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GPU implementation of hamming distance #541

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@felixpetschko felixpetschko commented Aug 19, 2024 •
edited by grst
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Hamming distance implementation with numba.cuda for GPU support.
This is built on top of the changes in Hamming distance implementation with Numba #512

@grst:

felixpetschko and others added 30 commits April 29, 2024 13:28
@felixpetschko
take static methods out of tcrdist
bad62d8
@felixpetschko
made _tcrdist_mat a normal class method
72565bf
@felixpetschko
parent method NumbaDistanceCalculator extracted
add8e7f
@felixpetschko
numba version of hamming distance implemented
e9c0642
@felixpetschko
hamming numba tests passed and reference test added
68e0493
@felixpetschko
hamming numba distance calculator implemented and tested
ef0fa7d
@felixpetschko
n_jobs parameter handling done in NumbaDistanceCalculator superclass
0b15f8b
@felixpetschko
documentation adapted
46bfc14
@felixpetschko
removed unnecessary import
e339e14
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7da4519 
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@felixpetschko
hamming distance with numba parallelization implemented
82b0259
@felixpetschko
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scirpy…
b2d28d3 
… into numba_hamming
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[pre-commit.ci] auto fixes from pre-commit.com hooks
249e626 
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@felixpetschko
imports fixed
2fccc6a
@felixpetschko
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scirpy…
9ee1a2b 
… into numba_hamming
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a68ab53 
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@felixpetschko
implemented parallelization with n_jobs and n_blocks for hamming and …
d68a10b 
…tcrdist distance metrics
@felixpetschko
performance optimization for hamming and tcrdist
0005e63
@felixpetschko
more documentation added
6f16a3e
@felixpetschko
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scirpy…
6b32311 
… into numba_hamming
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[pre-commit.ci] auto fixes from pre-commit.com hooks
ad13f52 
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@felixpetschko
documentation adapted
08ad838
@felixpetschko
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scirpy…
a8d9846 
… into numba_hamming
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
b86030c 
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@felixpetschko
documentation adapted
2fb8254
@felixpetschko
Merge branch 'numba_hamming' of https://github.com/felixpetschko/scirpy…
bb0f430 
… into numba_hamming
@felixpetschko
signature of _calc_dist_mat_block changed
80ae271
@felixpetschko
the alphabet for the hamming distance is now the unique characters oc…
91c1dea 
…curing in all sequences
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@grst
Merge branch 'main' into numba_hamming
a0627b4
felixpetschko and others added 24 commits February 5, 2025 10:37
@felixpetschko
refactored
2b8cf41
@felixpetschko
merge
8783b27
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9784d77 
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@grst
Update meta.yaml
10a7577
@grst
Merge branch 'main' into gpu_hamming
8b2d5bf
@grst
Update meta.yaml
4b40c08
@grst
Update meta.yaml
825775c
@felixpetschko
removed time measurement prints and added progress bar
2b677a7
@felixpetschko
removed cuda synchronize statements used for performance testing
f446f82
@felixpetschko
added parameters gpu_n_blocks and gpu_block_width
d1fc102
@felixpetschko
added parameter documentation
48a66dc
@felixpetschko
cleaned up hamming kernel
641985f
@felixpetschko
catch sequence conversion error by retrying with non ascii implementa…
751387d 
…tion
@felixpetschko
use parameters gpu_n_blocks and gpu_block_width for testing
2d5067a
@felixpetschko
adapted documentation about n_blocks
231603c
@felixpetschko
Merge branch 'gpu_hamming' of https://github.com/felixpetschko/scirpy …
b2d0bd6 
…into gpu_hamming
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[pre-commit.ci] auto fixes from pre-commit.com hooks
9729e10 
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@felixpetschko
adapted error handling for ascii UnicodeError
4508cf5
@felixpetschko
Merge branch 'gpu_hamming' of https://github.com/felixpetschko/scirpy …
7036ad5 
…into gpu_hamming
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[pre-commit.ci] auto fixes from pre-commit.com hooks
f0c809c 
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@felixpetschko
removed reference to :class:`~scirpy.ir_dist.metrics.GPUHammingDistan…
571bffc 
…ceCalculator` in documentation
@felixpetschko
Merge branch 'gpu_hamming' of https://github.com/felixpetschko/scirpy …
ad5757e 
…into gpu_hamming
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@grst
WIP: update docs
a1d509e
grst
grst reviewed Feb 9, 2025
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