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Sparse in-mem HNSW graph #4888

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Sparse in-mem HNSW graph #4888

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@ray6080 ray6080 commented Feb 12, 2025

Description

Introduce SparseInMemHNSWGraph, which is more space-efficient, as the upper layer for InMemHNSWIndex during index construction.

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github-actions bot commented Feb 12, 2025

Benchmark Result

Master commit hash: dfabf90eab17ec0dc0f87d18464152412e1fd8ee
Branch commit hash: 5351c3a194a4c3e2171f04e79c4ba1a629111e2d

Query Group Query Name Mean Time - Commit (ms) Mean Time - Master (ms) Diff
aggregation q24 742.45 736.85 5.60 (0.76%)
aggregation q28 6379.45 6358.04 21.40 (0.34%)
filter q14 143.85 128.29 15.56 (12.13%)
filter q15 145.23 126.50 18.73 (14.81%)
filter q16 320.14 306.18 13.96 (4.56%)
filter q17 462.29 446.79 15.50 (3.47%)
filter q18 1926.94 1922.93 4.01 (0.21%)
filter zonemap-node 107.14 88.87 18.27 (20.56%)
filter zonemap-node-lhs-cast 105.61 90.75 14.86 (16.38%)
filter zonemap-node-null 105.46 90.66 14.80 (16.33%)
filter zonemap-rel 5688.28 5394.15 294.13 (5.45%)
fixed_size_expr_evaluator q07 599.11 581.95 17.16 (2.95%)
fixed_size_expr_evaluator q08 828.49 801.57 26.91 (3.36%)
fixed_size_expr_evaluator q09 827.07 803.44 23.63 (2.94%)
fixed_size_expr_evaluator q10 260.64 236.67 23.97 (10.13%)
fixed_size_expr_evaluator q11 253.91 229.64 24.27 (10.57%)
fixed_size_expr_evaluator q12 250.59 231.70 18.89 (8.15%)
fixed_size_expr_evaluator q13 1470.19 1465.25 4.95 (0.34%)
fixed_size_seq_scan q23 134.58 111.76 22.82 (20.42%)
join q29 715.24 703.37 11.87 (1.69%)
join q30 10690.08 11083.57 -393.49 (-3.55%)
join q31 5.43 9.98 -4.55 (-45.57%)
join SelectiveTwoHopJoin 57.46 59.99 -2.53 (-4.21%)
ldbc_snb_ic q35 2699.55 2607.02 92.53 (3.55%)
ldbc_snb_ic q36 478.11 485.56 -7.45 (-1.53%)
ldbc_snb_is q32 5.06 4.47 0.59 (13.11%)
ldbc_snb_is q33 15.48 14.83 0.65 (4.40%)
ldbc_snb_is q34 1.23 1.25 -0.02 (-1.36%)
multi-rel multi-rel-large-scan 1404.23 1392.59 11.65 (0.84%)
multi-rel multi-rel-lookup 25.08 32.54 -7.46 (-22.94%)
multi-rel multi-rel-small-scan 91.63 102.16 -10.53 (-10.30%)
order_by q25 147.38 131.92 15.46 (11.72%)
order_by q26 470.60 452.45 18.15 (4.01%)
order_by q27 1461.59 1420.37 41.22 (2.90%)
recursive_join recursive-join-bidirection 313.02 296.22 16.80 (5.67%)
recursive_join recursive-join-dense 7401.56 7444.01 -42.45 (-0.57%)
recursive_join recursive-join-path 24164.21 24117.33 46.88 (0.19%)
recursive_join recursive-join-sparse 1055.29 1057.45 -2.16 (-0.20%)
recursive_join recursive-join-trail 7395.44 7418.08 -22.64 (-0.31%)
scan_after_filter q01 188.72 175.01 13.71 (7.83%)
scan_after_filter q02 174.24 159.85 14.39 (9.00%)
shortest_path_ldbc100 q37 91.01 97.65 -6.63 (-6.79%)
shortest_path_ldbc100 q38 382.15 377.28 4.87 (1.29%)
shortest_path_ldbc100 q39 61.96 64.85 -2.89 (-4.45%)
shortest_path_ldbc100 q40 466.89 464.15 2.74 (0.59%)
var_size_expr_evaluator q03 2110.99 2149.45 -38.46 (-1.79%)
var_size_expr_evaluator q04 2237.16 2203.44 33.72 (1.53%)
var_size_expr_evaluator q05 2721.30 2620.11 101.19 (3.86%)
var_size_expr_evaluator q06 1341.70 1345.39 -3.70 (-0.27%)
var_size_seq_scan q19 1516.90 1459.82 57.08 (3.91%)
var_size_seq_scan q20 2491.02 2352.12 138.90 (5.91%)
var_size_seq_scan q21 2313.83 2311.06 2.76 (0.12%)
var_size_seq_scan q22 130.48 128.13 2.35 (1.83%)

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codecov bot commented Feb 12, 2025 •
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Codecov Report

Attention: Patch coverage is 92.79279% with 8 lines in your changes missing coverage. Please review.

Project coverage is 86.56%. Comparing base (bf8c8b8) to head (4a9b75b).
Report is 335 commits behind head on master.

Files with missing lines Patch % Lines
src/storage/index/hnsw_graph.cpp 87.71% 7 Missing ⚠️
src/include/storage/index/hnsw_graph.h 97.67% 1 Missing ⚠️
Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #4888   +/-   ##
=======================================
  Coverage   86.55%   86.56%           
=======================================
  Files        1409     1409           
  Lines       60916    61012   +96     
  Branches     7493     7501    +8     
=======================================
+ Hits        52726    52813   +87     
- Misses       8021     8030    +9     
  Partials      169      169

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@ray6080 ray6080 marked this pull request as ready for review February 13, 2025 05:35
@ray6080 ray6080 requested review from andyfengHKU and removed request for benjaminwinger February 13, 2025 05:36
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github-actions bot commented Feb 15, 2025

Benchmark Result

Master commit hash: 0e61d7391827730cb6df21ce4abd40b02e227171
Branch commit hash: 63a7b73c83b984a5398acf94e7dfa5c625c36063

Query Group Query Name Mean Time - Commit (ms) Mean Time - Master (ms) Diff
aggregation q24 733.37 725.06 8.31 (1.15%)
aggregation q28 6355.42 6365.47 -10.05 (-0.16%)
filter q14 134.75 127.96 6.79 (5.31%)
filter q15 135.53 125.90 9.63 (7.65%)
filter q16 309.36 302.95 6.42 (2.12%)
filter q17 452.65 447.74 4.91 (1.10%)
filter q18 1942.70 1927.66 15.03 (0.78%)
filter zonemap-node 97.33 88.86 8.47 (9.53%)
filter zonemap-node-lhs-cast 97.77 89.13 8.64 (9.70%)
filter zonemap-node-null 97.03 90.69 6.33 (6.98%)
filter zonemap-rel 5493.43 5604.53 -111.11 (-1.98%)
fixed_size_expr_evaluator q07 579.48 571.83 7.65 (1.34%)
fixed_size_expr_evaluator q08 811.95 802.87 9.08 (1.13%)
fixed_size_expr_evaluator q09 812.12 799.89 12.23 (1.53%)
fixed_size_expr_evaluator q10 244.81 236.77 8.04 (3.39%)
fixed_size_expr_evaluator q11 237.35 231.22 6.13 (2.65%)
fixed_size_expr_evaluator q12 234.93 227.30 7.63 (3.36%)
fixed_size_expr_evaluator q13 1464.09 1449.45 14.64 (1.01%)
fixed_size_seq_scan q23 121.44 110.52 10.92 (9.88%)
join q29 702.08 713.01 -10.93 (-1.53%)
join q30 9768.09 10109.53 -341.44 (-3.38%)
join q31 4.25 7.46 -3.21 (-43.04%)
join SelectiveTwoHopJoin 55.39 58.13 -2.74 (-4.71%)
ldbc_snb_ic q35 2716.53 2680.25 36.27 (1.35%)
ldbc_snb_ic q36 487.89 477.54 10.35 (2.17%)
ldbc_snb_is q32 6.04 3.90 2.14 (54.85%)
ldbc_snb_is q33 13.91 12.09 1.82 (15.09%)
ldbc_snb_is q34 1.18 1.14 0.03 (3.00%)
multi-rel multi-rel-large-scan 1323.69 1372.62 -48.93 (-3.56%)
multi-rel multi-rel-lookup 20.61 10.87 9.75 (89.66%)
multi-rel multi-rel-small-scan 96.93 96.04 0.89 (0.92%)
order_by q25 137.79 136.56 1.23 (0.90%)
order_by q26 459.64 451.63 8.00 (1.77%)
order_by q27 1397.03 1413.47 -16.43 (-1.16%)
recursive_join recursive-join-bidirection 298.15 293.37 4.79 (1.63%)
recursive_join recursive-join-dense 7361.24 7358.13 3.11 (0.04%)
recursive_join recursive-join-path 23939.47 24082.51 -143.04 (-0.59%)
recursive_join recursive-join-sparse 1061.97 1056.68 5.30 (0.50%)
recursive_join recursive-join-trail 7356.57 7316.10 40.48 (0.55%)
scan_after_filter q01 179.18 173.03 6.15 (3.56%)
scan_after_filter q02 165.19 159.90 5.29 (3.31%)
shortest_path_ldbc100 q37 96.22 88.39 7.83 (8.86%)
shortest_path_ldbc100 q38 343.96 352.52 -8.56 (-2.43%)
shortest_path_ldbc100 q39 63.82 65.89 -2.07 (-3.14%)
shortest_path_ldbc100 q40 444.33 443.60 0.73 (0.17%)
var_size_expr_evaluator q03 2066.50 2102.24 -35.74 (-1.70%)
var_size_expr_evaluator q04 2269.38 2202.42 66.95 (3.04%)
var_size_expr_evaluator q05 2610.38 2673.80 -63.42 (-2.37%)
var_size_expr_evaluator q06 1331.07 1339.30 -8.23 (-0.61%)
var_size_seq_scan q19 1439.93 1453.15 -13.22 (-0.91%)
var_size_seq_scan q20 2470.32 2538.69 -68.37 (-2.69%)
var_size_seq_scan q21 2287.75 2321.33 -33.58 (-1.45%)
var_size_seq_scan q22 130.33 127.85 2.48 (1.94%)

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github-actions bot commented Feb 20, 2025

Benchmark Result

Master commit hash: bf8c8b88cbdeb1a10e58e53a07a156ea72932d40
Branch commit hash: c7114b7923917ee409cac02a4703e4b7c35adffc

Query Group Query Name Mean Time - Commit (ms) Mean Time - Master (ms) Diff
aggregation q24 725.46 722.70 2.76 (0.38%)
aggregation q28 6356.04 6396.89 -40.85 (-0.64%)
filter q14 126.39 130.34 -3.95 (-3.03%)
filter q15 125.77 125.08 0.69 (0.55%)
filter q16 305.37 306.73 -1.35 (-0.44%)
filter q17 451.28 448.03 3.25 (0.73%)
filter q18 1926.66 1934.88 -8.21 (-0.42%)
filter zonemap-node 89.04 94.15 -5.11 (-5.43%)
filter zonemap-node-lhs-cast 90.76 90.39 0.37 (0.41%)
filter zonemap-node-null 90.68 89.94 0.74 (0.82%)
filter zonemap-rel 5626.43 5587.69 38.75 (0.69%)
fixed_size_expr_evaluator q07 572.74 570.73 2.01 (0.35%)
fixed_size_expr_evaluator q08 800.53 801.53 -1.00 (-0.13%)
fixed_size_expr_evaluator q09 802.62 800.49 2.13 (0.27%)
fixed_size_expr_evaluator q10 237.03 236.62 0.41 (0.17%)
fixed_size_expr_evaluator q11 229.98 230.25 -0.27 (-0.12%)
fixed_size_expr_evaluator q12 228.40 226.52 1.88 (0.83%)
fixed_size_expr_evaluator q13 1454.77 1458.46 -3.70 (-0.25%)
fixed_size_seq_scan q23 113.42 108.92 4.50 (4.13%)
join q29 775.90 768.96 6.94 (0.90%)
join q30 10073.93 11630.24 -1556.32 (-13.38%)
join q31 5.72 8.94 -3.22 (-36.00%)
join SelectiveTwoHopJoin 53.81 57.24 -3.42 (-5.98%)
ldbc_snb_ic q35 2750.09 2621.22 128.87 (4.92%)
ldbc_snb_ic q36 489.33 484.63 4.70 (0.97%)
ldbc_snb_is q32 4.63 5.68 -1.06 (-18.59%)
ldbc_snb_is q33 13.12 15.43 -2.31 (-14.95%)
ldbc_snb_is q34 1.35 1.20 0.15 (12.87%)
multi-rel multi-rel-large-scan 1324.79 1499.32 -174.53 (-11.64%)
multi-rel multi-rel-lookup 20.55 44.94 -24.39 (-54.27%)
multi-rel multi-rel-small-scan 92.27 88.16 4.11 (4.67%)
order_by q25 128.81 134.53 -5.72 (-4.25%)
order_by q26 454.02 461.64 -7.62 (-1.65%)
order_by q27 1413.93 1407.49 6.44 (0.46%)
recursive_join recursive-join-bidirection 308.36 305.79 2.58 (0.84%)
recursive_join recursive-join-dense 6416.55 7092.58 -676.03 (-9.53%)
recursive_join recursive-join-path 23740.44 23969.41 -228.98 (-0.96%)
recursive_join recursive-join-sparse 1053.17 1047.42 5.75 (0.55%)
recursive_join recursive-join-trail 6703.53 7036.01 -332.49 (-4.73%)
scan_after_filter q01 173.91 172.68 1.23 (0.71%)
scan_after_filter q02 158.59 157.25 1.34 (0.85%)
shortest_path_ldbc100 q37 86.57 82.22 4.35 (5.29%)
shortest_path_ldbc100 q38 341.39 325.19 16.20 (4.98%)
shortest_path_ldbc100 q39 62.60 60.50 2.10 (3.47%)
shortest_path_ldbc100 q40 410.17 299.15 111.02 (37.11%)
var_size_expr_evaluator q03 2110.43 2073.31 37.12 (1.79%)
var_size_expr_evaluator q04 2210.34 2212.19 -1.85 (-0.08%)
var_size_expr_evaluator q05 2637.00 2644.54 -7.54 (-0.29%)
var_size_expr_evaluator q06 1332.31 1329.93 2.38 (0.18%)
var_size_seq_scan q19 1470.53 1470.74 -0.21 (-0.01%)
var_size_seq_scan q20 2569.08 2772.24 -203.16 (-7.33%)
var_size_seq_scan q21 2315.06 2392.45 -77.39 (-3.23%)
var_size_seq_scan q22 126.57 125.08 1.48 (1.19%)

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ray6080 commented Jun 9, 2025

Done in #5499.

@ray6080 ray6080 closed this Jun 9, 2025
@ray6080 ray6080 deleted the vector-index branch July 22, 2025 03:44
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