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Fix OMP_NUM_THREADS bug #885

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Merged
merged 4 commits into from
Mar 5, 2025
Merged

Fix OMP_NUM_THREADS bug #885

merged 4 commits into from
Mar 5, 2025

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RobertoDF
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@RobertoDF RobertoDF commented Mar 5, 2025 •
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Hi,

if OMP_NUM_THREADS is not set already it will be set to a string instead of a int here below.

Kilosort/kilosort/spikedetect.py

Lines 74 to 83 in 326a00d

with warnings.catch_warnings():
warnings.filterwarnings("ignore", message="")
# Prevents memory leak for KMeans when using MKL on Windows
msg = 'KMeans is known to have a memory leak on Windows with MKL'
nthread = os.environ.get('OMP_NUM_THREADS', msg)
os.environ['OMP_NUM_THREADS'] = '7'
model = KMeans(n_clusters=ops['settings']['n_templates'], n_init = 10).fit(clips)
wTEMP = torch.from_numpy(model.cluster_centers_).to(device).float()
wTEMP = wTEMP / (wTEMP**2).sum(1).unsqueeze(1)**.5
os.environ['OMP_NUM_THREADS'] = nthread

This was happening on my windows machine and crashing the code.
7 seems to work fine, the msg text is currently unused, not sure it is important to keep it or not.

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codecov-commenter commented Mar 5, 2025 •
edited
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Codecov Report

Attention: Patch coverage is 0% with 5 lines in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (d8ba42f) to head (aca577f).
Report is 548 commits behind head on main.

Files with missing lines Patch % Lines
kilosort/spikedetect.py 0.00% 5 Missing ⚠️
Additional details and impacted files 
@@          Coverage Diff           @@
##            main    #885    +/-   ##
======================================
  Coverage   0.00%   0.00%            
======================================
  Files         32      33     +1     
  Lines       4649    5633   +984     
======================================
- Misses      4649    5633   +984

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RobertoDF and others added 3 commits March 5, 2025 13:06
@jacobpennington
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Thanks for catching that. Changes have been corrected, waiting for tests before merging.

@jacobpennington jacobpennington merged commit 07980b2 into MouseLand:main Mar 5, 2025
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@RobertoDF RobertoDF deleted the Fix-OMP_NUM_THREADS branch March 5, 2025 19:31
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@RobertoDF @codecov-commenter @jacobpennington