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#!/usr/bin/env python
## Test of ParallelTransfer-based gap junctions. Assumes the presence
## of a conductance-based half-gap junction model ggap.mod
import sys, os, itertools, argparse, time
import numpy as np
from neuron import h
cells = []
gjlist = []
vrecs = []
stims = []
class MyCell:
_ids = itertools.count(0)
def __repr__(self):
return "MyCell[%d]" % self.id
def __init__(self):
self.id = next(self._ids)
# create the morphology and connect it
self.soma = h.Section(name="soma", cell=self)
self.dend = h.Section(name="dend", cell=self)
self.dend.connect(self.soma(0.5))
self.soma.insert("pas")
self.dend.insert("pas")
self.dend(0.5).pas.e = -65
self.soma(0.5).pas.e = -65
## Creates half-gap junction mechanism
def mkgap(pc, sec, gid, secpos, sgid, dgid, w, gjlist):
myrank = int(pc.id())
seg = sec(secpos)
gj = h.ggap(seg)
gj.g = w
pc.source_var(seg._ref_v, sgid, sec=sec)
pc.target_var(gj, gj._ref_vgap, dgid)
if myrank == 0:
print(
"mkgap: gid %i: sec=%s sgid=%i dgid=%i w=%f"
% (gid, str(sec), sgid, dgid, w)
)
gjlist.append(gj)
return gj
def mkcells(pc, ngids):
nranks = int(pc.nhost())
myrank = int(pc.id())
assert nranks <= ngids
for gid in range(ngids):
if gid % nranks == myrank:
cell = MyCell()
nc = h.NetCon(cell.soma(0.5)._ref_v, None, sec=cell.soma)
pc.set_gid2node(gid, myrank)
pc.cell(gid, nc, 1)
cells.append(cell)
# Current injection into section
stim = h.IClamp(cell.soma(0.5))
if gid % 2 == 0:
stim.delay = 10
else:
stim.delay = 20
stim.dur = 20
stim.amp = 10
stims.append(stim)
# Record membrane potential
v = h.Vector()
v.record(cell.dend(0.5)._ref_v)
vrecs.append(v)
if myrank == 0:
print(
"Rank %i: created gid %i; stim delay = %.02f"
% (myrank, gid, stim.delay)
)
## Creates gap junctional connections:
## The first halfgap is created on even gids and gid 0 and the second
## halfgap is created on odd gids.
def mkgjs(pc, ngids):
nranks = int(pc.nhost())
myrank = int(pc.id())
ggid = 2e6 ## gap junction id range is intended to not overlap with gid range
for gid in range(0, ngids, 2):
# source gid: all even gids
src = gid
# destination gid: all odd gids
dst = gid + 1
# source gap junction gid
sgid = ggid
# destination gap junction gid
dgid = ggid + 1
# if the source gid exists on this rank, create the half gap from src to dst
if pc.gid_exists(src) > 0:
cell = pc.gid2cell(src)
sec = cell.dend
ggap = mkgap(pc, sec, gid, 0.5, sgid, dgid, 1.0, gjlist)
# if the destination gid exists on this rank, create the half gap from dst to src
if pc.gid_exists(dst) > 0:
cell = pc.gid2cell(dst)
sec = cell.dend
ggap = mkgap(pc, sec, gid, 0.5, dgid, sgid, 1.0, gjlist)
ggid += 2
def main():
parser = argparse.ArgumentParser(description="Parallel transfer test.")
parser.add_argument(
"--sparse-partrans",
dest="sparse_partrans",
default=False,
action="store_true",
help="use sparse parallel transfer",
)
parser.add_argument(
"--result-prefix",
default=".",
help="place output files in given directory (must exist before launch)",
)
parser.add_argument(
"--ngids", default=2, type=int, help="number of gids to create (must be even)"
)
args, unknown = parser.parse_known_args()
pc = h.ParallelContext()
myrank = int(pc.id())
mkcells(pc, args.ngids)
mkgjs(pc, args.ngids)
pc.setup_transfer()
if args.sparse_partrans:
if hasattr(h, "nrn_sparse_partrans"):
h.nrn_sparse_partrans = 1
rec_t = h.Vector()
rec_t.record(h._ref_t)
wt = time.time()
h.dt = 0.25
pc.set_maxstep(10)
h.finitialize(-65)
pc.psolve(500)
total_wt = time.time() - wt
gjtime = pc.vtransfer_time()
print("rank %d: parallel transfer time: %.02f" % (myrank, gjtime))
print("rank %d: total compute time: %.02f" % (myrank, total_wt))
output = itertools.chain(
[np.asarray(rec_t.to_python())],
[np.asarray(vrec.to_python()) for vrec in vrecs],
)
np.savetxt(
"%s/ParGJ_%04i.dat" % (args.result_prefix, myrank),
np.column_stack(tuple(output)),
)
pc.runworker()
pc.done()
h.quit()
main()
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