Subject: Re: [PATCH 07/15] commit-graph: new filter ver. that fixes murmur3

From: SZEDER Gábor <[email-masked]>
Date: Sat, 26 Aug 2023 17:06:10 +0200

On Mon, Aug 21, 2023 at 05:44:15PM -0400, Taylor Blau wrote:
> From: Jonathan Tan <[email-masked]>
> 
> The murmur3 implementation in bloom.c has a bug when converting series
> of 4 bytes into network-order integers when char is signed (which is
> controllable by a compiler option, and the default signedness of char is
> platform-specific). When a string contains characters with the high bit
> set, this bug causes results that, although internally consistent within
> Git, does not accord with other implementations of murmur3 (thus,
> the changed path filters wouldn't be readable by other off-the-shelf
> implementatios of murmur3) and even with Git binaries that were compiled
> with different signedness of char. This bug affects both how Git writes
> changed path filters to disk and how Git interprets changed path filters
> on disk.
> 
> Therefore, introduce a new version (2) of changed path filters that
> corrects this problem. The existing version (1) is still supported and
> is still the default, but users should migrate away from it as soon
> as possible.
> 
> Because this bug only manifests with characters that have the high bit
> set, it may be possible that some (or all) commits in a given repo would
> have the same changed path filter both before and after this fix is
> applied. However, in order to determine whether this is the case, the
> changed paths would first have to be computed, at which point it is not
> much more expensive to just compute a new changed path filter.
> 
> So this patch does not include any mechanism to "salvage" changed path
> filters from repositories. There is also no "mixed" mode - for each
> invocation of Git, reading and writing changed path filters are done
> with the same version number; this version number may be explicitly
> stated (typically if the user knows which version they need) or
> automatically determined from the version of the existing changed path
> filters in the repository.
> 
> There is a change in write_commit_graph(). graph_read_bloom_data()
> makes it possible for chunk_bloom_data to be non-NULL but
> bloom_filter_settings to be NULL, which causes a segfault later on. I
> produced such a segfault while developing this patch, but couldn't find
> a way to reproduce it neither after this complete patch (or before),
> but in any case it seemed like a good thing to include that might help
> future patch authors.
> 
> The value in t0095 was obtained from another murmur3 implementation
> using the following Go source code:
> 
>   package main
> 
>   import "fmt"
>   import "github.com/spaolacci/murmur3"
> 
>   func main() {
>           fmt.Printf("%x\n", murmur3.Sum32([]byte("Hello world!")))
>           fmt.Printf("%x\n", murmur3.Sum32([]byte{0x99, 0xaa, 0xbb, 0xcc, 0xdd, 0xee, 0xff}))
>   }
> 
> Signed-off-by: Jonathan Tan <[email-masked]>
> Signed-off-by: Junio C Hamano <[email-masked]>
> Signed-off-by: Taylor Blau <[email-masked]>
> ---
>  Documentation/config/commitgraph.txt |  5 +-
>  bloom.c                              | 69 +++++++++++++++++++-
>  bloom.h                              |  8 ++-
>  commit-graph.c                       | 32 ++++++++--
>  t/helper/test-bloom.c                |  9 ++-
>  t/t0095-bloom.sh                     |  8 +++
>  t/t4216-log-bloom.sh                 | 96 ++++++++++++++++++++++++++++
>  7 files changed, 214 insertions(+), 13 deletions(-)
> 
> diff --git a/Documentation/config/commitgraph.txt b/Documentation/config/commitgraph.txt
> index 2dc9170622..acc74a2f27 100644
> --- a/Documentation/config/commitgraph.txt
> +++ b/Documentation/config/commitgraph.txt
> @@ -15,7 +15,7 @@ commitGraph.readChangedPaths::
>  
>  commitGraph.changedPathsVersion::
>  	Specifies the version of the changed-path Bloom filters that Git will read and
> -	write. May be -1, 0 or 1.
> +	write. May be -1, 0, 1, or 2.
>  +
>  Defaults to -1.
>  +
> @@ -28,4 +28,7 @@ filters when instructed to write.
>  If 1, Git will only read version 1 Bloom filters, and will write version 1
>  Bloom filters.
>  +
> +If 2, Git will only read version 2 Bloom filters, and will write version 2
> +Bloom filters.
> ++
>  See linkgit:git-commit-graph[1] for more information.
> diff --git a/bloom.c b/bloom.c
> index 3e78cfe79d..ebef5cfd2f 100644
> --- a/bloom.c
> +++ b/bloom.c
> @@ -66,7 +66,64 @@ int load_bloom_filter_from_graph(struct commit_graph *g,
>   * Not considered to be cryptographically secure.
>   * Implemented as described in https://en.wikipedia.org/wiki/MurmurHash#Algorithm
>   */
> -uint32_t murmur3_seeded(uint32_t seed, const char *data, size_t len)
> +uint32_t murmur3_seeded_v2(uint32_t seed, const char *data, size_t len)

Nit: MurmurHash3 implementations in C/C++ (apart from the sample
implementation on Wikipedia), and other hash functions taking data
pointer and buffer size parameters in general, have a 'const void
*data' parameter, not 'const char*'.

> +{
> +	const uint32_t c1 = 0xcc9e2d51;
> +	const uint32_t c2 = 0x1b873593;
> +	const uint32_t r1 = 15;
> +	const uint32_t r2 = 13;
> +	const uint32_t m = 5;
> +	const uint32_t n = 0xe6546b64;
> +	int i;
> +	uint32_t k1 = 0;
> +	const char *tail;
> +
> +	int len4 = len / sizeof(uint32_t);
> +
> +	uint32_t k;
> +	for (i = 0; i < len4; i++) {
> +		uint32_t byte1 = (uint32_t)(unsigned char)data[4*i];
> +		uint32_t byte2 = ((uint32_t)(unsigned char)data[4*i + 1]) << 8;
> +		uint32_t byte3 = ((uint32_t)(unsigned char)data[4*i + 2]) << 16;
> +		uint32_t byte4 = ((uint32_t)(unsigned char)data[4*i + 3]) << 24;
> +		k = byte1 | byte2 | byte3 | byte4;
> +		k *= c1;
> +		k = rotate_left(k, r1);
> +		k *= c2;
> +
> +		seed ^= k;
> +		seed = rotate_left(seed, r2) * m + n;
> +	}
> +
> +	tail = (data + len4 * sizeof(uint32_t));
> +
> +	switch (len & (sizeof(uint32_t) - 1)) {
> +	case 3:
> +		k1 ^= ((uint32_t)(unsigned char)tail[2]) << 16;
> +		/*-fallthrough*/
> +	case 2:
> +		k1 ^= ((uint32_t)(unsigned char)tail[1]) << 8;
> +		/*-fallthrough*/
> +	case 1:
> +		k1 ^= ((uint32_t)(unsigned char)tail[0]) << 0;
> +		k1 *= c1;
> +		k1 = rotate_left(k1, r1);
> +		k1 *= c2;
> +		seed ^= k1;
> +		break;
> +	}
> +
> +	seed ^= (uint32_t)len;
> +	seed ^= (seed >> 16);
> +	seed *= 0x85ebca6b;
> +	seed ^= (seed >> 13);
> +	seed *= 0xc2b2ae35;
> +	seed ^= (seed >> 16);
> +
> +	return seed;
> +}
> +
> +static uint32_t murmur3_seeded_v1(uint32_t seed, const char *data, size_t len)
>  {
>  	const uint32_t c1 = 0xcc9e2d51;
>  	const uint32_t c2 = 0x1b873593;
> @@ -131,8 +188,14 @@ void fill_bloom_key(const char *data,
>  	int i;
>  	const uint32_t seed0 = 0x293ae76f;
>  	const uint32_t seed1 = 0x7e646e2c;
> -	const uint32_t hash0 = murmur3_seeded(seed0, data, len);
> -	const uint32_t hash1 = murmur3_seeded(seed1, data, len);
> +	uint32_t hash0, hash1;
> +	if (settings->hash_version == 2) {
> +		hash0 = murmur3_seeded_v2(seed0, data, len);
> +		hash1 = murmur3_seeded_v2(seed1, data, len);
> +	} else {
> +		hash0 = murmur3_seeded_v1(seed0, data, len);
> +		hash1 = murmur3_seeded_v1(seed1, data, len);
> +	}
>  
>  	key->hashes = (uint32_t *)xcalloc(settings->num_hashes, sizeof(uint32_t));
>  	for (i = 0; i < settings->num_hashes; i++)
> diff --git a/bloom.h b/bloom.h
> index 1e4f612d2c..138d57a86b 100644
> --- a/bloom.h
> +++ b/bloom.h
> @@ -8,9 +8,11 @@ struct commit_graph;
>  struct bloom_filter_settings {
>  	/*
>  	 * The version of the hashing technique being used.
> -	 * We currently only support version = 1 which is
> +	 * The newest version is 2, which is
>  	 * the seeded murmur3 hashing technique implemented
> -	 * in bloom.c.
> +	 * in bloom.c. Bloom filters of version 1 were created
> +	 * with prior versions of Git, which had a bug in the
> +	 * implementation of the hash function.
>  	 */
>  	uint32_t hash_version;
>  
> @@ -80,7 +82,7 @@ int load_bloom_filter_from_graph(struct commit_graph *g,
>   * Not considered to be cryptographically secure.
>   * Implemented as described in https://en.wikipedia.org/wiki/MurmurHash#Algorithm
>   */
> -uint32_t murmur3_seeded(uint32_t seed, const char *data, size_t len);
> +uint32_t murmur3_seeded_v2(uint32_t seed, const char *data, size_t len);
>  
>  void fill_bloom_key(const char *data,
>  		    size_t len,
> diff --git a/commit-graph.c b/commit-graph.c
> index da99f15fdf..f7322c4fff 100644
> --- a/commit-graph.c
> +++ b/commit-graph.c
> @@ -304,17 +304,26 @@ static int graph_read_oid_lookup(const unsigned char *chunk_start,
>  	return 0;
>  }
>  
> +struct graph_read_bloom_data_context {
> +	struct commit_graph *g;
> +	int *commit_graph_changed_paths_version;
> +};
> +
>  static int graph_read_bloom_data(const unsigned char *chunk_start,
>  				  size_t chunk_size, void *data)
>  {
> -	struct commit_graph *g = data;
> +	struct graph_read_bloom_data_context *c = data;
> +	struct commit_graph *g = c->g;
>  	uint32_t hash_version;
> -	g->chunk_bloom_data = chunk_start;
>  	hash_version = get_be32(chunk_start);
>  
> -	if (hash_version != 1)
> +	if (*c->commit_graph_changed_paths_version == -1) {
> +		*c->commit_graph_changed_paths_version = hash_version;
> +	} else if (hash_version != *c->commit_graph_changed_paths_version) {
>  		return 0;
> +	}
>  
> +	g->chunk_bloom_data = chunk_start;
>  	g->bloom_filter_settings = xmalloc(sizeof(struct bloom_filter_settings));
>  	g->bloom_filter_settings->hash_version = hash_version;
>  	g->bloom_filter_settings->num_hashes = get_be32(chunk_start + 4);
> @@ -402,10 +411,14 @@ struct commit_graph *parse_commit_graph(struct repo_settings *s,
>  	}
>  
>  	if (s->commit_graph_changed_paths_version) {
> +		struct graph_read_bloom_data_context context = {
> +			.g = graph,
> +			.commit_graph_changed_paths_version = &s->commit_graph_changed_paths_version
> +		};
>  		pair_chunk(cf, GRAPH_CHUNKID_BLOOMINDEXES,
>  			   &graph->chunk_bloom_indexes);
>  		read_chunk(cf, GRAPH_CHUNKID_BLOOMDATA,
> -			   graph_read_bloom_data, graph);
> +			   graph_read_bloom_data, &context);
>  	}
>  
>  	if (graph->chunk_bloom_indexes && graph->chunk_bloom_data) {
> @@ -2376,6 +2389,13 @@ int write_commit_graph(struct object_directory *odb,
>  	}
>  	if (!commit_graph_compatible(r))
>  		return 0;
> +	if (r->settings.commit_graph_changed_paths_version < -1
> +	    || r->settings.commit_graph_changed_paths_version > 2) {
> +		warning(_("attempting to write a commit-graph, but "
> +			  "'commitgraph.changedPathsVersion' (%d) is not supported"),
> +			r->settings.commit_graph_changed_paths_version);
> +		return 0;
> +	}
>  
>  	CALLOC_ARRAY(ctx, 1);
>  	ctx->r = r;
> @@ -2388,6 +2408,8 @@ int write_commit_graph(struct object_directory *odb,
>  	ctx->write_generation_data = (get_configured_generation_version(r) == 2);
>  	ctx->num_generation_data_overflows = 0;
>  
> +	bloom_settings.hash_version = r->settings.commit_graph_changed_paths_version == 2
> +		? 2 : 1;
>  	bloom_settings.bits_per_entry = git_env_ulong("GIT_TEST_BLOOM_SETTINGS_BITS_PER_ENTRY",
>  						      bloom_settings.bits_per_entry);
>  	bloom_settings.num_hashes = git_env_ulong("GIT_TEST_BLOOM_SETTINGS_NUM_HASHES",
> @@ -2417,7 +2439,7 @@ int write_commit_graph(struct object_directory *odb,
>  		g = ctx->r->objects->commit_graph;
>  
>  		/* We have changed-paths already. Keep them in the next graph */
> -		if (g && g->chunk_bloom_data) {
> +		if (g && g->bloom_filter_settings) {
>  			ctx->changed_paths = 1;
>  			ctx->bloom_settings = g->bloom_filter_settings;
>  		}
> diff --git a/t/helper/test-bloom.c b/t/helper/test-bloom.c
> index aabe31d724..3cbc0a5b50 100644
> --- a/t/helper/test-bloom.c
> +++ b/t/helper/test-bloom.c
> @@ -50,6 +50,7 @@ static void get_bloom_filter_for_commit(const struct object_id *commit_oid)
>  
>  static const char *bloom_usage = "\n"
>  "  test-tool bloom get_murmur3 <string>\n"
> +"  test-tool bloom get_murmur3_seven_highbit\n"
>  "  test-tool bloom generate_filter <string> [<string>...]\n"
>  "  test-tool bloom get_filter_for_commit <commit-hex>\n";
>  
> @@ -64,7 +65,13 @@ int cmd__bloom(int argc, const char **argv)
>  		uint32_t hashed;
>  		if (argc < 3)
>  			usage(bloom_usage);
> -		hashed = murmur3_seeded(0, argv[2], strlen(argv[2]));
> +		hashed = murmur3_seeded_v2(0, argv[2], strlen(argv[2]));
> +		printf("Murmur3 Hash with seed=0:0x%08x\n", hashed);
> +	}
> +
> +	if (!strcmp(argv[1], "get_murmur3_seven_highbit")) {
> +		uint32_t hashed;
> +		hashed = murmur3_seeded_v2(0, "\x99\xaa\xbb\xcc\xdd\xee\xff", 7);
>  		printf("Murmur3 Hash with seed=0:0x%08x\n", hashed);
>  	}
>  
> diff --git a/t/t0095-bloom.sh b/t/t0095-bloom.sh
> index b567383eb8..c8d84ab606 100755
> --- a/t/t0095-bloom.sh
> +++ b/t/t0095-bloom.sh
> @@ -29,6 +29,14 @@ test_expect_success 'compute unseeded murmur3 hash for test string 2' '
>  	test_cmp expect actual
>  '
>  
> +test_expect_success 'compute unseeded murmur3 hash for test string 3' '
> +	cat >expect <<-\EOF &&
> +	Murmur3 Hash with seed=0:0xa183ccfd
> +	EOF
> +	test-tool bloom get_murmur3_seven_highbit >actual &&
> +	test_cmp expect actual
> +'
> +
>  test_expect_success 'compute bloom key for empty string' '
>  	cat >expect <<-\EOF &&
>  	Hashes:0x5615800c|0x5b966560|0x61174ab4|0x66983008|0x6c19155c|0x7199fab0|0x771ae004|
> diff --git a/t/t4216-log-bloom.sh b/t/t4216-log-bloom.sh
> index 2d4a3fefee..775e59d864 100755
> --- a/t/t4216-log-bloom.sh
> +++ b/t/t4216-log-bloom.sh
> @@ -447,4 +447,100 @@ test_expect_success 'version 1 changed-path used when version 1 requested' '
>  	)
>  '
>  
> +test_expect_success 'version 1 changed-path not used when version 2 requested' '
> +	(
> +		cd highbit1 &&
> +		git config --add commitgraph.changedPathsVersion 2 &&
> +		test_bloom_filters_not_used "-- $CENT"
> +	)
> +'
> +
> +test_expect_success 'version 1 changed-path used when autodetect requested' '
> +	(
> +		cd highbit1 &&
> +		git config --add commitgraph.changedPathsVersion -1 &&
> +		test_bloom_filters_used "-- $CENT"
> +	)
> +'
> +
> +test_expect_success 'when writing another commit graph, preserve existing version 1 of changed-path' '
> +	test_commit -C highbit1 c1double "$CENT$CENT" &&
> +	git -C highbit1 commit-graph write --reachable --changed-paths &&

Nit: Since there is a subshell cd-ing into the 'highbit1' directory
anyway, it would look clearer to put these two commands into that
subshell as well.
This applies to some of the later test cases as well.

> +	(
> +		cd highbit1 &&
> +		git config --add commitgraph.changedPathsVersion -1 &&
> +		echo "options: bloom(1,10,7) read_generation_data" >expect &&
> +		test-tool read-graph >full &&
> +		grep options full >actual &&
> +		test_cmp expect actual
> +	)
> +'
> +
> +test_expect_success 'set up repo with high bit path, version 2 changed-path' '
> +	git init highbit2 &&
> +	git -C highbit2 config --add commitgraph.changedPathsVersion 2 &&
> +	test_commit -C highbit2 c2 "$CENT" &&
> +	git -C highbit2 commit-graph write --reachable --changed-paths
> +'
> +
> +test_expect_success 'check value of version 2 changed-path' '
> +	(
> +		cd highbit2 &&
> +		echo "c01f" >expect &&
> +		get_first_changed_path_filter >actual &&
> +		test_cmp expect actual
> +	)
> +'
> +
> +test_expect_success 'version 2 changed-path used when version 2 requested' '
> +	(
> +		cd highbit2 &&
> +		test_bloom_filters_used "-- $CENT"

This test_bloom_filter_used helper runs two pathspec-limited 'git log'
invocations, one with disabled and the other with enabled
commit-graph, and thus with disabled and enabled modified path Bloom
filters, and compares their output.

One of the flaws of the current modified path Bloom filters
implementation is that it doesn't check Bloom filters for root
commits.

In several of the above test cases test_bloom_filters_used is invoked
in a repository with only a root commit, so they don't check that
the output is the same with and without Bloom filters.

> +	)
> +'
> +
> +test_expect_success 'version 2 changed-path not used when version 1 requested' '
> +	(
> +		cd highbit2 &&
> +		git config --add commitgraph.changedPathsVersion 1 &&
> +		test_bloom_filters_not_used "-- $CENT"
> +	)
> +'
> +
> +test_expect_success 'version 2 changed-path used when autodetect requested' '
> +	(
> +		cd highbit2 &&
> +		git config --add commitgraph.changedPathsVersion -1 &&
> +		test_bloom_filters_used "-- $CENT"
> +	)
> +'
> +
> +test_expect_success 'when writing another commit graph, preserve existing version 2 of changed-path' '
> +	test_commit -C highbit2 c2double "$CENT$CENT" &&
> +	git -C highbit2 commit-graph write --reachable --changed-paths &&
> +	(
> +		cd highbit2 &&
> +		git config --add commitgraph.changedPathsVersion -1 &&
> +		echo "options: bloom(2,10,7) read_generation_data" >expect &&
> +		test-tool read-graph >full &&
> +		grep options full >actual &&
> +		test_cmp expect actual
> +	)
> +'
> +
> +test_expect_success 'when writing commit graph, do not reuse changed-path of another version' '
> +	git init doublewrite &&
> +	test_commit -C doublewrite c "$CENT" &&
> +	git -C doublewrite config --add commitgraph.changedPathsVersion 1 &&
> +	git -C doublewrite commit-graph write --reachable --changed-paths &&
> +	git -C doublewrite config --add commitgraph.changedPathsVersion 2 &&
> +	git -C doublewrite commit-graph write --reachable --changed-paths &&
> +	(
> +		cd doublewrite &&
> +		echo "c01f" >expect &&
> +		get_first_changed_path_filter >actual &&
> +		test_cmp expect actual
> +	)
> +'

The string "split" occurs twice in this patch series, but only in
patch hunk contexts, and it doesn't occur at all in the previous long
thread about the original patch series.

Unfortunately, split commit-graphs weren't really considered in the
design of the modified path Bloom filters feature, and layers with
different Bloom filter settings weren't considered at all.  I've
reported it back then, but the fixes so far were incomplete, and e.g.
the test cases shown in

  https://public-inbox.org/git/[email-masked]/

still fail.

Since the interaction of different versions and split commit-graphs
was neither mentioned in any of the commit messages nor discussed
during the previous rounds, and there isn't any test case excercising
it, and since the Bloom filter version information is stored in the
same 'g->bloom_filter_settings' structure as the number of hashes, I'm
afraid (though haven't actually checked) that handling commit-graph
layers with different Bloom filter versions is prone to the same
issues as well.