
h.stdinit()
h.finitialize(env.v_init)
env.pc.barrier()
if env.optldbal or env.optlptbal:
cx(env)
ld_bal(env)
if env.optlptbal:
lpt_bal(env)