Improve GPU Hamming distance computation - #723

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felixpetschko:performance/gpu-hamming-improvements

Commits on Jul 22, 2026

Add GPU hamming improvements
felixpetschko
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880a882
Change cutoff guard to <=125
felixpetschko
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3d40391
Add parameter guards for block size parameters
felixpetschko
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d053bee
Add tests for different block size parameters
felixpetschko
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5200588
Adapt GPUHammingDistanceCalculator doc string
felixpetschko
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5b89ab2
Change sequence length array data type to int32
felixpetschko
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7718e2c
Avoid unnecessary dtype copies in GPU hamming transfers
felixpetschko
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9d3252d
Replace asserts with exceptions
felixpetschko
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80ee4c5
Transform guarding assert into error
felixpetschko
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dada164
Remove benchmarking option
felixpetschko
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6887bf3
Skip calculation of blocks under diagonal
felixpetschko
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86391e7
Update block skipping
felixpetschko
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1ab2ffb
Update block skipping to work with tqdm
felixpetschko
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701b860
Remove logic to only compute upper triangular half for symmetric result blocks within Hamming kernel itself
felixpetschko
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c82add0
Extend test cases to cover block skipping
felixpetschko
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4884d50
Update changelog
felixpetschko
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efa31eb
Add GPU hamming integration test
felixpetschko
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a2bba48
Prevent out-of-bounds writes in GPU Hamming kernel
felixpetschko
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940d3a0
Handle excess blocks in GPU Hamming calculator
felixpetschko
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d5eef6e
Support joblib blocks in GPU Hamming calculator
felixpetschko
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0530c30

Commits on Jul 23, 2026

Balance symmetric distance blocks and use fixed GPU tile sizes
felixpetschko
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4c9f30e
Improve GPU Hamming block sizing and buffer handling
felixpetschko
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6d22b8b
Change parameter names
felixpetschko
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c5938ab
Log tile retry info
felixpetschko
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7f4b593
Test maximum GPU Hamming cutoff
felixpetschko
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14e0bcf
Extend large dataset tutorial
felixpetschko
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9fea04d
Reformat
felixpetschko
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717974b

Commits on Jul 26, 2026

Adapt input array memory management
felixpetschko
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7feb2b4