chunked: store cache as binary and use a bloom filter #1870

giuseppe · 2024-03-27T11:47:13Z

The bloom filter itself is useful to reduce page faults with the mmap'ed cache files, as it reduces lookups.

Storing the file as a binary instead reduces the file size considerably, with the quay.io/giuseppe/zstd-chunked:fedora-{38,39,40}{,-updated} images I see:

before:

# find -name '=Y2h1bmtlZC1tYW5pZmVzdC1jYWNoZQ==' -exec stat -c '%s' \{\} \;2547644
2575163
2547644
2476816
2462835
2533346

after:

# find -name '=Y2h1bmtlZC1tYW5pZmVzdC1jYWNoZQ==' -exec stat -c '%s' \{\} \;
1319206
1312332
1275803
1270629
1297565

so it is ~50% size reduction

openshift-ci · 2024-03-27T11:47:19Z

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This pull-request has been approved by: giuseppe

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giuseppe · 2024-03-27T11:50:29Z

@kolyshkin @mtrmac @rhatdan some more improvements to the cache file

mtrmac

Thanks so much for splitting this into smaller commits. That made the review very enjoyable.

pkg/chunked/cache_linux_test.go

mtrmac · 2024-03-27T19:42:34Z

pkg/chunked/cache_linux.go

@@ -154,6 +162,19 @@ fallback:
 	return buf, nil, err
 }

+func getBinaryDigest(stringDigest string) ([]byte, error) {
+	d, err := digest.Parse(stringDigest)


Consider having this function accept a digest.Digest instead, and pushing the digest.Parse to callers; on various code paths that compute the digest, that can avoid a digest.Validate (regex evaluation).

OTOH then the other code paths must call Parse or Validate if dealing with untrusted data.

pkg/chunked/cache_linux.go

mtrmac · 2024-03-27T19:45:23Z

pkg/chunked/cache_linux.go

+	if err != nil {
+		return nil, err
+	}
+	digest := append([]byte(d.Algorithm()+":"), digestBytes...)


(More space could be saved by using a single byte to index into a table of algorithm names, or something like that, at the cost of even more complexity. Possibly not worth it, and definitely not blocking this PR.)

mtrmac · 2024-03-27T21:16:02Z

pkg/chunked/cache_linux.go

+		bloomFilter: bloomFilter,
+		digestLen:   int(digestLen),
+		fnames:      fnames,
+		fnamesLen:   int(fnamesLen),


(Nit: I’d aesthetically prefer if the type declaration, and the two constructors, were all listing the fields in the same order — and if that order were somehow consistent. Here we have (data, len) for file names, but (len, data) for tags, for example.)

pkg/chunked/cache_linux.go

mtrmac · 2024-03-27T21:22:27Z

pkg/chunked/cache_linux_test.go

@@ -164,7 +167,8 @@ func TestWriteCache(t *testing.T) {
 			if digest != r.ChunkDigest {
 				t.Error("wrong digest found")
 			}
-			expectedLocation := generateFileLocation(r.Name, uint64(r.ChunkOffset), uint64(r.ChunkSize))
+			expectedLocation, err := generateFileLocation(0, uint64(r.ChunkOffset), uint64(r.ChunkSize))


Non-blocking: Testing this with at least two distinct paths, to truly exercise the indexing logic, would be nice.

pkg/chunked/cache_linux.go

pkg/chunked/bloom_filter_test.go

giuseppe · 2024-04-08T11:13:28Z

the PR is ready for review

rhatdan · 2024-04-08T14:19:32Z

@mtrmac needs another review.

pkg/chunked/cache_linux.go

pkg/chunked/bloom_filter.go

pkg/chunked/cache_linux.go

mtrmac

I’m sorry about the delayed response.

pkg/chunked/cache_linux.go

giuseppe · 2024-04-09T08:41:03Z

I've fixed your comments, except #1870 (comment). What would you like me to do here?

mtrmac · 2024-04-09T15:14:16Z

pkg/chunked/cache_linux.go

 // are stored.  $DIGEST has length digestLen stored in the cache file file header.
-func generateTag(digest string, offset, len uint64) string {
-	return fmt.Sprintf("%s%.20d@%.20d", digest, offset, len)
+func appendTag(digest []byte, offset, len uint64) ([]byte, error) {


(Absolutely non-blocking: the error value is always nil now.)

pkg/chunked/bloom_filter.go

pkg/chunked/cache_linux.go

mtrmac · 2024-04-09T15:27:29Z

I've fixed your comments, except #1870 (comment). What would you like me to do here?

https://github.com/containers/storage/pull/1870/files#r1557856169 , or perhaps I’m missing something.

rhatdan · 2024-04-16T11:07:16Z

@giuseppe This is waiting on you now?

kolyshkin

Left some very minor comments. Overall it looks like a good case for protobuf, or is that an overkill?

It looks like appendBinaryDigest's first argument is always []byte{}. First, it could be nil, second, if it's not ever used maybe drop it (and rename the function to getBinaryDigest).

kolyshkin · 2024-04-16T18:58:56Z

pkg/chunked/cache_linux.go

 	var vdata bytes.Buffer
+	var tagsBuffer bytes.Buffer


nit:

var vdata, tagsBuffer bytes.Buffer

kolyshkin · 2024-04-16T19:29:08Z

pkg/chunked/cache_linux.go

 		return "", 0, 0
 	}

 	nElements := len(cacheFile.tags) / cacheFile.tagLen

 	i := sort.Search(nElements, func(i int) bool {
-		d := byteSliceAsString(cacheFile.tags[i*cacheFile.tagLen : i*cacheFile.tagLen+cacheFile.digestLen])


nit: with this change, func byteSliceAsString (defined above) can also be removed.

kolyshkin · 2024-04-16T23:20:52Z

pkg/chunked/cache_linux.go

-func generateTag(digest string, offset, len uint64) string {
-	return fmt.Sprintf("%s%.20d@%.20d", digest, offset, len)
+func generateTag(digest []byte, offset, len uint64) []byte {
+	tag := append(digest[:], []byte(fmt.Sprintf("%.20d@%.20d", offset, len))...)


Can you please explain the need for [:] after digest here? I am staring at it and can't see why it's needed.

Also, []byte() conversion is redundant here, in Go you can append a string... to a []byte slice.

this code is replaced by a next commit. I'll squash the two patches so it will just disappear

kolyshkin · 2024-04-16T23:42:35Z

pkg/chunked/cache_linux.go

+	sort.Slice(tags, func(i, j int) bool {
+		return bytes.Compare(tags[i], tags[j]) == -1
+	})


Easier to use slices.SortFunc(tags, bytes.Compare) here

had to revert this change as we are using go 1.20

(BTW we are now agreed on updating to Go 1.21 (around containers/skopeo#2297 ). That would probably be a separate PR.)

kolyshkin · 2024-04-16T23:53:41Z

pkg/chunked/cache_linux.go

 	for _, k := range toc {
 		if k.Digest != "" {
+			digest, err := appendBinaryDigest([]byte{}, k.Digest)


nit: you can use nil instead of []byte{} here -- appending to nil slice is fine.

kolyshkin · 2024-04-17T00:05:33Z

pkg/chunked/bloom_filter_test.go

 	var tagsBuffer bytes.Buffer
 	var vdata bytes.Buffer
+	var fnames bytes.Buffer


nit:

var tagsBuffer, vdata, fnames bytes.Buffer

(unless you don't like that style; to me it's less repetition)

kolyshkin · 2024-04-17T00:08:27Z

pkg/chunked/cache_linux.go

+		nameBytes := []byte(name)
+
+		if err := binary.Write(&fnames, binary.LittleEndian, uint32(len(nameBytes))); err != nil {
+			return 0, err
+		}
+		if _, err := fnames.Write(nameBytes); err != nil {
+			return 0, err
+		}


You can avoid []byte conversion here, using name directly (as in len(name) and fnames.WriteString(name))

Signed-off-by: Giuseppe Scrivano <[email protected]>

giuseppe · 2024-04-19T10:40:44Z

thanks @mtrmac and @kolyshkin. I've addressed your last comments and pushed a new version

mtrmac

LGTM otherwise.

pkg/chunked/cache_linux.go

use the binary representation for a given digest, it helps reducing the file size by ~25%. Signed-off-by: Giuseppe Scrivano <[email protected]>

it helps reducing the cache file size by ~25%. Signed-off-by: Giuseppe Scrivano <[email protected]>

Signed-off-by: Giuseppe Scrivano <[email protected]>

use a bloom filter to speed up lookup of digests in a cache file. The biggest advantage is that it reduces page faults with the mmap'ed cache file. Signed-off-by: Giuseppe Scrivano <[email protected]>

so that the same file path is stored only once in the cache file. After this change, the cache file measured on the fedora:{38,39,40} images is in average ~6% smaller. Signed-off-by: Giuseppe Scrivano <[email protected]>

it reduces the cache file size by ~3%. Signed-off-by: Giuseppe Scrivano <[email protected]>

Signed-off-by: Giuseppe Scrivano <[email protected]>

mtrmac · 2024-04-19T19:34:59Z

/lgtm

Thanks!

openshift-ci bot added the do-not-merge/work-in-progress label Mar 27, 2024

openshift-ci bot added the approved label Mar 27, 2024

giuseppe changed the title ~~chunked: use a bloom filter to speed up cache lookup and store file as binary~~ chunked: store cache as binary and use a bloom filter Mar 27, 2024

giuseppe force-pushed the chunked-bloom-filter branch from f4f29dd to ba6657b Compare March 27, 2024 11:50

giuseppe force-pushed the chunked-bloom-filter branch 2 times, most recently from fb5a6e7 to de1dff9 Compare March 27, 2024 13:11

mtrmac reviewed Mar 27, 2024

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giuseppe force-pushed the chunked-bloom-filter branch from de1dff9 to 9f2b6a3 Compare March 28, 2024 22:22

giuseppe marked this pull request as ready for review April 4, 2024 07:41

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mtrmac reviewed Apr 8, 2024

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giuseppe force-pushed the chunked-bloom-filter branch from 9f2b6a3 to d986219 Compare April 9, 2024 08:36

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chunked: move cache file generation to separate function

397943b

Signed-off-by: Giuseppe Scrivano <[email protected]>

giuseppe force-pushed the chunked-bloom-filter branch from d986219 to 0820a2a Compare April 19, 2024 10:40

giuseppe force-pushed the chunked-bloom-filter branch from 0820a2a to 6d8fc8e Compare April 19, 2024 13:55

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chunked: store digest in binary format

3347254

use the binary representation for a given digest, it helps reducing the file size by ~25%. Signed-off-by: Giuseppe Scrivano <[email protected]>

giuseppe added 6 commits April 19, 2024 21:28

chunked: store file offset and length in binary format

e6793e3

it helps reducing the cache file size by ~25%. Signed-off-by: Giuseppe Scrivano <[email protected]>

chunked: add implementation for a bloom filter

6668761

Signed-off-by: Giuseppe Scrivano <[email protected]>

chunked: use a bloom filter to speedup lookup

e9a96e0

use a bloom filter to speed up lookup of digests in a cache file. The biggest advantage is that it reduces page faults with the mmap'ed cache file. Signed-off-by: Giuseppe Scrivano <[email protected]>

chunked: store file names separately

59ac039

so that the same file path is stored only once in the cache file. After this change, the cache file measured on the fedora:{38,39,40} images is in average ~6% smaller. Signed-off-by: Giuseppe Scrivano <[email protected]>

chunked: store file locations as binary

9619a53

it reduces the cache file size by ~3%. Signed-off-by: Giuseppe Scrivano <[email protected]>

chunked: bump version number for cache file

065a2f3

Signed-off-by: Giuseppe Scrivano <[email protected]>

giuseppe force-pushed the chunked-bloom-filter branch from 6d8fc8e to 065a2f3 Compare April 19, 2024 19:28

openshift-ci bot assigned mtrmac Apr 19, 2024

openshift-ci bot added the lgtm label Apr 19, 2024

openshift-merge-bot bot merged commit d227439 into containers:main Apr 19, 2024
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chunked: store cache as binary and use a bloom filter #1870

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chunked: store cache as binary and use a bloom filter #1870

chunked: store cache as binary and use a bloom filter #1870

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