def test_domain_decomposition_exceptions(self):
nranks = 1
rank = 0
if (mpi_enabled):
comm = arb.mpi_comm()
context = arb.context(threads=1, gpu_id=None, mpi=comm)
nranks = context.ranks
rank = context.rank
else:
context = arb.context(threads=1, gpu_id=None)
recipe = gj_symmetric(nranks)
hint1 = arb.partition_hint()
hint1.prefer_gpu = False
hint1.cpu_group_size = 0
hints1 = dict([(arb.cell_kind.cable, hint1)])
with self.assertRaisesRegex(RuntimeError,
"unable to perform load balancing because cell_kind::cable has invalid suggested cpu_cell_group size of 0"):
decomp1 = arb.partition_load_balance(recipe, context, hints1)
hint2 = arb.partition_hint()
hint2.prefer_gpu = True
hint2.gpu_group_size = 0
hints2 = dict([(arb.cell_kind.cable, hint2)])
with self.assertRaisesRegex(RuntimeError,
"unable to perform load balancing because cell_kind::cable has invalid suggested gpu_cell_group size of 0"):
decomp2 = arb.partition_load_balance(recipe, context, hints2)
def test_exceptions_context_arbmpi(self):
alloc = arb.proc_allocation()
with self.assertRaisesRegex(
RuntimeError, "mpi must be None, or an MPI communicator"):
arb.context(mpi='MPI_COMM_WORLD')
with self.assertRaisesRegex(
RuntimeError, "mpi must be None, or an MPI communicator"):
arb.context(alloc, mpi=0)
def test_domain_decomposition_heterogenous_MC(self):
if (mpi_enabled):
comm = arb.mpi_comm()
context = arb.context(threads=1, gpu_id=None, mpi=comm)
else:
context = arb.context(threads=1, gpu_id=None)
N = context.ranks
I = context.rank
# 10 cells per domain
n_local = 10
n_global = n_local * N
n_local_groups = n_local # 1 cell per group
recipe = hetero_recipe(n_global)
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_local)
self.assertEqual(decomp.num_global_cells, n_global)
self.assertEqual(len(decomp.groups), n_local)
b = I * n_local
e = (I + 1) * n_local
gids = list(range(b,e))
for gid in gids:
self.assertEqual(I, decomp.gid_domain(gid))
# Each cell group contains 1 cell of kind cable
# Each group should also be tagged for cpu execution
grps = list(range(n_local_groups))
kind_lists = dict()
for i in grps:
grp = decomp.groups[i]
self.assertEqual(len(grp.gids), 1)
k = grp.kind
if k not in kind_lists:
kind_lists[k] = []
kind_lists[k].append(grp.gids[0])
self.assertEqual(grp.backend, arb.backend.multicore)
kinds = [arb.cell_kind.cable, arb.cell_kind.spike_source]
for k in kinds:
gids = kind_lists[k]
self.assertEqual(len(gids), int(n_local/2))
for gid in gids:
self.assertEqual(k, recipe.cell_kind(gid))
def test_domain_decomposition_hints(self):
n_cells = 20
recipe = hetero_recipe(n_cells)
context = arb.context()
# The hints perfer the multicore backend, so the decomposition is expected
# to never have cell groups on the GPU, regardless of whether a GPU is
# available or not.
cable_hint = arb.partition_hint()
cable_hint.prefer_gpu = False
cable_hint.cpu_group_size = 3
spike_hint = arb.partition_hint()
spike_hint.prefer_gpu = False
spike_hint.cpu_group_size = 4
hints = dict([(arb.cell_kind.cable, cable_hint),
(arb.cell_kind.spike_source, spike_hint)])
decomp = arb.partition_load_balance(recipe, context, hints)
exp_cable_groups = [[0, 2, 4], [6, 8, 10], [12, 14, 16], [18]]
exp_spike_groups = [[1, 3, 5, 7], [9, 11, 13, 15], [17, 19]]
cable_groups = []
spike_groups = []
for g in decomp.groups:
self.assertTrue(g.kind == arb.cell_kind.cable
or g.kind == arb.cell_kind.spike_source)
if (g.kind == arb.cell_kind.cable):
cable_groups.append(g.gids)
elif (g.kind == arb.cell_kind.spike_source):
spike_groups.append(g.gids)
self.assertEqual(exp_cable_groups, cable_groups)
self.assertEqual(exp_spike_groups, spike_groups)
def test_domain_decomposition_heterogenous_GPU(self):
n_cells = 10
recipe = hetero_recipe(n_cells)
context = arb.context(threads=1, gpu_id=0)
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_cells)
self.assertEqual(decomp.num_global_cells, n_cells)
# one cell group with n_cells/2 on gpu, and n_cells/2 groups on cpu
expected_groups = int(n_cells / 2) + 1
self.assertEqual(len(decomp.groups), expected_groups)
grps = range(expected_groups)
n = 0
# iterate over each group and test its properties
for i in grps:
grp = decomp.groups[i]
k = grp.kind
if (k == arb.cell_kind.cable):
self.assertEqual(grp.backend, arb.backend.gpu)
self.assertEqual(len(grp.gids), int(n_cells / 2))
for gid in grp.gids:
self.assertTrue(gid % 2 == 0)
n += 1
elif (k == arb.cell_kind.spike_source):
self.assertEqual(grp.backend, arb.backend.multicore)
self.assertEqual(len(grp.gids), 1)
self.assertTrue(grp.gids[0] % 2)
n += 1
self.assertEqual(n_cells, n)
def test_domain_decomposition_heterogenous_CPU(self):
n_cells = 10
recipe = hetero_recipe(n_cells)
context = arb.context()
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_cells)
self.assertEqual(decomp.num_global_cells, n_cells)
self.assertEqual(len(decomp.groups), n_cells)
gids = list(range(n_cells))
for gid in gids:
self.assertEqual(0, decomp.gid_domain(gid))
# Each cell group contains 1 cell of kind cable
# Each group should also be tagged for cpu execution
grps = list(range(n_cells))
kind_lists = dict()
for i in grps:
grp = decomp.groups[i]
self.assertEqual(len(grp.gids), 1)
k = grp.kind
if k not in kind_lists:
kind_lists[k] = []
kind_lists[k].append(grp.gids[0])
self.assertEqual(grp.backend, arb.backend.multicore)
kinds = [arb.cell_kind.cable, arb.cell_kind.spike_source]
for k in kinds:
gids = kind_lists[k]
self.assertEqual(len(gids), int(n_cells / 2))
for gid in gids:
self.assertEqual(k, recipe.cell_kind(gid))
def run(dT, n_pairs=1, do_plots=False):
recipe = single_recipe(dT, n_pairs)
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
sim = arbor.simulation(recipe, domains, context)
sim.record(arbor.spike_recording.all)
reg_sched = arbor.regular_schedule(0.1)
handle_mem = sim.sample((0, 0), reg_sched)
handle_g = sim.sample((0, 1), reg_sched)
handle_apost = sim.sample((0, 2), reg_sched)
handle_apre = sim.sample((0, 3), reg_sched)
handle_weight_plastic = sim.sample((0, 4), reg_sched)
sim.run(tfinal=600)
if do_plots:
print("Plotting detailed results ...")
for (handle, var) in [(handle_mem, 'U'), (handle_g, "g"),
(handle_apost, "apost"), (handle_apre, "apre"),
(handle_weight_plastic, "weight_plastic")]:
data, meta = sim.samples(handle)[0]
df = pandas.DataFrame({'t/ms': data[:, 0], var: data[:, 1]})
seaborn.relplot(data=df, kind="line", x="t/ms", y=var,
ci=None).savefig(
'single_cell_stdp_result_{}.svg'.format(var))
weight_plastic, meta = sim.samples(handle_weight_plastic)[0]
return weight_plastic[:, 1][-1]
def test_context(self):
ctx = arb.context(threads=42, gpu_id=None)
self.assertFalse(ctx.has_mpi)
self.assertFalse(ctx.has_gpu)
self.assertEqual(ctx.threads, 42)
self.assertEqual(ctx.ranks, 1)
self.assertEqual(ctx.rank, 0)
def test_context_allocation_mpi4py(self):
comm = arb.mpi_comm(mpi.COMM_WORLD)
# test context with alloc and mpi
alloc = arb.proc_allocation()
ctx = arb.context(alloc, comm)
self.assertEqual(ctx.threads, alloc.threads)
self.assertTrue(ctx.has_mpi)
def test_default_context(self):
ctx = arb.context()
# test that by default context has 1 thread and no GPU, no MPI
self.assertFalse(ctx.has_mpi)
self.assertFalse(ctx.has_gpu)
self.assertEqual(ctx.threads, 1)
self.assertEqual(ctx.ranks, 1)
self.assertEqual(ctx.rank, 0)
def test_context_allocation(self):
alloc = arb.proc_allocation()
# test context construction with proc_allocation()
ctx = arb.context(alloc)
self.assertEqual(ctx.threads, alloc.threads)
self.assertEqual(ctx.has_gpu, alloc.has_gpu)
self.assertEqual(ctx.ranks, 1)
self.assertEqual(ctx.rank, 0)
def test_context_avail_threads(self):
# test that 'avail_threads' returns at least 1.
ctx = arb.context(threads = 'avail_threads', gpu_id = None)
self.assertFalse(ctx.has_mpi)
self.assertFalse(ctx.has_gpu)
self.assertTrue(ctx.threads >= 1)
self.assertEqual(ctx.ranks, 1)
self.assertEqual(ctx.rank, 0)
def test_domain_decomposition_nonsymmetric(self):
nranks = 1
rank = 0
if (mpi_enabled):
comm = arb.mpi_comm()
context = arb.context(threads=1, gpu_id=None, mpi=comm)
nranks = context.ranks
rank = context.rank
else:
context = arb.context(threads=1, gpu_id=None)
recipe = gj_non_symmetric(nranks)
decomp = arb.partition_load_balance(recipe, context)
cells_per_rank = nranks
# check groups
i = 0
for gid in range(rank * cells_per_rank, (rank + 1) * cells_per_rank):
if (gid % nranks == rank - 1):
continue
elif (gid % nranks == rank and rank != nranks - 1):
cg = [gid, gid + cells_per_rank]
self.assertEqual(cg,
decomp.groups[len(decomp.groups) - 1].gids)
else:
cg = [gid]
self.assertEqual(cg, decomp.groups[i].gids)
i += 1
# check gid_domains
for gid in range(recipe.num_cells()):
group = int(gid / cells_per_rank)
idx = gid % cells_per_rank
ngroups = nranks
if (idx == group - 1):
self.assertEqual(group - 1, decomp.gid_domain(gid))
elif (idx == group and group != ngroups - 1):
self.assertEqual(group, decomp.gid_domain(gid))
else:
self.assertEqual(group, decomp.gid_domain(gid))
def test_domain_decomposition_homogenous_GPU(self):
if (mpi_enabled):
comm = arb.mpi_comm()
context = arb.context(threads=1, gpu_id=0, mpi=comm)
else:
context = arb.context(threads=1, gpu_id=0)
N = context.ranks
I = context.rank
# 10 cells per domain
n_local = 10
n_global = n_local * N
recipe = homo_recipe(n_global)
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_local)
self.assertEqual(decomp.num_global_cells, n_global)
self.assertEqual(len(decomp.groups), 1)
b = I * n_local
e = (I + 1) * n_local
gids = list(range(b,e))
for gid in gids:
self.assertEqual(I, decomp.gid_domain(gid))
# Each cell group contains 1 cell of kind cable
# Each group should also be tagged for gpu execution
grp = decomp.groups[0]
self.assertEqual(len(grp.gids), n_local)
self.assertEqual(grp.gids[0], b)
self.assertEqual(grp.gids[-1], e-1)
self.assertEqual(grp.backend, arb.backend.gpu)
self.assertEqual(grp.kind, arb.cell_kind.cable)
def run():
v = options.parse_arguments().verbosity
comm = arb.mpi_comm(mpi.COMM_WORLD)
alloc = arb.proc_allocation()
ctx = arb.context(alloc, comm)
rank = ctx.rank
if rank == 0:
runner = unittest.TextTestRunner(verbosity=v)
else:
sys.stdout = open(os.devnull, 'w')
runner = unittest.TextTestRunner(stream=sys.stdout)
runner.run(suite())
def init_sim(self):
comm = A.mpi_comm()
context = A.context(threads=1, gpu_id=None, mpi=A.mpi_comm())
self.rank = context.rank
self.ranks = context.ranks
recipe = lifN_recipe(context.ranks)
dd = A.partition_load_balance(recipe, context)
# Confirm decomposition has gid 0 on rank 0, ..., gid N-1 on rank N-1.
self.assertEqual(1, dd.num_local_cells)
local_groups = dd.groups
self.assertEqual(1, len(local_groups))
self.assertEqual([self.rank], local_groups[0].gids)
return A.simulation(recipe, dd, context)
def context():
"""
Fixture that produces an MPI sensitive `arbor.context`
"""
args = [arbor.proc_allocation()]
if _mpi_enabled:
if not arbor.mpi_is_initialized():
print("Context fixture initializing mpi", flush=True)
arbor.mpi_init()
atexit.register(_finalize_mpi)
if _mpi4py_enabled:
from mpi4py.MPI import COMM_WORLD as comm
else:
comm = arbor.mpi_comm()
args.append(comm)
return arbor.context(*args)
def run():
v = options.parse_arguments().verbosity
if not arb.mpi_is_initialized():
arb.mpi_init()
comm = arb.mpi_comm()
alloc = arb.proc_allocation()
ctx = arb.context(alloc, comm)
rank = ctx.rank
if rank == 0:
runner = unittest.TextTestRunner(verbosity=v)
else:
sys.stdout = open(os.devnull, 'w')
runner = unittest.TextTestRunner(stream=sys.stdout)
runner.run(suite())
if not arb.mpi_is_finalized():
arb.mpi_finalize()
def test_domain_decomposition_homogenous_CPU(self):
n_cells = 10
recipe = homo_recipe(n_cells)
context = arb.context()
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_cells)
self.assertEqual(decomp.num_global_cells, n_cells)
self.assertEqual(len(decomp.groups), n_cells)
gids = list(range(n_cells))
for gid in gids:
self.assertEqual(0, decomp.gid_domain(gid))
# Each cell group contains 1 cell of kind cable
# Each group should also be tagged for cpu execution
for i in gids:
grp = decomp.groups[i]
self.assertEqual(len(grp.gids), 1)
self.assertEqual(grp.gids[0], i)
self.assertEqual(grp.backend, arb.backend.multicore)
self.assertEqual(grp.kind, arb.cell_kind.cable)
def test_domain_decomposition_homogenous_GPU(self):
n_cells = 10
recipe = homo_recipe(n_cells)
context = arb.context(threads=1, gpu_id=0)
decomp = arb.partition_load_balance(recipe, context)
self.assertEqual(decomp.num_local_cells, n_cells)
self.assertEqual(decomp.num_global_cells, n_cells)
self.assertEqual(len(decomp.groups), 1)
gids = range(n_cells)
for gid in gids:
self.assertEqual(0, decomp.gid_domain(gid))
# Each cell group contains 1 cell of kind cable
# Each group should also be tagged for gpu execution
grp = decomp.groups[0]
self.assertEqual(len(grp.gids), n_cells)
self.assertEqual(grp.gids[0], 0)
self.assertEqual(grp.gids[-1], n_cells - 1)
self.assertEqual(grp.backend, arb.backend.gpu)
self.assertEqual(grp.kind, arb.cell_kind.cable)
def test_domain_decomposition_exceptions(self):
n_cells = 20
recipe = hetero_recipe(n_cells)
context = arb.context()
# The hints perfer the multicore backend, so the decomposition is expected
# to never have cell groups on the GPU, regardless of whether a GPU is
# available or not.
cable_hint = arb.partition_hint()
cable_hint.prefer_gpu = False
cable_hint.cpu_group_size = 0
spike_hint = arb.partition_hint()
spike_hint.prefer_gpu = False
spike_hint.gpu_group_size = 1
hints = dict([(arb.cell_kind.cable, cable_hint),
(arb.cell_kind.spike_source, spike_hint)])
with self.assertRaisesRegex(
RuntimeError,
"unable to perform load balancing because cell_kind::cable has invalid suggested cpu_cell_group size of 0"
):
decomp = arb.partition_load_balance(recipe, context, hints)
cable_hint = arb.partition_hint()
cable_hint.prefer_gpu = False
cable_hint.cpu_group_size = 1
spike_hint = arb.partition_hint()
spike_hint.prefer_gpu = True
spike_hint.gpu_group_size = 0
hints = dict([(arb.cell_kind.cable, cable_hint),
(arb.cell_kind.spike_source, spike_hint)])
with self.assertRaisesRegex(
RuntimeError,
"unable to perform load balancing because cell_kind::spike_source has invalid suggested gpu_cell_group size of 0"
):
decomp = arb.partition_load_balance(recipe, context, hints)
def test_simulation(self):
rcp = recipe()
ctx = arb.context()
dom = arb.partition_load_balance(rcp, ctx)
sim = arb.simulation(rcp, dom, ctx)
sim.run(tfinal=30)
if gid==0:
sched = arbor.explicit_schedule([1])
return [arbor.event_generator(arbor.cell_member(0,0), 0.1, sched)]
return []
def probes(self, gid):
return [arbor.cable_probe_membrane_voltage('"root"')]
def global_properties(self, kind):
return self.props
comm = arbor.mpi_comm()
print(comm)
# (10) Set up the hardware context
context = arbor.context(threads=20, gpu_id=None, mpi=comm)
print(context)
# (11) Set up and start the meter manager
meters = arbor.meter_manager()
meters.start(context)
# (12) Instantiate recipe
ncells = 50
recipe = ring_recipe(ncells)
meters.checkpoint('recipe-create', context)
# (13) Define a hint at to the execution.
hint = arbor.partition_hint()
hint.prefer_gpu = True
hint.gpu_group_size = 1000
d = 10
return [
arbor.connection(arbor.cell_member(src, 0),
arbor.cell_member(gid, 0), w, d)
]
# Attach a generator to the first cell in the ring.
def event_generators(self, gid):
if gid == 0:
sched = arbor.explicit_schedule([1])
return [arbor.event_generator(arbor.cell_member(0, 0), 0.1, sched)]
return []
nthreads = 1
context = arbor.context(threads=nthreads, gpu_id=None)
meters = arbor.meter_manager()
meters.start(context)
# Create a recipe
recipe = ring_recipe(1000)
meters.checkpoint('recipe-create', context) # checkpoint
# Perform decomposition
decomp = arbor.partition_load_balance(recipe, context)
meters.checkpoint('load-balance', context) # checkpoint
# Create the simulation
sim = arbor.simulation(recipe, decomp, context)
# Attach a spike recorder
def test_probe_addr_metadata(self):
recipe = cc_recipe()
context = A.context()
dd = A.partition_load_balance(recipe, context)
sim = A.simulation(recipe, dd, context)
all_cv_cables = [A.cable(0, 0, 1)]
m = sim.probe_metadata((0, 0))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.0), m[0])
m = sim.probe_metadata((0, 1))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 2))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.02), m[0])
m = sim.probe_metadata((0, 3))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.03), m[0])
m = sim.probe_metadata((0, 4))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 5))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 6))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.06), m[0])
m = sim.probe_metadata((0, 7))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 8))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.08), m[0].location)
self.assertEqual(1, m[0].multiplicity)
self.assertEqual(0, m[0].target)
m = sim.probe_metadata((0, 9))
self.assertEqual(1, len(m))
self.assertEqual(1, len(m[0]))
self.assertEqual(A.location(0, 0.09), m[0][0].location)
self.assertEqual(1, m[0][0].multiplicity)
self.assertEqual(1, m[0][0].target)
m = sim.probe_metadata((0, 10))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.10), m[0])
m = sim.probe_metadata((0, 11))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 12))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.12), m[0])
m = sim.probe_metadata((0, 13))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 14))
self.assertEqual(1, len(m))
self.assertEqual(A.location(0, 0.14), m[0])
m = sim.probe_metadata((0, 15))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
m = sim.probe_metadata((0, 16))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
self.props.catalogue = arb.load_catalogue(cat)
d = arb.decor()
d.paint('(all)', 'dummy')
d.set_property(Vm=0.0)
self.cell = arb.cable_cell(self.tree, arb.label_dict(), d)
def global_properties(self, _):
return self.props
def num_cells(self):
return 1
def cell_kind(self, gid):
return arb.cell_kind.cable
def cell_description(self, gid):
return self.cell
if not Path(cat).is_file():
print("""Catalogue not found in this directory.
Please ensure it has been compiled by calling")
<arbor>/scripts/build-catalogue cat <arbor>/python/examples/cat
where <arbor> is the location of the arbor source tree.""")
exit(1)
rcp = recipe()
ctx = arb.context()
dom = arb.partition_load_balance(rcp, ctx)
sim = arb.simulation(rcp, dom, ctx)
sim.run(tfinal=30)
def gap_junction_on(self, gid):
return []
def event_generators(self, gid):
return []
def global_properties(self, gid):
return self.the_props
recipe = single_recipe(cell, [probe])
# (4) Create an execution context
context = arbor.context()
# (5) Create a domain decomposition
domains = arbor.partition_load_balance(recipe, context)
# (6) Create a simulation
sim = arbor.simulation(recipe, domains, context)
# Instruct the simulation to record the spikes and sample the probe
sim.record(arbor.spike_recording.all)
probe_id = arbor.cell_member(0, 0)
handle = sim.sample(probe_id, arbor.regular_schedule(0.02))
# Attach a generator to the first cell in the ring.
def event_generators(self, gid):
if gid==0:
sched = arbor.explicit_schedule([1])
return [arbor.event_generator(arbor.cell_member(0,0), 0.1, sched)]
return []
# Define one probe (for measuring voltage at the soma) on each cell.
def num_probes(self, gid):
return 1
def get_probe(self, id):
loc = arbor.location(0, 0) # at the soma
return arbor.cable_probe('voltage', id, loc)
context = arbor.context(threads=12, gpu_id=None)
print(context)
meters = arbor.meter_manager()
meters.start(context)
ncells = 4
recipe = ring_recipe(ncells)
print(f'{recipe}')
meters.checkpoint('recipe-create', context)
decomp = arbor.partition_load_balance(recipe, context)
print(f'{decomp}')
hint = arbor.partition_hint()
def test_context_arbmpi(self):
comm = arb.mpi_comm()
# test context with mpi
ctx = arb.context(mpi=comm)
self.assertTrue(ctx.has_mpi)
def test_context_mpi4py(self):
comm = arb.mpi_comm(mpi.COMM_WORLD)
# test context with mpi
ctx = arb.context(mpi=comm)
self.assertTrue(ctx.has_mpi)