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# ParallelContext transfer functionality tests.
# This uses nonsense models and values to verify transfer takes place correctly.
import sys
from io import StringIO
from neuron import h
# h.nrnmpi_init()
pc = h.ParallelContext()
rank = pc.id()
nhost = pc.nhost()
if nhost > 1:
if rank == 0:
print("nhost > 1 so calls to expect_error will return without testing.")
def expect_error(callable, args, sec=None):
"""
Execute callable(args) and assert that it generated an error.
If sec is not None, executes callable(args, sec=sec)
Skips if nhost > 1 as all hoc_execerror end in MPI_ABORT
Does not work well with nrniv launch since hoc_execerror messages do not
pass through sys.stderr.
"""
if nhost > 1:
return
old_stderr = sys.stderr
sys.stderr = my_stderr = StringIO()
err = 0
try:
if sec:
callable(*args, sec=sec)
else:
callable(*args)
except:
err = 1
errmes = my_stderr.getvalue()
sys.stderr = old_stderr
if errmes:
errmes = errmes.splitlines()[0]
errmes = errmes[(errmes.find(":") + 2) :]
print("expect_error: %s" % errmes)
if err == 0:
print("expect_error: no err for %s%s" % (str(callable), str(args)))
assert err
# HGap POINT_PROCESS via ChannelBUilder.
# Cannot use with extracellular.
ks = h.KSChan(1)
ks.name("HGap")
ks.iv_type(0)
ks.gmax(0)
ks.erev(0)
# Cell with enough nonsense stuff to exercise transfer possibilities.
class Cell:
def __init__(self):
self.soma = h.Section(name="soma", cell=self)
self.soma.diam = 10.0
self.soma.L = 10.0
self.soma.insert("na_ion") # can use nai as transfer source
# can use POINT_PROCESS range variable as targets
self.ic = h.IClamp(self.soma(0.5))
self.vc = h.SEClamp(self.soma(0.5))
self.vc.rs = 1e9 # no voltage clamp current
self.hgap = [None for _ in range(2)] # filled by mkgaps
def run():
pc.setup_transfer()
h.finitialize()
h.fadvance()
model = None # Global allows teardown of model
def teardown():
"""
destroy model
"""
global model
pc.gid_clear()
model = None
def mkmodel(ncell):
"""
Destroy existing model and re-create with ncell Cells.
"""
global model
if model:
teardown()
cells = {}
for gid in range(rank, ncell, nhost):
cells[gid] = Cell()
pc.set_gid2node(gid, rank)
pc.cell(gid, h.NetCon(cells[gid].soma(0.5)._ref_v, None, sec=cells[gid].soma))
model = (cells, ncell)
def mkgaps(gids):
"""For list of gids, full gap, right to left"""
gidset = set()
for gid in gids:
g = [gid, (gid + 1) % model[1]]
sids = [i + 1000 for i in g]
for i, j in enumerate([1, 0]):
if pc.gid_exists(g[i]):
cell = model[0][g[i]]
if g[i] not in gidset: # source var sid cannot be used twice
pc.source_var(cell.soma(0.5)._ref_v, sids[i], sec=cell.soma)
gidset.add(g[i])
assert cell.hgap[j] is None
cell.hgap[j] = h.HGap(cell.soma(0.5))
pc.target_var(cell.hgap[j], cell.hgap[j]._ref_e, sids[j])
cell.hgap[j].gmax = 0.0001
def transfer1(amp1=True):
"""
round robin transfer v to ic.amp and vc.amp1, nai to vc.amp2
"""
ncell = model[1]
for gid, cell in model[0].items():
s = cell.soma
srcsid = gid
tarsid = (gid + 1) % ncell
pc.source_var(s(0.5)._ref_v, srcsid, sec=s)
pc.source_var(s(0.5)._ref_nai, srcsid + ncell, sec=s)
pc.target_var(cell.ic, cell.ic._ref_amp, tarsid)
if amp1:
pc.target_var(cell.vc, cell.vc._ref_amp1, tarsid)
pc.target_var(cell.vc, cell.vc._ref_amp2, tarsid + ncell)
def init_values():
"""
Initialize sources to their sid values and targets to 0
This allows substantive test that source values make it to targets.
"""
ncell = model[1]
for gid, c in model[0].items():
c.soma(0.5).v = gid
c.soma(0.5).nai = gid + ncell
c.ic.amp = 0
c.vc.amp1 = 0
c.vc.amp2 = 0
def check_values():
"""
Verify that target values are equal to source values.
"""
values = {}
for gid, c in model[0].items():
vi = c.soma(0.5).v
if h.ismembrane("extracellular", sec=c.soma):
vi += c.soma(0.5).vext[0]
values[gid] = {
"v": vi,
"nai": c.soma(0.5).nai,
"amp": c.ic.amp,
"amp1": c.vc.amp1,
"amp2": c.vc.amp2,
}
x = pc.py_gather(values, 0)
if rank == 0:
values = {}
for v in x:
values.update(v)
ncell = len(values)
for gid in values:
v1 = values[gid]
v2 = values[(gid + ncell - 1) % ncell]
assert v1["v"] == v2["amp"]
assert v1["v"] == v2["amp1"]
assert v1["nai"] == v2["amp2"]
def test_partrans():
# no transfer targets or sources.
mkmodel(4)
run()
# invalid source or target sid.
if 0 in model[0]:
cell = model[0][0]
s = cell.soma
expect_error(pc.source_var, (s(0.5)._ref_v, -1), sec=s)
expect_error(pc.target_var, (cell.ic, cell.ic._ref_amp, -1))
# target with no source.
if pc.gid_exists(1):
cell = pc.gid2cell(1)
pc.target_var(cell.ic, cell.ic._ref_amp, 1)
expect_error(run, ())
mkmodel(4)
# source with no target (not an error).
if pc.gid_exists(1):
cell = pc.gid2cell(1)
pc.source_var(cell.soma(0.5)._ref_v, 1, sec=cell.soma)
run()
# No point process for target
if pc.gid_exists(1):
cell = pc.gid2cell(1)
pc.target_var(cell.vc._ref_amp3, 1)
try:
run() # ok if test_fast_imem.py not prior
except:
pass
pc.nthread(2)
expect_error(run, ()) # Do not know the POINT_PROCESS target
pc.nthread(1)
# Wrong sec for source ref and wrong point process for target ref.
mkmodel(1)
if pc.gid_exists(0):
cell = pc.gid2cell(0)
sec = h.Section(name="dend")
expect_error(pc.source_var, (cell.soma(0.5)._ref_v, 1), sec=sec)
expect_error(pc.source_var, (cell.soma(0.5)._ref_nai, 2), sec=sec)
del sec
expect_error(pc.target_var, (cell.ic, cell.vc._ref_amp3, 1))
# source sid already in use
expect_error(pc.source_var, (cell.soma(0.5)._ref_nai, 1), sec=cell.soma)
# partrans update: could not find parameter index
# pv2node checks the parent
mkmodel(1)
s1 = h.Section(name="dend")
s2 = h.Section(name="soma")
ic = h.IClamp(s1(0.5))
pc.source_var(s1(0)._ref_v, rank, sec=s1)
pc.target_var(ic, ic._ref_amp, rank)
run()
assert s1(0).v == ic.amp
"""
# but following changes the source node and things get screwed up
# because of continuing to use a freed Node*. The solution is
# beyond the scope of this pull request and would involve replacing
# description in terms of Node* with (Section*, arc_position)
s1.connect(s2(.5))
run()
print(s1(0).v, ic.amp)
assert(s1(0).v == ic.amp)
"""
# non_vsrc_update property disappears from Node*
s1.insert("pas") # not allowed to uninsert ions :(
pc.source_var(s1(0.5)._ref_e_pas, rank + 10, sec=s1)
pc.target_var(ic, ic._ref_delay, rank + 10)
run()
assert s1(0.5).e_pas == ic.delay
s1.uninsert("pas")
expect_error(run, ())
teardown()
del ic, s1, s2
# missing setup_transfer
mkmodel(4)
transfer1()
expect_error(h.finitialize, (-65,))
# round robin transfer v to ic.amp and vc.amp1, nai to vc.amp2
ncell = 5
mkmodel(ncell)
transfer1()
init_values()
run()
check_values()
# nrnmpi_int_alltoallv_sparse
h.nrn_sparse_partrans = 1
mkmodel(5)
transfer1()
init_values()
run()
check_values()
h.nrn_sparse_partrans = 0
# impedance error (number of gap junction not equal to number of pc.transfer_var)
imp = h.Impedance()
if 0 in model[0]:
imp.loc(model[0][0].soma(0.5))
expect_error(imp.compute, (1, 1))
del imp
# For impedance, pc.target_var requires that its first arg be a reference to the POINT_PROCESS"
mkmodel(2)
if pc.gid_exists(0):
cell = pc.gid2cell(0)
pc.source_var(cell.soma(0.5)._ref_v, 1000, sec=cell.soma)
cell.hgap[1] = h.HGap(cell.soma(0.5))
pc.target_var(cell.hgap[1], cell.hgap[1]._ref_e, 1001)
if pc.gid_exists(1):
cell = pc.gid2cell(1)
pc.source_var(cell.soma(0.5)._ref_v, 1001, sec=cell.soma)
cell.hgap[0] = h.HGap(cell.soma(0.5))
pc.target_var(cell.hgap[0], cell.hgap[0]._ref_e, 1000)
pc.setup_transfer()
imp = h.Impedance()
h.finitialize(-65)
if pc.gid_exists(0):
imp.loc(pc.gid2cell(0).soma(0.5))
expect_error(imp.compute, (10, 1, 100))
del imp, cell
# impedance
ncell = 5
mkmodel(ncell)
mkgaps(list(range(ncell - 1)))
pc.setup_transfer()
imp = h.Impedance()
h.finitialize(-65)
if 0 in model[0]:
imp.loc(model[0][0].soma(0.5))
niter = imp.compute(10, 1, 100)
if rank == 0:
print("impedance iterations=%d" % niter)
# tickle execution of target_ptr_update for one more line of coverage.
if 0 in model[0]:
model[0][0].hgap[1].loc(model[0][0].soma(0))
model[0][0].hgap[1].loc(model[0][0].soma(0.5))
niter = imp.compute(10, 1, 100)
del imp
# CoreNEURON gap file generation
mkmodel(ncell)
transfer1()
# following is a bit tricky and need some user help in the docs.
# cannot be cache_efficient if general sparse matrix solver in effect.
cvode = h.CVode()
assert cvode.use_mxb(0) == 0
assert cvode.cache_efficient(1) == 1
pc.setup_transfer()
h.finitialize(-65)
pc.nrncore_write("tmp")
# CoreNEURON: one thread empty of gaps
mkmodel(1)
transfer1()
s = h.Section("dend")
pc.set_gid2node(rank + 10, rank)
pc.cell(rank + 10, h.NetCon(s(0.5)._ref_v, None, sec=s))
pc.nthread(2)
pc.setup_transfer()
h.finitialize(-65)
pc.nrncore_write("tmp")
pc.nthread(1)
teardown()
del s
# There are single thread circumstances where target POINT_PROCESS is needed
s = h.Section("dend")
pc.set_gid2node(rank, rank)
pc.cell(rank, h.NetCon(s(0.5)._ref_v, None, sec=s))
pc.source_var(s(0.5)._ref_v, rank, sec=s)
ic = h.IClamp(s(0.5))
pc.target_var(ic._ref_amp, rank)
pc.setup_transfer()
expect_error(h.finitialize, (-65,))
teardown()
del ic, s
# threads
mkmodel(ncell)
transfer1()
pc.nthread(2)
init_values()
run()
check_values()
pc.nthread(1)
# extracellular means use v = vm+vext[0]
for cell in model[0].values():
cell.soma.insert("extracellular")
init_values()
run()
check_values()
teardown()
if __name__ == "__main__":
test_partrans()
pc.barrier()
h.quit()
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