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Fixed unnecessary Pool creation in searchlight #386

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Merged
mihaic merged 3 commits into from
Oct 16, 2018
Merged

Fixed unnecessary Pool creation in searchlight #386

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fca04f5
Fixed unnecessary Pool creation in searchlight
davidt0x Oct 15, 2018
ac2cf6e
Fixed some lint errors.
davidt0x Oct 16, 2018
dbfe054
Added test for searchlight with pool_size=1
davidt0x Oct 16, 2018
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39 changes: 29 additions & 10 deletions brainiak/searchlight/searchlight.py
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Original file line number Diff line number Diff line change
Expand Up @@ -420,18 +420,37 @@ def run_block_function(self, block_fn, extra_block_fn_params=None,
processes = usable_cpus
else:
processes = min(pool_size, usable_cpus)
with Pool(processes) as pool:

if processes > 1:
with Pool(processes) as pool:
for idx, block in enumerate(self.blocks):
result = pool.apply_async(
block_fn,
([subproblem[idx] for subproblem in self.subproblems],
self.submasks[idx],
self.sl_rad,
self.bcast_var,
extra_block_fn_params))
results.append((block[0], result))
local_outputs = [(result[0], result[1].get())
for result in results]
else:
# If we only are using one CPU core, no need to create a Pool,
# cause an underlying fork(), and send the data to that process.
# Just do it here in serial. This will save copying the memory
# and will stop a fork() which can cause problems in some MPI
# implementations.
for idx, block in enumerate(self.blocks):
result = pool.apply_async(
block_fn,
([subproblem[idx] for subproblem in self.subproblems],
self.submasks[idx],
self.sl_rad,
self.bcast_var,
extra_block_fn_params))
subprob_list = [subproblem[idx]
for subproblem in self.subproblems]
result = block_fn(
subprob_list,
self.submasks[idx],
self.sl_rad,
self.bcast_var,
extra_block_fn_params)
results.append((block[0], result))
local_outputs = [(result[0], result[1].get())
for result in results]
local_outputs = [(result[0], result[1]) for result in results]

# Collect results
global_outputs = self.comm.gather(local_outputs)
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30 changes: 30 additions & 0 deletions tests/searchlight/test_searchlight.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,36 @@ def test_searchlight_with_cube():
assert global_outputs[i, j, k] is None


def test_searchlight_with_cube_poolsize_1():
sl = Searchlight(sl_rad=3)
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
dim0, dim1, dim2 = (50, 50, 50)
ntr = 30
nsubj = 3
mask = np.zeros((dim0, dim1, dim2), dtype=np.bool)
data = [np.empty((dim0, dim1, dim2, ntr), dtype=np.object)
if i % size == rank
else None
for i in range(0, nsubj)]

# Put a spot in the mask
mask[10:17, 10:17, 10:17] = True

sl.distribute(data, mask)
global_outputs = sl.run_searchlight(cube_sfn, pool_size=1)

if rank == 0:
assert global_outputs[13, 13, 13] == 1.0
global_outputs[13, 13, 13] = None

for i in range(global_outputs.shape[0]):
for j in range(global_outputs.shape[1]):
for k in range(global_outputs.shape[2]):
assert global_outputs[i, j, k] is None


def diamond_sfn(l, msk, myrad, bcast_var):
assert not np.any(msk[~Diamond(3).mask_])
if np.all(msk[Diamond(3).mask_]):
Expand Down