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Re: [PATCH 4/9] commit-graph: document bloom filter format

From
Jakub Narebski <jnareb@gmail.com>
Date
Jan 7, 2020, 14:46 UTC
Message-ID
<86h817xr1i.fsf@gmail.com>
In-Reply-To
<3182a11f7c07af834ba71dc7861742458754eb91.1576879520.git.gitgitgadget@gmail.com>
"Garima Singh via GitGitGadget" <gitgitgadget@gmail.com> writes:
Show 10 quoted lines
> From: Garima Singh <garima.singh@microsoft.com>
>
> Update the technical documentation for commit-graph-format with BIDX
> and BDAT chunk information.
>
> RFC Notes:
> 1. [Call for advice] We specifically mention that we are using Bloom
>    filters in this technical document. Should this document also be
>    made open to other data structures in the future, with versioning
>    information?

I'm not sure. In theory we might want to switch to another probabilistic set inclusion query structure, like xor filters or cuckoo hashing.

On one hand side we could use separate chunks (e.g. XIDX, XDAT for xor filters), on the other hand we need only one such structure. On the gripping hand this can be left for the future, if needed.

Sidenote: using Bloom filters is somewhat encoded in the name of chunk
(B from Bloom filter).  I don't have a better poposal for 4-char name
(XIDX / XDAT for cXange?  CHDX / CHDT for CHange?  FIDX / FDAT for
changed Files?... I don't know).
Show 6 quoted lines
>
> 2. [Call for advice] We are also not describing the explicit nature
>    of how we store the bloom filter binary data. Would it be useful
>    to document details about the hash algorithm, the number of hashes
>    and the specific seed values we are using in a separate document,
>    or perhaps in a separate section in this document?

I think it would be best to keep description of the commit graph format concise. The details about Bloom filter implementation would be better put in Documentation/technical/commit-graph.txt in my opinion, together with reasoning behind it (perhaps borrowing from Derrick Stolee blog post).

This could be done as a separate patch.
Show 17 quoted lines
>
> Helped-by: Derrick Stolee <dstolee@microsoft.com>
> Signed-off-by: Garima Singh <garima.singh@microsoft.com>
> ---
>  Documentation/technical/commit-graph-format.txt | 17 +++++++++++++++++
>  1 file changed, 17 insertions(+)
>
> diff --git a/Documentation/technical/commit-graph-format.txt b/Documentation/technical/commit-graph-format.txt
> index a4f17441ae..6497f19f08 100644
> --- a/Documentation/technical/commit-graph-format.txt
> +++ b/Documentation/technical/commit-graph-format.txt
> @@ -17,6 +17,9 @@ metadata, including:
>  - The parents of the commit, stored using positional references within
>    the graph file.
>  
> +- The bloom filter of the commit carrying the paths that were changed between
> +  the commit and it's first parent.
s/bloom/Bloom/ and s/it's/its/

I am not sure about exact wording, but I could at this time think of a better but concise way of stating it.

Show 13 quoted lines
> +
>  These positional references are stored as unsigned 32-bit integers
>  corresponding to the array position within the list of commit OIDs. Due
>  to some special constants we use to track parents, we can store at most
> @@ -93,6 +96,20 @@ CHUNK DATA:
>        positions for the parents until reaching a value with the most-significant
>        bit on. The other bits correspond to the position of the last parent.
>  
> +  Bloom Filter Index (ID: {'B', 'I', 'D', 'X'}) [Optional]
> +      For each commit we store the offset of its bloom filter in the BDAT chunk
> +      as follows:
> +      BIDX[i] = number of 8-byte words in all the bloom filters from commit 0 to
> +		commit i (inclusive)

I think it would be better for consistency and ease of reading to follow the example of OID Fanout (OIDF) chunk description:

 +  Bloom Filter Index (ID: {'B', 'I', 'D', 'X'}) (N * 4 bytes) [Optional]
 +      The ith entry, BIDX[i], stores the number of 8-byte word blocks
 +      in all Bloom filters from commit 0 up to commit i (inclusive)
 +      in lexicographical order.
Maybe even add the following to make implementing it easier:
 +      Data for Bloom filter for i-th commit spans from BIDX[i-1] to
 +      BIDX[i] (plus header length), where we take BIDX[-1] to be 0.

Is it possible for (BIDX[i] - BIDX[i-1]) to be zero (no Bloom filter), for example for commits with more than 512 changes? Or is this case handled by 1 8-byte word Bloom filter of all bits sets to '1', i.e. 0xffffffffffffffff?

How the case of too many changes is distingushed from the case of no changes (`git commit --allow-empty`, or `git merge --ours`)? Is the case of no changes uninteresting, i.e. Bloom filter consisting of zero, that is with all bits set to '0'?

> +
> +  Bloom Filter Data (ID: {'B', 'D', 'A', 'T'}) [Optional]
> +      * It starts with three 32 bit integers for the

I would say "It starts with the header consisting of three unsigned 32-bit integers:" (but current version is not bad).

I wonder if this metadata should perhaps be put in a separate chunk, BMET... (Bloom filter METadata).

> +	    - version of the hash algorithm being used

This number not only encodes that the base hash algorithm being used is 32-bit Murmur3 hash, but that 'k' hashes used in the computation are created out of Murmur3 hash using double hashing technique, and specifies two specific seed values for this double hashing technique.

[Maybe we should store those two seed values here too?]

It might be important to say that the currently supported version is '1', and if Git encounters unknown hashing algorithm version it should not use Bloom filter data.

Unless we store encoded _name_ of the hash algorithm, e.g. bytes 'm','u','r','3' for MurmurHash3_32... though it is about more than a base hash.

Do we need whole 4 bytes for hash version, or is it for ease of use and alignment?

> +	    - the number of hashes used in the computation

All right. Perhaps we should test in the future patches that the value different from the default of 7 would also work.

Also 8-bits / 1 byte for number of hashes (hash functions) should be enough: as I have written in prevous reply there is no need for k > 32.

> +	    - the number of bits per entry

This is important for construction of Bloom filter, but I think it is not necessary to use it -- so it may not be necessary to store it.

Would also fit in a single byte: we don't need exceedingly low false positive probability.

We could use it to estimate the false positive probability, and...
> +	  * The rest of the chunk is the concatenation of all the computed bloom 
> +	  filters for the commits in lexicographic order.
  +	 * The rest of the chunk is the concatenation of all the computed Bloom 
  +	   filters for the commits in lexicographic order.

It would be, I think, a good idea to make it explicit that BDAT is present iff BIDX is present (iff == if and only if), i.e. that either both or neither of those chunks should be present.

> +
>    Base Graphs List (ID: {'B', 'A', 'S', 'E'}) [Optional]
>        This list of H-byte hashes describe a set of B commit-graph files that
>        form a commit-graph chain. The graph position for the ith commit in this
Best,
-- 
Jakub Narębski
Previous: Garima Singh via GitGitGadgetNext: Garima Singh via GitGitGadget
Message 7 of 159 in “[RFC] Changed Paths Bloom Filters”
  1. 0/9 [RFC] Changed Paths Bloom FiltersGarima Singh via GitGitGadget, Dec 20, 2019
  2. 1/9 commit-graph: add --changed-paths option to writeGarima Singh via GitGitGadget, Dec 20, 2019
  3. Jakub NarebskiJan 1, 2020
  4. 3/9 commit-graph: use MAX_NUM_CHUNKSGarima Singh via GitGitGadget, Dec 20, 2019
  5. Jakub NarebskiJan 7, 2020
  6. 4/9 commit-graph: document bloom filter formatGarima Singh via GitGitGadget, Dec 20, 2019
  7. Jakub NarebskiJan 7, 2020
  8. 8/9 revision.c: use bloom filters to speed up path based revision walksGarima Singh via GitGitGadget, Dec 20, 2019
  9. Jakub NarebskiJan 11, 2020
  10. Garima SinghJan 15, 2020
  11. 7/9 commit-graph: reuse existing bloom filters during write.Garima Singh via GitGitGadget, Dec 20, 2019
  12. Jakub NarebskiJan 9, 2020
  13. 9/9 commit-graph: add GIT_TEST_COMMIT_GRAPH_BLOOM_FILTERS test flagGarima Singh via GitGitGadget, Dec 20, 2019
  14. Jakub NarebskiJan 11, 2020
  15. Garima SinghJan 15, 2020
  16. 5/9 commit-graph: write changed path bloom filters to commit-graph file.Garima Singh via GitGitGadget, Dec 20, 2019
  17. Jakub NarebskiJan 7, 2020
  18. Garima SinghJan 14, 2020
  19. 6/9 commit-graph: test commit-graph write --changed-pathsGarima Singh via GitGitGadget, Dec 20, 2019
  20. Jakub NarebskiJan 8, 2020
  21. 2/9 commit-graph: write changed paths bloom filtersGarima Singh via GitGitGadget, Dec 20, 2019
  22. Philip OakleyDec 21, 2019
  23. Jakub NarebskiJan 6, 2020
  24. Garima SinghJan 13, 2020
  25. Junio C HamanoDec 20, 2019
  26. Christian CouderDec 22, 2019
  27. Jeff KingDec 22, 2019
  28. Jakub NarebskiJan 1, 2020
  29. Jeff KingDec 22, 2019
  30. 1/3 commit-graph: examine changed-path objects in pack orderJeff King, Dec 22, 2019
  31. Derrick StoleeDec 27, 2019
  32. Jeff KingDec 29, 2019
  33. Jeff KingDec 29, 2019
  34. Derrick StoleeDec 30, 2019
  35. Derrick StoleeDec 30, 2019
  36. 2/3 commit-graph: free large diffs, tooJeff King, Dec 22, 2019
  37. Derrick StoleeDec 27, 2019
  38. 3/3 commit-graph: stop using full rev_info for diffsJeff King, Dec 22, 2019
  39. Derrick StoleeDec 27, 2019
  40. Derrick StoleeDec 26, 2019
  41. Jeff KingDec 29, 2019
  42. Derrick StoleeDec 27, 2019
  43. Jeff KingDec 29, 2019
  44. Derrick StoleeDec 30, 2019
  45. Junio C HamanoDec 30, 2019
  46. Jakub NarebskiDec 31, 2019
  47. Garima SinghJan 13, 2020
  48. Jakub NarebskiJan 20, 2020
  49. Garima SinghJan 21, 2020
  50. Jakub NarebskiFeb 2, 2020
  51. Emily ShafferJan 21, 2020
  52. Garima SinghJan 27, 2020
  53. Jakub NarebskiFeb 1, 2020
  54. 00/11 Changed Paths Bloom FiltersGarima Singh via GitGitGadget, Feb 5, 2020
  55. 01/11 commit-graph: use MAX_NUM_CHUNKSGarima Singh via GitGitGadget, Feb 5, 2020
  56. Jakub NarebskiFeb 9, 2020
  57. 04/11 commit-graph: compute Bloom filters for changed pathsGarima Singh via GitGitGadget, Feb 5, 2020
  58. Jakub NarebskiFeb 17, 2020
  59. Garima SinghFeb 22, 2020
  60. Jakub NarebskiFeb 23, 2020
  61. 05/11 commit-graph: examine changed-path objects in pack orderJeff King via GitGitGadget, Feb 5, 2020
  62. Jakub NarebskiFeb 18, 2020
  63. Garima SinghFeb 24, 2020
  64. 06/11 commit-graph: examine commits by generation numberDerrick Stolee via GitGitGadget, Feb 5, 2020
  65. Jakub NarebskiFeb 19, 2020
  66. Garima SinghFeb 24, 2020
  67. 02/11 bloom: core Bloom filter implementation for changed pathsGarima Singh via GitGitGadget, Feb 5, 2020
  68. Jakub NarebskiFeb 15, 2020
  69. Jakub NarebskiFeb 16, 2020
  70. Garima SinghFeb 22, 2020
  71. Jakub NarebskiFeb 23, 2020
  72. Garima SinghFeb 24, 2020
  73. Jakub NarebskiFeb 24, 2020
  74. 03/11 diff: halt tree-diff early after max_changesDerrick Stolee via GitGitGadget, Feb 5, 2020
  75. Jakub NarebskiFeb 17, 2020
  76. Garima SinghFeb 22, 2020
  77. 07/11 commit-graph: write Bloom filters to commit graph fileGarima Singh via GitGitGadget, Feb 5, 2020
  78. Jakub NarebskiFeb 19, 2020
  79. Garima SinghFeb 24, 2020
  80. Jakub NarebskiFeb 25, 2020
  81. Garima SinghFeb 25, 2020
  82. 08/11 commit-graph: reuse existing Bloom filters during write.Garima Singh via GitGitGadget, Feb 5, 2020
  83. Jakub NarebskiFeb 20, 2020
  84. Garima SinghFeb 24, 2020
  85. 11/11 commit-graph: add GIT_TEST_COMMIT_GRAPH_CHANGED_PATHS test flagGarima Singh via GitGitGadget, Feb 5, 2020
  86. Jakub NarebskiFeb 22, 2020
  87. 10/11 revision.c: use Bloom filters to speed up path based revision walksGarima Singh via GitGitGadget, Feb 5, 2020
  88. Jakub NarebskiFeb 21, 2020
  89. Jakub NarebskiFeb 21, 2020
  90. 09/11 commit-graph: add --changed-paths option to write subcommandGarima Singh via GitGitGadget, Feb 5, 2020
  91. Jakub NarebskiFeb 20, 2020
  92. Garima SinghFeb 24, 2020
  93. Jakub NarebskiFeb 25, 2020
  94. Bryan TurnerFeb 20, 2020
  95. Garima SinghFeb 22, 2020
  96. SZEDER GáborFeb 7, 2020
  97. Garima SinghFeb 7, 2020
  98. Derrick StoleeFeb 7, 2020
  99. SZEDER GáborFeb 7, 2020
  100. Derrick StoleeFeb 7, 2020
  101. Garima SinghFeb 11, 2020
  102. Jakub NarebskiFeb 8, 2020
  103. Garima SinghFeb 21, 2020
  104. Junio C HamanoMar 29, 2020
  105. 00/16 Changed Paths Bloom FiltersGarima Singh via GitGitGadget, Mar 30, 2020
  106. 01/16 commit-graph: define and use MAX_NUM_CHUNKSGarima Singh via GitGitGadget, Mar 30, 2020
  107. 02/16 bloom.c: add the murmur3 hash implementationGarima Singh via GitGitGadget, Mar 30, 2020
  108. 03/16 bloom.c: introduce core Bloom filter constructsGarima Singh via GitGitGadget, Mar 30, 2020
  109. 06/16 commit-graph: compute Bloom filters for changed pathsGarima Singh via GitGitGadget, Mar 30, 2020
  110. 05/16 diff: halt tree-diff early after max_changesDerrick Stolee via GitGitGadget, Mar 30, 2020
  111. 04/16 bloom.c: core Bloom filter implementation for changed paths.Garima Singh via GitGitGadget, Mar 30, 2020
  112. 07/16 commit-graph: examine changed-path objects in pack orderJeff King via GitGitGadget, Mar 30, 2020
  113. 10/16 commit-graph: write Bloom filters to commit graph fileGarima Singh via GitGitGadget, Mar 30, 2020
  114. 13/16 revision.c: use Bloom filters to speed up path based revision walksGarima Singh via GitGitGadget, Mar 30, 2020
  115. 14/16 revision.c: add trace2 stats around Bloom filter usageGarima Singh via GitGitGadget, Mar 30, 2020
  116. 15/16 t4216: add end to end tests for git log with Bloom filtersGarima Singh via GitGitGadget, Mar 30, 2020
  117. 16/16 commit-graph: add GIT_TEST_COMMIT_GRAPH_CHANGED_PATHS test flagGarima Singh via GitGitGadget, Mar 30, 2020
  118. 12/16 commit-graph: add --changed-paths option to write subcommandGarima Singh via GitGitGadget, Mar 30, 2020
  119. 09/16 diff: skip batch object download when possibleGarima Singh via GitGitGadget, Mar 30, 2020
  120. 08/16 commit-graph: examine commits by generation numberGarima Singh via GitGitGadget, Mar 30, 2020
  121. 11/16 commit-graph: reuse existing Bloom filters during writeGarima Singh via GitGitGadget, Mar 30, 2020
  122. 00/15 Changed Paths Bloom FiltersGarima Singh via GitGitGadget, Apr 6, 2020
  123. 01/15 commit-graph: define and use MAX_NUM_CHUNKSGarima Singh via GitGitGadget, Apr 6, 2020
  124. 03/15 bloom.c: introduce core Bloom filter constructsGarima Singh via GitGitGadget, Apr 6, 2020
  125. 02/15 bloom.c: add the murmur3 hash implementationGarima Singh via GitGitGadget, Apr 6, 2020
  126. 05/15 diff: halt tree-diff early after max_changesDerrick Stolee via GitGitGadget, Apr 6, 2020
  127. SZEDER GáborAug 4, 2020
  128. Derrick StoleeAug 4, 2020
  129. SZEDER GáborAug 4, 2020
  130. Derrick StoleeAug 4, 2020
  131. Derrick StoleeAug 5, 2020
  132. 04/15 bloom.c: core Bloom filter implementation for changed paths.Garima Singh via GitGitGadget, Apr 6, 2020
  133. SZEDER GáborJun 27, 2020
  134. 06/15 commit-graph: compute Bloom filters for changed pathsGarima Singh via GitGitGadget, Apr 6, 2020
  135. 07/15 commit-graph: examine changed-path objects in pack orderJeff King via GitGitGadget, Apr 6, 2020
  136. 10/15 commit-graph: reuse existing Bloom filters during writeGarima Singh via GitGitGadget, Apr 6, 2020
  137. SZEDER GáborJun 19, 2020
  138. Junio C HamanoJun 19, 2020
  139. SZEDER GáborJul 27, 2020
  140. 09/15 commit-graph: write Bloom filters to commit graph fileGarima Singh via GitGitGadget, Apr 6, 2020
  141. SZEDER GáborMay 29, 2020
  142. Derrick StoleeMay 29, 2020
  143. SZEDER GáborMay 31, 2020
  144. commit-graph: fix "Writing out commit graph" progress counterSZEDER Gábor, Jul 9, 2020
  145. Derrick StoleeJul 9, 2020
  146. Derrick StoleeJul 9, 2020
  147. 08/15 commit-graph: examine commits by generation numberGarima Singh via GitGitGadget, Apr 6, 2020
  148. 13/15 revision.c: add trace2 stats around Bloom filter usageGarima Singh via GitGitGadget, Apr 6, 2020
  149. 14/15 t4216: add end to end tests for git log with Bloom filtersGarima Singh via GitGitGadget, Apr 6, 2020
  150. 12/15 revision.c: use Bloom filters to speed up path based revision walksGarima Singh via GitGitGadget, Apr 6, 2020
  151. SZEDER GáborJun 26, 2020
  152. 11/15 commit-graph: add --changed-paths option to write subcommandGarima Singh via GitGitGadget, Apr 6, 2020
  153. SZEDER GáborJun 7, 2020
  154. 15/15 commit-graph: add GIT_TEST_COMMIT_GRAPH_CHANGED_PATHS test flagGarima Singh via GitGitGadget, Apr 6, 2020
  155. Derrick StoleeApr 8, 2020
  156. Junio C HamanoApr 8, 2020
  157. Jakub NarębskiApr 8, 2020
  158. Taylor BlauApr 12, 2020
  159. Garima SinghMar 5, 2020

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