def prun(tstop, restore=False):
pc.set_maxstep(10 * ms)
h.finitialize(-65 * mV)
if restore == "SaveState":
ns = h.SaveState()
sf = h.File("state%d.bin" % pc.id())
ns.fread(sf)
ns.restore(0) # event queue restored
sf.close()
elif restore == "BBSaveState":
cp_out_to_in() # prepare for restore.
bbss = h.BBSaveState()
bbss.restore_test()
else:
pc.psolve(tstop / 2)
# SaveState save
ss = h.SaveState()
ss.save()
sf = h.File("state%d.bin" % pc.id())
ss.fwrite(sf)
sf.close()
# BBSaveState Save
cnt = h.List("PythonObject").count()
for i in range(1):
bbss = h.BBSaveState()
bbss.save_test()
bbss = None
assert h.List("PythonObject").count() == cnt
pc.psolve(tstop)
def run2(tstop, mode=None):
pc.set_maxstep(10)
h.finitialize()
if mode == "save_test":
pc.psolve(tstop / 2)
h.BBSaveState().save_test()
elif mode == "restore_test":
cp_out_to_in()
h.BBSaveState().restore_test()
pc.psolve(tstop)
def srun(tsave, tstop):
cvode = h.CVode()
qm = cvode.queue_mode()
print("srun tsave=%g tstop=%g start=%g delay=%g %s" %
(tsave, tstop, ns.start, nsnc.delay, "binq" if qm else ""))
run(tsave)
st = spiketime.c()
sg = spikegid.c()
bbss = h.BBSaveState()
bbss.save("allcell_bbss.dat")
qm = 0
if qm:
print("after save")
h.CVode().print_event_queue()
h.finitialize(-65)
spiketime.resize(0)
spikegid.resize(0)
bbss.restore("allcell_bbss.dat")
if qm:
print("after restore")
h.CVode().print_event_queue()
pc.psolve(tstop)
st.append(spiketime)
sg.append(spikegid)
spiketime.copy(st)
spikegid.copy(sg)
print(" %d spikes" % len(spiketime))
def test_6(): # Test BBSaveState.ignore
rmfiles()
model = Ring(5, 0)
syn = model.cells[0].syn
prun(1)
h.finitialize(-65)
g_expect = syn.g
pc.psolve(20)
g_actual = syn.g
bbss = h.BBSaveState()
bbss.ignore(syn)
bbss.save("allcell-bbss.dat")
h.finitialize(-65)
bbss.restore("allcell-bbss.dat")
print(g_expect, g_actual, syn.g)
assert syn.g == g_expect
h.finitialize(-65)
pc.psolve(20)
bbss.ignore(syn)
bbss.ignore()
bbss.save("allcell-bbss.dat")
h.finitialize(-65)
bbss.restore("allcell-bbss.dat")
print(g_expect, g_actual, syn.g)
assert abs((syn.g - g_actual) / (syn.g + g_actual)) < 1e-12
pc.gid_clear()
def test_7(): # save a ring with n cells and extra section, restore n-1 cells
rmfiles()
model = Ring(5, 0)
model.cells[0].foo = h.Section(name="foo", cell=model.cells[0])
prun(5)
v_expect = model.cells[0].soma(0.5).v
bbss = h.BBSaveState()
bbss.save_test()
model = Ring(4, 0)
prun(0.1)
bbss = h.BBSaveState()
cp_out_to_in()
bbss.restore_test()
print(v_expect, model.cells[0].soma(0.5).v)
assert abs(v_expect - model.cells[0].soma(0.5).v) < 1e-13
pc.gid_clear()
def prun(tstop, mode=None):
pc.set_maxstep(10 * ms)
h.finitialize(-65 * mV)
if mode == "save_test": # integrate to tstop/2 and save
pc.psolve(tstop / 2)
bbss = h.BBSaveState()
bbss.save_test() # creates separate file in bbss_out for each piece
elif mode == "save_test_bin":
pc.psolve(tstop / 2)
bbss = h.BBSaveState()
bbss.save_test_bin(
) # like save_test but binary wholecell in binbufout
elif mode == "save":
pc.psolve(tstop / 2)
bbss = h.BBSaveState()
bbss.save("allcell-bbss.dat") # single file for everything (nhost==1!)
elif mode == "restore_test":
cp_out_to_in() # prepare for restore.
bbss = h.BBSaveState()
bbss.restore_test()
elif mode == "restore_test_bin":
subprocess_run("mkdir binbufin")
subprocess_run("cp binbufout/* binbufin")
bbss = h.BBSaveState()
bbss.restore_test_bin()
elif mode == "restore":
bbss = h.BBSaveState()
bbss.restore("allcell-bbss.dat")
bbss.vector_play_init() # just for coverage as there are none.
pc.psolve(tstop) # integrate the rest of the way
def test_3():
rmfiles()
hl = hlist()
npo = hl.count()
stdspikes = {
0.0: [
1.975000000099995,
21.300000000099324,
39.70000000010047,
58.05000000010464,
76.4000000001088,
94.80000000011299,
],
1.0: [
5.9250000001000505,
24.800000000099125,
43.32500000010129,
61.725000000105474,
80.10000000010965,
98.47500000011382,
],
2.0: [
9.900000000099972,
28.40000000009892,
46.950000000102115,
65.3750000001063,
83.77500000011048,
],
3.0: [
13.900000000099745,
32.15000000009875,
50.600000000102945,
69.02500000010713,
87.45000000011132,
],
4.0: [
17.900000000099517,
36.02500000009963,
54.32500000010379,
72.70000000010796,
91.12500000011215,
],
}
ring = Ring(3, 2)
assert hl.count() == npo
prun(100 * ms)
if "usetable_hh" not in dir(h): # coreneuron has different hh.mod
stdspikes = get_all_spikes(ring)
compare_dicts(get_all_spikes(ring), stdspikes)
stdspikes_after_50 = {}
for gid in stdspikes:
stdspikes_after_50[gid] = [
spk_t for spk_t in stdspikes[gid] if spk_t >= 50.0
]
prun(100 * ms, mode="save_test") # at tstop/2 does a BBSaveState.save
assert hl.count() == npo
compare_dicts(get_all_spikes(ring), stdspikes)
prun(100 * ms,
mode="restore_test") # BBSaveState restore to start at t = tstop/2
assert hl.count() == npo
compare_dicts(get_all_spikes(ring), stdspikes_after_50)
# while we are at it check the BBSaveState binary file mode.
prun(100 * ms, mode="save_test_bin")
compare_dicts(get_all_spikes(ring), stdspikes)
prun(100 * ms, mode="restore_test_bin")
compare_dicts(get_all_spikes(ring), stdspikes_after_50)
# while we are at it check the BBSaveState save/restore single file mode.
prun(100 * ms, mode="save")
compare_dicts(get_all_spikes(ring), stdspikes)
prun(100 * ms, mode="restore")
compare_dicts(get_all_spikes(ring), stdspikes_after_50)
assert hl.count() == npo
# save_request works but not very useful as save_gid and restore_gid
# not implemented.
pc.set_maxstep(10)
h.finitialize(-65)
gids = h.Vector()
sizes = h.Vector()
bbss = h.BBSaveState()
ngid = bbss.save_request(gids, sizes)
assert ngid == len(ring.cells)
# prints "not implemented"
bbss.save_gid()
bbss.restore_gid()
assert hl.count() == npo
del bbss
# binq
rmfiles()
h.CVode().queue_mode(1)
prun(100, mode="save")
compare_dicts(get_all_spikes(ring), stdspikes)
prun(100, mode="restore")
compare_dicts(get_all_spikes(ring), stdspikes_after_50)
prun(100, mode="save_test_bin")
compare_dicts(get_all_spikes(ring), stdspikes)
prun(100, mode="restore_test_bin")
compare_dicts(get_all_spikes(ring), stdspikes_after_50)
h.CVode().queue_mode(0)
pc.gid_clear()
def runBBSS():
svst = h.BBSaveState()
svst.save_test()