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manifest: add range annotations
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This change adds a "range annotation" feature to Annotators , which
are computations that aggregate some value over a specific key range within
within a level. Level-wide annotations are now computed internally as a
range annotation with a key range spanning the whole level. Range annotations
use the same B-tree caching behavior as regular annotations, so queries
remain fast even with thousands of tables because they avoid a sequential
iteration over a level's files.

This PR only sets up range annotations without changing any existing
behavior. However, there are a number of potential use cases for range
annotations which could be added next:
- Calculating the number of keys shadowed by a tombstone-dense key range,
  for use in the heuristic proposed at #3719
- Computing the total file size that a read compaction overlaps with,
  which is used to prevent read compactions that are too wide
  [here](https://github.com/cockroachdb/pebble/blob/9a4ea4dfc5a8129937e3fdc811ea87543d88565b/compaction_picker.go#L1930)
- Estimating disk usage for a key range without having to iterate over files,
  which is done [here](https://github.com/jbowens/pebble/blob/master/db.go#L2249)
- Calculating average value size and compression ratio for a key range,
  which we [currently use when estimating the potential space that compacting
  point tombstones would reclaim](https://github.com/jbowens/pebble/blob/646c6bab1af3c72dc7db59a0dcc38b5955fc15cc/table_stats.go#L350).
  Range annotations could also be used to implement the TODO from @jbowens.
- Estimating the reclaimed space from compacting range deletions, for which
  we also [currently use sequential iteration](https://github.com/jbowens/pebble/blob/master/table_stats.go#L557).
- Because annotations are in-memory, if we can find a way to refactor those
  last two without using I/O at all, then this would eliminate the need to
  defer table stats collection to a separate goroutine for newly written
  tables.
- Refactoring [`db.ScanStatistics`](https://github.com/jbowens/pebble/blob/646c6bab1af3c72dc7db59a0dcc38b5955fc15cc/db.go#L2823),
  which could increase performance significantly over the current
  implementation where we scan every key in the DB.
- Expand the LSM visualizer tool (#508) or the LSM viewer (#3339) to show
  aggregate statistics about key ranges. Range annotations would allow us to efficiently
  compute statistics including the # of sstables, # of keys, etc. in chunks
  of the keyspace and visualize this on a graph showing overlapping ranges
  from each level.

`BenchmarkNumFilesRangeAnnotation` shows that range annotations are
significantly faster than using `version.Overlaps` to aggregate over
a key range:
```
pkg: github.com/cockroachdb/pebble/internal/manifest
BenchmarkNumFilesRangeAnnotation/annotator-10         	  232282	      4716 ns/op	     112 B/op	       7 allocs/op
BenchmarkNumFilesRangeAnnotation/overlaps-10          	    2110	    545482 ns/op	     400 B/op	       9 allocs/op```
```
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@anish-shanbhag
anish-shanbhag committed Jul 26, 2024
1 parent 7920d96 commit 79bdbc1
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Showing 13 changed files with 648 additions and 584 deletions.
204 changes: 57 additions & 147 deletions compaction_picker.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -639,39 +639,13 @@ func compensatedSize(f *fileMetadata) uint64 {
return f.Size + fileCompensation(f)
}

// compensatedSizeAnnotator implements manifest.Annotator, annotating B-Tree
// nodes with the sum of the files' compensated sizes. Its annotation type is
// a *uint64. Compensated sizes may change once a table's stats are loaded
// asynchronously, so its values are marked as cacheable only if a file's
// stats have been loaded.
type compensatedSizeAnnotator struct {
}

var _ manifest.Annotator = compensatedSizeAnnotator{}

func (a compensatedSizeAnnotator) Zero(dst interface{}) interface{} {
if dst == nil {
return new(uint64)
}
v := dst.(*uint64)
*v = 0
return v
}

func (a compensatedSizeAnnotator) Accumulate(
f *fileMetadata, dst interface{},
) (v interface{}, cacheOK bool) {
vptr := dst.(*uint64)
*vptr = *vptr + compensatedSize(f)
return vptr, f.StatsValid()
}

func (a compensatedSizeAnnotator) Merge(src interface{}, dst interface{}) interface{} {
srcV := src.(*uint64)
dstV := dst.(*uint64)
*dstV = *dstV + *srcV
return dstV
}
// compensatedSizeAnnotator is a manifest.Annotator that annotates B-Tree
// nodes with the sum of the files' compensated sizes. Compensated sizes may
// change once a table's stats are loaded asynchronously, so its values are
// marked as cacheable only if a file's stats have been loaded.
var compensatedSizeAnnotator = manifest.SumAnnotator(func(f *fileMetadata) (uint64, bool) {
return compensatedSize(f), f.StatsValid()
})

// totalCompensatedSize computes the compensated size over a file metadata
// iterator. Note that this function is linear in the files available to the
Expand Down Expand Up @@ -912,10 +886,6 @@ func calculateSizeAdjust(inProgressCompactions []compactionInfo) [numLevels]leve
return sizeAdjust
}

func levelCompensatedSize(lm manifest.LevelMetadata) uint64 {
return *lm.Annotation(compensatedSizeAnnotator{}).(*uint64)
}

func (p *compactionPickerByScore) calculateLevelScores(
inProgressCompactions []compactionInfo,
) [numLevels]candidateLevelInfo {
Expand All @@ -932,7 +902,7 @@ func (p *compactionPickerByScore) calculateLevelScores(
}
sizeAdjust := calculateSizeAdjust(inProgressCompactions)
for level := 1; level < numLevels; level++ {
compensatedLevelSize := levelCompensatedSize(p.vers.Levels[level]) + sizeAdjust[level].compensated()
compensatedLevelSize := compensatedSizeAnnotator.LevelAnnotation(p.vers.Levels[level]) + sizeAdjust[level].compensated()
scores[level].compensatedScore = float64(compensatedLevelSize) / float64(p.levelMaxBytes[level])
scores[level].uncompensatedScore = float64(p.vers.Levels[level].Size()+sizeAdjust[level].actual()) / float64(p.levelMaxBytes[level])
}
Expand Down Expand Up @@ -1393,109 +1363,51 @@ func (p *compactionPickerByScore) addScoresToPickedCompactionMetrics(
}
}

// elisionOnlyAnnotator implements the manifest.Annotator interface,
// annotating B-Tree nodes with the *fileMetadata of a file meeting the
// obsolete keys criteria for an elision-only compaction within the subtree.
// If multiple files meet the criteria, it chooses whichever file has the
// lowest LargestSeqNum. The lowest LargestSeqNum file will be the first
// eligible for an elision-only compaction once snapshots less than or equal
// to its LargestSeqNum are closed.
type elisionOnlyAnnotator struct{}

var _ manifest.Annotator = elisionOnlyAnnotator{}

func (a elisionOnlyAnnotator) Zero(interface{}) interface{} {
return nil
}

func (a elisionOnlyAnnotator) Accumulate(f *fileMetadata, dst interface{}) (interface{}, bool) {
if f.IsCompacting() {
return dst, true
}
if !f.StatsValid() {
return dst, false
}
// Bottommost files are large and not worthwhile to compact just
// to remove a few tombstones. Consider a file ineligible if its
// own range deletions delete less than 10% of its data and its
// deletion tombstones make up less than 10% of its entries.
//
// TODO(jackson): This does not account for duplicate user keys
// which may be collapsed. Ideally, we would have 'obsolete keys'
// statistics that would include tombstones, the keys that are
// dropped by tombstones and duplicated user keys. See #847.
//
// Note that tables that contain exclusively range keys (i.e. no point keys,
// `NumEntries` and `RangeDeletionsBytesEstimate` are both zero) are excluded
// from elision-only compactions.
// TODO(travers): Consider an alternative heuristic for elision of range-keys.
if f.Stats.RangeDeletionsBytesEstimate*10 < f.Size &&
f.Stats.NumDeletions*10 <= f.Stats.NumEntries {
return dst, true
}
if dst == nil {
return f, true
} else if dstV := dst.(*fileMetadata); dstV.LargestSeqNum > f.LargestSeqNum {
return f, true
}
return dst, true
}

func (a elisionOnlyAnnotator) Merge(v interface{}, accum interface{}) interface{} {
if v == nil {
return accum
}
// If we haven't accumulated an eligible file yet, or f's LargestSeqNum is
// less than the accumulated file's, use f.
if accum == nil {
return v
}
f := v.(*fileMetadata)
accumV := accum.(*fileMetadata)
if accumV == nil || accumV.LargestSeqNum > f.LargestSeqNum {
return f
}
return accumV
}

// markedForCompactionAnnotator implements the manifest.Annotator interface,
// annotating B-Tree nodes with the *fileMetadata of a file that is marked for
// compaction within the subtree. If multiple files meet the criteria, it
// chooses whichever file has the lowest LargestSeqNum.
type markedForCompactionAnnotator struct{}

var _ manifest.Annotator = markedForCompactionAnnotator{}

func (a markedForCompactionAnnotator) Zero(interface{}) interface{} {
return nil
}

func (a markedForCompactionAnnotator) Accumulate(
f *fileMetadata, dst interface{},
) (interface{}, bool) {
if !f.MarkedForCompaction {
// Not marked for compaction; return dst.
return dst, true
}
return markedMergeHelper(f, dst)
}

func (a markedForCompactionAnnotator) Merge(v interface{}, accum interface{}) interface{} {
if v == nil {
return accum
}
accum, _ = markedMergeHelper(v.(*fileMetadata), accum)
return accum
}

// REQUIRES: f is non-nil, and f.MarkedForCompaction=true.
func markedMergeHelper(f *fileMetadata, dst interface{}) (interface{}, bool) {
if dst == nil {
return f, true
} else if dstV := dst.(*fileMetadata); dstV.LargestSeqNum > f.LargestSeqNum {
return f, true
}
return dst, true
// elisionOnlyAnnotator is a manifest.Annotator that annotates B-Tree
// nodes with the *fileMetadata of a file meeting the obsolete keys criteria
// for an elision-only compaction within the subtree. If multiple files meet
// the criteria, it chooses whichever file has the lowest LargestSeqNum. The
// lowest LargestSeqNum file will be the first eligible for an elision-only
// compaction once snapshots less than or equal to its LargestSeqNum are closed.
var elisionOnlyAnnotator = &manifest.Annotator[*fileMetadata]{
Aggregator: manifest.PickFileAggregator{
Filter: func(f *fileMetadata) (eligible bool, cacheOK bool) {
// Bottommost files are large and not worthwhile to compact just
// to remove a few tombstones. Consider a file eligible only if
// either its own range deletions delete at least 10% of its data or
// its deletion tombstones make at least 10% of its entries.
//
// TODO(jackson): This does not account for duplicate user keys
// which may be collapsed. Ideally, we would have 'obsolete keys'
// statistics that would include tombstones, the keys that are
// dropped by tombstones and duplicated user keys. See #847.
//
// Note that tables that contain exclusively range keys (i.e. no point keys,
// `NumEntries` and `RangeDeletionsBytesEstimate` are both zero) are excluded
// from elision-only compactions.
// TODO(travers): Consider an alternative heuristic for elision of range-keys.
deletionCriteria := f.Stats.RangeDeletionsBytesEstimate*10 >= f.Size || f.Stats.NumDeletions*10 > f.Stats.NumEntries
return !f.IsCompacting() && f.StatsValid() && deletionCriteria, f.StatsValid()
},
Compare: func(f1 *fileMetadata, f2 *fileMetadata) bool {
return f1.LargestSeqNum < f2.LargestSeqNum
},
},
}

// markedForCompactionAnnotator is a manifest.Annotator that annotates B-Tree
// nodes with the *fileMetadata of a file that is marked for compaction
// within the subtree. If multiple files meet the criteria, it chooses
// whichever file has the lowest LargestSeqNum.
var markedForCompactionAnnotator = &manifest.Annotator[*fileMetadata]{
Aggregator: manifest.PickFileAggregator{
Filter: func(f *fileMetadata) (eligible bool, cacheOK bool) {
return f.MarkedForCompaction, true
},
Compare: func(f1 *fileMetadata, f2 *fileMetadata) bool {
return f1.LargestSeqNum < f2.LargestSeqNum
},
},
}

// pickElisionOnlyCompaction looks for compactions of sstables in the
Expand All @@ -1506,11 +1418,10 @@ func (p *compactionPickerByScore) pickElisionOnlyCompaction(
if p.opts.private.disableElisionOnlyCompactions {
return nil
}
v := p.vers.Levels[numLevels-1].Annotation(elisionOnlyAnnotator{})
if v == nil {
candidate := elisionOnlyAnnotator.LevelAnnotation(p.vers.Levels[numLevels-1])
if candidate == nil {
return nil
}
candidate := v.(*fileMetadata)
if candidate.IsCompacting() || candidate.LargestSeqNum >= env.earliestSnapshotSeqNum {
return nil
}
Expand Down Expand Up @@ -1542,12 +1453,11 @@ func (p *compactionPickerByScore) pickElisionOnlyCompaction(
// the input level.
func (p *compactionPickerByScore) pickRewriteCompaction(env compactionEnv) (pc *pickedCompaction) {
for l := numLevels - 1; l >= 0; l-- {
v := p.vers.Levels[l].Annotation(markedForCompactionAnnotator{})
if v == nil {
candidate := markedForCompactionAnnotator.LevelAnnotation(p.vers.Levels[l])
if candidate == nil {
// Try the next level.
continue
}
candidate := v.(*fileMetadata)
if candidate.IsCompacting() {
// Try the next level.
continue
Expand Down
2 changes: 1 addition & 1 deletion compaction_picker_test.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -563,7 +563,7 @@ func TestCompactionPickerL0(t *testing.T) {
}
f.MarkedForCompaction = true
picker.vers.Stats.MarkedForCompaction++
picker.vers.Levels[l].InvalidateAnnotation(markedForCompactionAnnotator{})
markedForCompactionAnnotator.InvalidateLevelAnnotation(picker.vers.Levels[l])
return fmt.Sprintf("marked L%d.%s", l, f.FileNum)
}
}
Expand Down
2 changes: 1 addition & 1 deletion compaction_test.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2505,7 +2505,7 @@ func TestMarkedForCompaction(t *testing.T) {
}
f.MarkedForCompaction = true
vers.Stats.MarkedForCompaction++
vers.Levels[l].InvalidateAnnotation(markedForCompactionAnnotator{})
markedForCompactionAnnotator.InvalidateLevelAnnotation(vers.Levels[l])
return fmt.Sprintf("marked L%d.%s", l, f.FileNum)
}
}
Expand Down
16 changes: 8 additions & 8 deletions db.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1995,8 +1995,8 @@ func (d *DB) Metrics() *Metrics {
metrics.private.optionsFileSize = d.optionsFileSize

// TODO(jackson): Consider making these metrics optional.
metrics.Keys.RangeKeySetsCount = countRangeKeySetFragments(vers)
metrics.Keys.TombstoneCount = countTombstones(vers)
metrics.Keys.RangeKeySetsCount = rangeKeySetsAnnotator.MultiLevelAnnotation(vers.RangeKeyLevels[:])
metrics.Keys.TombstoneCount = tombstonesAnnotator.MultiLevelAnnotation(vers.Levels[:])

d.mu.versions.logLock()
metrics.private.manifestFileSize = uint64(d.mu.versions.manifest.Size())
Expand All @@ -2014,12 +2014,12 @@ func (d *DB) Metrics() *Metrics {
metrics.Flush.NumInProgress = 1
}
for i := 0; i < numLevels; i++ {
metrics.Levels[i].Additional.ValueBlocksSize = valueBlocksSizeForLevel(vers, i)
unknown, snappy, none, zstd := compressionTypesForLevel(vers, i)
metrics.Table.CompressedCountUnknown += int64(unknown)
metrics.Table.CompressedCountSnappy += int64(snappy)
metrics.Table.CompressedCountZstd += int64(zstd)
metrics.Table.CompressedCountNone += int64(none)
metrics.Levels[i].Additional.ValueBlocksSize = valueBlockSizeAnnotator.LevelAnnotation(vers.Levels[i])
compressionTypes := compressionTypeAnnotator.LevelAnnotation(vers.Levels[i])
metrics.Table.CompressedCountUnknown += int64(compressionTypes.unknown)
metrics.Table.CompressedCountSnappy += int64(compressionTypes.snappy)
metrics.Table.CompressedCountZstd += int64(compressionTypes.zstd)
metrics.Table.CompressedCountNone += int64(compressionTypes.none)
}

d.mu.Unlock()
Expand Down
2 changes: 1 addition & 1 deletion format_major_version.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ func (d *DB) markFilesLocked(findFn findFilesFunc) error {
// annotations will be out of date. Clear the compaction-picking
// annotation, so that it's recomputed the next time the compaction
// picker looks for a file marked for compaction.
vers.Levels[l].InvalidateAnnotation(markedForCompactionAnnotator{})
markedForCompactionAnnotator.InvalidateLevelAnnotation(vers.Levels[l])
}

// The 'marked-for-compaction' bit is persisted in the MANIFEST file
Expand Down
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