marin-dupekit 0.1.1

dupekit

Raison d'être: Home for the Rust code used for text deduplication.

Install

• Locally: This code is auto-magically built by uv via Cargo and Maturin. You might need to install them (e.g., brew install maturin rust on macOS).
• Cluster: This code is compiled as part of the Docker build (uv pip install -e ... step): Maturin builds the Rust code and places it in the system site-packages (e.g., /home/ray/anaconda3/lib/python3.11/site-packages/dupekit/dupekit.abi3.so).

[!NOTE] What about making dupekit a hybrid Python/Rust Maturin workspace? We tried and experienced issues getting the Docker build to work while keeping it simple—a simple Rust workspace helps keep the setup clean.

[!NOTE] Building from source requires a Rust toolchain (Cargo). Pre-built wheels are available from GitHub Releases for users who don't want to compile locally.

Benchmarking

The goal of these benchmarks is to test different ways of marshaling large text content between Python and Rust "foreign function interface" (wiki:FFI). These tests are designed to isolate the overhead of marshaling from the actual Rust computation (by doing minimal processing in Rust).

Dataset: 1 shard of HuggingFaceFW/fineweb-edu/sample/10BT (2.15 GB Parquet file, benchmarked on 250k out of 726k documents)

Install:

uv sync --all-packages --extra=benchmark --group dev

Benchmark (Takes a few minutes):

uv run pytest rust/dupekit/tests/bench/test_dedupe.py --run-benchmark --benchmark-min-rounds=20
uv run pytest rust/dupekit/tests/bench/test_marshaling.py --run-benchmark
uv run pytest rust/dupekit/tests/bench/test_batch_tuning.py --run-benchmark
uv run pytest rust/dupekit/tests/bench/test_io.py --run-benchmark
uv run pytest rust/dupekit/tests/bench/test_hashing.py --run-benchmark
uv run pytest rust/dupekit/tests/bench/test_minhash.py --run-benchmark

Note: Run separated by type of benchmark (otherwise results are mixed within one table)

Footprint (Note: sampling the stack might taint the mem measurements, so we disable benchmarking):

uv run pytest rust/dupekit/tests/bench/test_marshaling.py \
  --run-benchmark \
  --benchmark-disable \
  --memray \
  --native \
  --most-allocations=0

Results

Dedup: Rust vs. Python

---------------------------------------------------------------------------- benchmark 'Documents: Exact Deduplication': 2 tests ----------------------------------------------------------------------------
Name (time in ms)                             Min                 Max                Mean            StdDev              Median               IQR            Outliers       OPS            Rounds  Iterations
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_deduplication[rust-documents]         3.9872 (1.0)        5.2516 (1.0)        4.2341 (1.0)      0.1949 (1.0)        4.2247 (1.0)      0.2845 (1.0)          52;2  236.1805 (1.0)         188           1
test_deduplication[python-documents]     133.8747 (33.58)    157.3844 (29.97)    139.6233 (32.98)    7.7842 (39.94)    135.3300 (32.03)    9.6717 (34.00)         5;0    7.1621 (0.03)         20           1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------- benchmark 'Documents: Hash Generation': 2 tests ---------------------------------------------------------------------------
Name (time in ms)                       Min                 Max                Mean            StdDev              Median               IQR            Outliers       OPS            Rounds  Iterations
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_hashing[rust-documents]         2.2755 (1.0)        2.4842 (1.0)        2.3041 (1.0)      0.0301 (1.0)        2.2938 (1.0)      0.0381 (1.0)          50;9  434.0169 (1.0)         375           1
test_hashing[python-documents]     130.0445 (57.15)    132.3783 (53.29)    130.7795 (56.76)    0.6663 (22.13)    130.5910 (56.93)    0.6259 (16.44)         5;3    7.6465 (0.02)         20           1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------------- benchmark 'Paragraphs: Exact Deduplication': 2 tests ----------------------------------------------------------------------------
Name (time in ms)                              Min                 Max                Mean             StdDev              Median                IQR            Outliers      OPS            Rounds  Iterations
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_deduplication[rust-paragraphs]        85.4666 (1.0)      109.3652 (1.0)       90.2916 (1.0)       6.8294 (1.0)       87.3405 (1.0)       2.0275 (1.0)           4;4  11.0752 (1.0)          20           1
test_deduplication[python-paragraphs]     303.0885 (3.55)     342.9836 (3.14)     321.3022 (3.56)     13.8377 (2.03)     329.4886 (3.77)     25.1111 (12.39)         9;0   3.1123 (0.28)         20           1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------- benchmark 'Paragraphs: Hash Generation': 2 tests ---------------------------------------------------------------------------
Name (time in ms)                        Min                 Max                Mean             StdDev              Median               IQR            Outliers      OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_hashing[rust-paragraphs]        23.9739 (1.0)       26.9860 (1.0)       25.3823 (1.0)       0.4419 (1.0)       25.3160 (1.0)      0.2099 (1.0)           5;5  39.3975 (1.0)          38           1
test_hashing[python-paragraphs]     247.5415 (10.33)    321.4654 (11.91)    255.3421 (10.06)    19.0653 (43.15)    249.1948 (9.84)     1.7899 (8.53)          2;2   3.9163 (0.10)         20           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Marshaling

-------------------------------------------------------------------------------------------- benchmark: 7 tests -------------------------------------------------------------------------------------------
Name (time in ms)                    Min                   Max                  Mean             StdDev                Median                IQR            Outliers      OPS            Rounds  Iterations
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_arrow_giant                 86.4414 (1.0)         96.0537 (1.01)        90.0259 (1.0)       2.8582 (31.54)       90.4363 (1.0)       4.1787 (27.96)         3;0  11.1079 (1.0)          11           1
test_arrow_small                 94.4010 (1.09)        94.6679 (1.0)         94.5616 (1.05)      0.0906 (1.0)         94.5570 (1.05)      0.1494 (1.0)           5;0  10.5751 (0.95)         11           1
test_dicts_batched_stream     3,975.1581 (45.99)    3,979.7102 (42.04)    3,977.7639 (44.18)     1.8357 (20.26)    3,978.3399 (43.99)     2.8370 (18.98)         2;0   0.2514 (0.02)          5           1
test_dicts_batch              4,398.7191 (50.89)    4,421.9632 (46.71)    4,410.0489 (48.99)     8.7694 (96.78)    4,411.2232 (48.78)    12.0295 (80.50)         2;0   0.2268 (0.02)          5           1
test_dicts_loop               4,411.8727 (51.04)    4,457.0985 (47.08)    4,431.9081 (49.23)    19.8323 (218.86)   4,430.5465 (48.99)    35.6846 (238.78)        2;0   0.2256 (0.02)          5           1
test_rust_structs             4,449.5728 (51.47)    4,479.8173 (47.32)    4,465.2999 (49.60)    14.1041 (155.65)   4,472.5336 (49.46)    24.8971 (166.60)        3;0   0.2239 (0.02)          5           1
test_arrow_tiny               7,023.5789 (81.25)    7,064.2094 (74.62)    7,044.9691 (78.25)    19.4414 (214.55)   7,047.1538 (77.92)    37.8036 (252.96)        1;0   0.1419 (0.01)          5           1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

PyArrow Batch Size

--------------------------------------------------------------------------------------------- benchmark: 11 tests ----------------------------------------------------------------------------------------------
Name (time in ms)                         Min                   Max                  Mean             StdDev                Median                IQR            Outliers      OPS            Rounds  Iterations
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_arrow_batch_sizes[8192]          28.6030 (1.0)         32.0178 (1.07)        29.2802 (1.0)       0.8846 (4.75)        28.9333 (1.0)       0.7970 (3.52)          5;3  34.1528 (1.0)          34           1
test_arrow_batch_sizes[16384]         28.7303 (1.00)        30.8987 (1.03)        29.3111 (1.00)      0.5447 (2.92)        29.1404 (1.01)      0.5907 (2.61)          9;2  34.1168 (1.00)         33           1
test_arrow_batch_sizes[4096]          28.8488 (1.01)        30.1474 (1.01)        29.2876 (1.00)      0.3776 (2.03)        29.2212 (1.01)      0.6339 (2.80)         12;0  34.1441 (1.00)         34           1
test_arrow_batch_sizes[2048]          29.1493 (1.02)        30.4442 (1.02)        29.5710 (1.01)      0.3013 (1.62)        29.5505 (1.02)      0.3483 (1.54)         10;1  33.8169 (0.99)         32           1
test_arrow_batch_sizes[32768]         29.2200 (1.02)        29.9410 (1.0)         29.5896 (1.01)      0.1863 (1.0)         29.5706 (1.02)      0.2423 (1.07)         11;0  33.7956 (0.99)         34           1
test_arrow_batch_sizes[65536]         30.3973 (1.06)        31.3805 (1.05)        30.9409 (1.06)      0.2453 (1.32)        30.9829 (1.07)      0.2263 (1.0)           9;3  32.3197 (0.95)         33           1
test_arrow_batch_sizes[131072]        30.7074 (1.07)        33.1845 (1.11)        31.4322 (1.07)      0.6799 (3.65)        31.1102 (1.08)      0.8739 (3.86)          6;1  31.8145 (0.93)         32           1
test_arrow_batch_sizes[1024]          30.7724 (1.08)        32.6049 (1.09)        31.6173 (1.08)      0.5506 (2.96)        31.6311 (1.09)      0.9233 (4.08)         13;0  31.6283 (0.93)         30           1
test_arrow_batch_sizes[512]           33.8866 (1.18)        36.2981 (1.21)        34.5224 (1.18)      0.6189 (3.32)        34.2960 (1.19)      0.5087 (2.25)          6;3  28.9667 (0.85)         29           1
test_arrow_batch_sizes[128]           51.0530 (1.78)        56.3190 (1.88)        53.5492 (1.83)      1.6124 (8.65)        53.7474 (1.86)      2.3557 (10.41)         7;0  18.6744 (0.55)         18           1
test_arrow_batch_sizes[1]          2,781.2088 (97.23)    2,812.2547 (93.93)    2,797.8572 (95.55)    11.6892 (62.74)    2,801.0024 (96.81)    15.3956 (68.03)         2;0   0.3574 (0.01)          5           1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

I/O

------------------------------------------------------------------------------- benchmark: 4 tests ------------------------------------------------------------------------------
Name (time in s)          Min               Max              Mean            StdDev            Median               IQR            Outliers     OPS            Rounds  Iterations
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_rust_native       1.6757 (1.0)      1.6848 (1.0)      1.6794 (1.0)      0.0035 (1.26)     1.6783 (1.0)      0.0047 (1.73)          2;0  0.5955 (1.0)           5           1
test_arrow_giant       2.9501 (1.76)     2.9570 (1.76)     2.9521 (1.76)     0.0028 (1.0)      2.9511 (1.76)     0.0027 (1.0)           1;0  0.3387 (0.57)          5           1
test_arrow_small       3.3476 (2.00)     3.6588 (2.17)     3.5583 (2.12)     0.1241 (44.48)    3.5726 (2.13)     0.1289 (47.18)         1;0  0.2810 (0.47)          5           1
test_dicts_loop_io     7.3664 (4.40)     7.3913 (4.39)     7.3837 (4.40)     0.0101 (3.63)     7.3871 (4.40)     0.0113 (4.14)          1;0  0.1354 (0.23)          5           1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Hashing

--------------------------------------------------------------------------------------- benchmark: 6 tests ---------------------------------------------------------------------------------------
Name (time in ms)                     Min                Max               Mean            StdDev             Median               IQR            Outliers       OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_hash_rust_xxh3_64_batch       4.4886 (1.0)       4.9466 (1.0)       4.5860 (1.0)      0.0616 (1.57)      4.5939 (1.0)      0.0957 (2.52)         74;1  218.0558 (1.0)         210           1
test_hash_rust_xxh3_64_scalar      5.0276 (1.12)      5.3367 (1.08)      5.1276 (1.12)     0.0393 (1.0)       5.1307 (1.12)     0.0379 (1.0)         41;12  195.0244 (0.89)        190           1
test_hash_rust_xxh3_128            6.1686 (1.37)      6.5772 (1.33)      6.2901 (1.37)     0.1098 (2.79)      6.2334 (1.36)     0.1731 (4.56)         37;0  158.9811 (0.73)        160           1
test_hash_rust_blake3             28.7743 (6.41)     29.0392 (5.87)     28.8919 (6.30)     0.0593 (1.51)     28.8799 (6.29)     0.0709 (1.87)         10;1   34.6118 (0.16)         35           1
test_hash_rust_blake2             54.1043 (12.05)    55.0271 (11.12)    54.4180 (11.87)    0.3711 (9.43)     54.1916 (11.80)    0.7337 (19.34)         5;0   18.3763 (0.08)         19           1
test_hash_python_blake2b          84.0109 (18.72)    84.1698 (17.02)    84.0611 (18.33)    0.0465 (1.18)     84.0469 (18.30)    0.0595 (1.57)          3;0   11.8961 (0.05)         12           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Mem Footprin (sorted from high to low):

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_rust_structs at the high watermark

	 📦 Total memory allocated: 4.3GiB
	 📏 Total allocations: 21
	 📊 Histogram of allocation sizes: | ▃█▁▃|

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_dicts_batch at the high watermark

	 📦 Total memory allocated: 3.3GiB
	 📏 Total allocations: 20
	 📊 Histogram of allocation sizes: |  ▁█▂|

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_dicts_loop at the high watermark

	 📦 Total memory allocated: 3.3GiB
	 📏 Total allocations: 19
	 📊 Histogram of allocation sizes: |  ▁█▂|

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_arrow_giant at the high watermark

	 📦 Total memory allocated: 64.9MiB
	 📏 Total allocations: 36
	 📊 Histogram of allocation sizes: |▅█   |

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_dicts_batched_stream at the high watermark

	 📦 Total memory allocated: 28.1MiB
	 📏 Total allocations: 7
	 📊 Histogram of allocation sizes: |█▄▄▄▄|

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_arrow_tiny at the high watermark

	 📦 Total memory allocated: 22.0MiB
	 📏 Total allocations: 37
	 📊 Histogram of allocation sizes: |█▇   |

Allocation results for rust/dupekit/tests/bench/test_marshaling.py::test_arrow_small at the high watermark

	 📦 Total memory allocated: 551.7KiB
	 📏 Total allocations: 42
	 📊 Histogram of allocation sizes: |▂█▁  |

Statement of attribution:

• This code was seeded from nelson-liu/rbloom-gcs.
• Bloom filters were originally proposed in (Bloom, 1970). Furthermore, this implementation makes use of a constant recommended by (L'Ecuyer, 1999) for redistributing the entropy of a single hash over multiple integers using a linear congruential generator.