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Merged
jhprinz merged 20 commits into from
Apr 22, 2015
Merged

[WIP] Faster SequentialEnsemble #204

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b8d903f
Start of cache in SequentialEnsemble.
dwhswenson Apr 3, 2015
d74bd44
More caching in SeqEns
dwhswenson Apr 4, 2015
007a6a0
Cache setup (no usage) works with tests.
dwhswenson Apr 4, 2015
7012596
Skeleton of testSequentialEnsembleCaching
dwhswenson Apr 5, 2015
ee02afd
Merge remote-tracking branch 'upstream/master' into faster_sequential…
dwhswenson Apr 5, 2015
e2f13f6
Cache resets when function changes.
dwhswenson Apr 5, 2015
e61ece0
Changing trajectory resets cache
dwhswenson Apr 5, 2015
8b5a85e
Merge remote-tracking branch 'upstream/master' into faster_sequential…
dwhswenson Apr 7, 2015
83d10fa
Merge remote-tracking branch 'upstream/master' into faster_sequential…
dwhswenson Apr 8, 2015
f05fe7c
Start to new EnsembleCache class
dwhswenson Apr 8, 2015
a8686c9
Start on a couple more tests
dwhswenson Apr 9, 2015
783070e
Tests for the EnsembleCache object finished.
dwhswenson Apr 9, 2015
56a1ffa
Rewrite cache reset to allow using same traj 2x
dwhswenson Apr 10, 2015
4541151
Starting to use the caching in SeqEns
dwhswenson Apr 12, 2015
df3cad6
Yes we can_append! (With caching)
dwhswenson Apr 21, 2015
023c564
Fast can_append
dwhswenson Apr 21, 2015
48c4f2c
Prepend too?
dwhswenson Apr 21, 2015
2cf260f
Faster SequentialEnsembles; but still optimizing
dwhswenson Apr 22, 2015
5930624
Merge remote-tracking branch 'upstream/master' into faster_sequential…
dwhswenson Apr 22, 2015
dafd7a1
Much faster, tho more room for optimization left.
dwhswenson Apr 22, 2015
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Rewrite cache reset to allow using same traj 2x 
Also skeletons for test of seq ens cache
  • Loading branch information
@dwhswenson
dwhswenson committed Apr 10, 2015
commit 56a1ffadd41a0c34073a98dd5f1278c80b95c7ce
45 changes: 29 additions & 16 deletions openpathsampling/ensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,25 +40,39 @@ def __init__(self, direction=None):
self.direction = direction
self.contents = { }

def bad_direction_error(self):
raise RuntimeError("EnsembleCache.direction = " +
str(self.direction) + " invalid.") #nocover

def check(self, trajectory=None, reset=None):
"""Checks and resets (if necessary) the ensemble cache.
"""
if trajectory is not None:
lentraj = len(trajectory)
# if the first frame has changed, we should reset
if reset is None:
reset = (
self.direction > 0 and (
trajectory[0] != self.start_frame or
lentraj - 1 != self.last_length or
(lentraj > 1 and trajectory[-2] != self.prev_last_frame)
)
) or (
self.direction < 0 and (
trajectory[-1] != self.start_frame or
lentraj - 1 != self.last_length or
(lentraj > 1 and trajectory[1] != self.prev_last_frame)
)
)
lentraj = len(trajectory)
if self.direction > 0:
if trajectory[0] != self.start_frame:
reset = True
else:
if lentraj == self.last_length:
reset = (trajectory[-1] != self.prev_last_frame)
elif lentraj == self.last_length + 1:
reset = (trajectory[-2] != self.prev_last_frame)
else:
reset = True
elif self.direction < 0:
if trajectory[-1] != self.start_frame:
reset = True
else:
if lentraj == self.last_length:
reset = (trajectory[0] != self.prev_last_frame)
elif lentraj == self.last_length + 1:
reset = (trajectory[1] != self.prev_last_frame)
else:
reset = True
else:
self.bad_direction_error()
else:
reset = True

Expand All @@ -74,8 +88,7 @@ def check(self, trajectory=None, reset=None):
self.last_length = len(trajectory)
self.contents = { }
else:
raise RuntimeWarning("EnsembleCache.direction = " +
str(self.direction) + " invalid.")
self.bad_direction_error()
# by returning reset, we allow the functions that call this to reset
# other things as well
self.last_length = len(trajectory)
Expand Down
39 changes: 37 additions & 2 deletions openpathsampling/tests/testensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -868,6 +868,17 @@ def test_trajectory_by_frame(self):
self.rev.check(self.traj[-2:])
assert_equal(self._was_cache_reset(self.rev), False)

def test_same_traj_twice_no_reset(self):
# tests for forward
self.fwd.check(self.traj)
assert_equal(self._was_cache_reset(self.fwd), True)
self.fwd.contents = { 'test' : 'object' }
self.fwd.check(self.traj)
#assert_equal(self._was_cache_reset(self.fwd), False)
# tests for backward
raise SkipTest


def test_trajectory_skips_frame(self):
# tests for forward
self.fwd.check(self.traj[0:1])
Expand Down Expand Up @@ -903,9 +914,8 @@ def test_trajectory_middle_frame_changes(self):
assert_equal(self._was_cache_reset(self.rev), True)


class testSequentialEnsembleCache(testEnsembleCache):
class testSequentialEnsembleCache(EnsembleCacheTest):
def setUp(self):
super(testSequentialEnsembleCache, self).setUp()
self.inX = AllInXEnsemble(vol1)
self.outX = AllOutXEnsemble(vol1)
self.length1 = LengthEnsemble(1)
Expand All @@ -920,6 +930,31 @@ def setUp(self):


def test_sequential_caching_can_append(self):
#cache = self.pseudo_minus._cache_can_append
assert_equal(self.pseudo_minus.can_append(self.traj[0:1]), True)
#assert_equal(self._was_cache_reset(cache), True)
for i in range(1, len(self.traj)-1):
assert_equal(self.pseudo_minus.can_append(self.traj[0:i+1]), True)
#assert_equal(self._was_cache_reset(cache), False)
assert_equal(self.pseudo_minus.can_append(self.traj), False)
#assert_equal(self._was_cache_reset(cache), False)

def test_sequential_caching_resets(self):
#cache = self.pseudo_minus._cache_can_append
assert_equal(self.pseudo_minus.can_append(self.traj[2:3]), True)
assert_equal(self.pseudo_minus(self.traj[2:3]), False)
#assert_equal(self._was_cache_reset(cache), True)
assert_equal(self.pseudo_minus.can_append(self.traj[2:4]), True)
assert_equal(self.pseudo_minus(self.traj[2:4]), False)
#assert_equal(self._was_cache_reset(cache), True)
for i in range(4, len(self.traj)-1):
assert_equal(self.pseudo_minus.can_append(self.traj[2:i+1]), True)
assert_equal(self.pseudo_minus(self.traj[2:i+1]), False)
#assert_equal(self._was_cache_reset(cache), False)
assert_equal(self.pseudo_minus.can_append(self.traj[2:]), False)
assert_equal(self.pseudo_minus(self.traj[2:]), False)
#assert_equal(self._was_cache_reset(cache), False)
# TODO: same story backward
raise SkipTest

def test_sequential_caching_call(self):
Expand Down