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ALL: allow to change number of threads used for kdtree #353

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ALL: allow to change number of threads used for kdtree #353

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houndci-bot reviewed Dec 6, 2021
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pytim/gitim.py
@@ -66,6 +66,8 @@ class GITIM(Interface):
:param bool warnings: Print warnings
:param bool autoassign: If true (default) detect the interface
every time a new frame is selected.
:param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball
If -1 is given all CPU threads are used (default: -1)
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line too long (89 > 79 characters)

pytim/gitim.py
@@ -66,6 +66,8 @@ class GITIM(Interface):
:param bool warnings: Print warnings
:param bool autoassign: If true (default) detect the interface
every time a new frame is selected.
:param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball
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line too long (97 > 79 characters)

pytim/interface.py
>>> print(repr(inter.atoms))
<AtomGroup with 855 atoms>

>>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True,workers=1)
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line too long (129 > 79 characters)

pytim/interface.py
@@ -519,7 +524,11 @@ def _():
<AtomGroup with 2025 atoms>


>>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True)
>>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True,workers=-1)
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line too long (130 > 79 characters)

pytim/interface.py
@@ -171,7 +176,7 @@ def _define_cluster_group(self):
# the smaller clusters of the other phase
labels, counts, neighbors = utilities.do_cluster_analysis_dbscan(
self.cluster_group, cluster_cut,
self.cluster_threshold_density, self.molecular)
self.cluster_threshold_density, self.molecular,workers=self.workers)
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line too long (84 > 79 characters)
missing whitespace after ','

pytim/sasa.py
@@ -60,6 +60,8 @@ class SASA(GITIM):
:param bool warnings: Print warnings
:param bool autoassign: If true (default) detect the interface
every time a new frame is selected.
:param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball
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line too long (97 > 79 characters)

pytim/utilities_dbscan.py
@@ -56,7 +59,7 @@ def do_cluster_analysis_dbscan(group,

neighborhoods = np.array([
np.array(neighbors)
for neighbors in tree.query_ball_point(points, cluster_cut, n_jobs=-1)
for neighbors in tree.query_ball_point(points, cluster_cut, workers=workers)
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line too long (84 > 79 characters)

pytim/utilities_dbscan.py
@@ -46,6 +46,9 @@ def do_cluster_analysis_dbscan(group,
clusters. This is on average O(N log N) thanks to the O(log N)
scaling of the kdtree.

To avoid problems in environments with limited resources,
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trailing whitespace

pytim/utilities_dbscan.py
@@ -31,7 +31,7 @@ def determine_samples(threshold_density, cluster_cut, n_neighbors):
def do_cluster_analysis_dbscan(group,
cluster_cut,
threshold_density=None,
molecular=True):
molecular=True,workers=1):
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missing whitespace after ','

pytim/willard_chandler.py
:param bool autoassign: If true (default) detect the interface
every time a new frame is selected.
:param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball
If -1 is given all CPU threads are used (default: -1)
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line too long (87 > 79 characters)

@Marcello-Sega Marcello-Sega linked an issue Dec 6, 2021 that may be closed by this pull request
multiple kdtree threads might create issues on clusters #352
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fixes #352

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multiple kdtree threads might create issues on clusters
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