fix: series file index compaction (#23916) (#27068)

Co-authored-by: davidby-influx <72418212+davidby-influx@users.noreply.github.com>
closes influxdata/EAR#3643

Author: devanbenz

tsdb/series_partition.go

@@ -5,12 +5,14 @@ import (
 	"encoding/binary"
 	"errors"
 	"fmt"
+	"math"
 	"os"
 	"path/filepath"
 	"sync"
 
 	"github.com/influxdata/influxdb/v2/logger"
 	"github.com/influxdata/influxdb/v2/models"
+	errors2 "github.com/influxdata/influxdb/v2/pkg/errors"
 	"github.com/influxdata/influxdb/v2/pkg/limiter"
 	"github.com/influxdata/influxdb/v2/pkg/rhh"
 	"go.uber.org/zap"
@@ -87,7 +89,7 @@ func (p *SeriesPartition) Open() error {
 		p.index = NewSeriesIndex(p.IndexPath())
 		if err := p.index.Open(); err != nil {
 			return err
-		} else if err := p.index.Recover(p.segments); err != nil {
+		} else if err = p.index.Recover(p.segments); err != nil {
 			return err
 		}
 
@@ -565,94 +567,108 @@ func (c *SeriesPartitionCompactor) Compact(p *SeriesPartition) error {
 	return nil
 }
 
-func (c *SeriesPartitionCompactor) compactIndexTo(index *SeriesIndex, seriesN uint64, segments []*SeriesSegment, path string) error {
-	hdr := NewSeriesIndexHeader()
-	hdr.Count = seriesN
-	hdr.Capacity = pow2((int64(hdr.Count) * 100) / SeriesIndexLoadFactor)
-
-	// Allocate space for maps.
-	keyIDMap := make([]byte, (hdr.Capacity * SeriesIndexElemSize))
-	idOffsetMap := make([]byte, (hdr.Capacity * SeriesIndexElemSize))
+var errDone error = errors.New("done")
 
-	// Reindex all partitions.
-	var entryN int
-	for _, segment := range segments {
-		errDone := errors.New("done")
+func (c *SeriesPartitionCompactor) compactIndexTo(index *SeriesIndex, seriesN uint64, segments []*SeriesSegment, path string) (err error) {
 
-		if err := segment.ForEachEntry(func(flag uint8, id uint64, offset int64, key []byte) error {
+	hdr := NewSeriesIndexHeader()
+	var keyIDMap []byte
+	var idOffsetMap []byte
+
+	hdr.Count = math.MaxUint64
+	// seriesN is the current size of the index.  Because it may contain tombstones
+	// for deleted series, we recalculate that number (as seriesCount) without the
+	// deleted series as we rebuild the index.	If the count of existing series does
+	// not equal the seriesN passed in (meaning there were tombstones), we rebuild
+	// the index a second time with the correct size.
+	seriesCount := seriesN
+	for {
+		seriesN = seriesCount
+		seriesCount = uint64(0)
+		// This only loops if there are deleted entries, which shrinks the size
+		hdr.Capacity = pow2((int64(seriesN) * 100) / SeriesIndexLoadFactor)
+		// Allocate space for maps, guaranteeing slices are initialized to zero
+		keyIDMap = make([]byte, hdr.Capacity*SeriesIndexElemSize)
+		idOffsetMap = make([]byte, hdr.Capacity*SeriesIndexElemSize)
+
+		// Reindex all partitions.
+		var entryN int
+		for _, segment := range segments {
+
+			if err = segment.ForEachEntry(func(flag uint8, id uint64, offset int64, key []byte) error {
+
+				// Make sure we don't go past the offset where the compaction began.
+				if offset > index.maxOffset {
+					return errDone
+				}
 
-			// Make sure we don't go past the offset where the compaction began.
-			if offset > index.maxOffset {
-				return errDone
-			}
+				// Check for cancellation periodically.
+				if entryN++; entryN%1000 == 0 {
+					select {
+					case <-c.cancel:
+						return ErrSeriesPartitionCompactionCancelled
+					default:
+					}
+				}
 
-			// Check for cancellation periodically.
-			if entryN++; entryN%1000 == 0 {
-				select {
-				case <-c.cancel:
-					return ErrSeriesPartitionCompactionCancelled
+				// Only process insert entries.
+				switch flag {
+				case SeriesEntryInsertFlag:
+					// does not fallthrough
+				case SeriesEntryTombstoneFlag:
+					return nil
 				default:
+					return fmt.Errorf("unexpected series partition log entry flag: %d", flag)
 				}
-			}
-
-			// Only process insert entries.
-			switch flag {
-			case SeriesEntryInsertFlag: // fallthrough
-			case SeriesEntryTombstoneFlag:
-				return nil
-			default:
-				return fmt.Errorf("unexpected series partition log entry flag: %d", flag)
-			}
 
-			// Save max series identifier processed.
-			hdr.MaxSeriesID, hdr.MaxOffset = id, offset
+				// Save max series identifier processed.
+				hdr.MaxSeriesID, hdr.MaxOffset = id, offset
 
-			// Ignore entry if tombstoned.
-			if index.IsDeleted(id) {
-				return nil
+				// Ignore entry if tombstoned.
+				if index.IsDeleted(id) {
+					return nil
+				}
+				seriesCount++
+				// Insert into maps.
+				c.insertIDOffsetMap(idOffsetMap, hdr.Capacity, id, offset)
+				return c.insertKeyIDMap(keyIDMap, hdr.Capacity, segments, key, offset, id)
+			}); err == errDone {
+				break
+			} else if err != nil {
+				return err
 			}
-
-			// Insert into maps.
-			c.insertIDOffsetMap(idOffsetMap, hdr.Capacity, id, offset)
-			return c.insertKeyIDMap(keyIDMap, hdr.Capacity, segments, key, offset, id)
-		}); err == errDone {
+		}
+		hdr.Count = seriesCount
+		if seriesN != seriesCount {
+			continue
+		} else {
 			break
-		} else if err != nil {
-			return err
 		}
 	}
-
 	// Open file handler.
 	f, err := os.Create(path)
 	if err != nil {
 		return err
 	}
-	defer f.Close()
-
+	defer errors2.Capture(&err, f.Close)()
 	// Calculate map positions.
 	hdr.KeyIDMap.Offset, hdr.KeyIDMap.Size = SeriesIndexHeaderSize, int64(len(keyIDMap))
 	hdr.IDOffsetMap.Offset, hdr.IDOffsetMap.Size = hdr.KeyIDMap.Offset+hdr.KeyIDMap.Size, int64(len(idOffsetMap))
 
 	// Write header.
-	if _, err := hdr.WriteTo(f); err != nil {
+	if _, err = hdr.WriteTo(f); err != nil {
 		return err
 	}
 
 	// Write maps.
-	if _, err := f.Write(keyIDMap); err != nil {
+	if _, err = f.Write(keyIDMap); err != nil {
 		return err
 	} else if _, err := f.Write(idOffsetMap); err != nil {
 		return err
 	}
 
-	// Sync & close.
-	if err := f.Sync(); err != nil {
-		return err
-	} else if err := f.Close(); err != nil {
-		return err
-	}
-
-	return nil
+	// Sync, then deferred close
+	return f.Sync()
 }
 
 func (c *SeriesPartitionCompactor) insertKeyIDMap(dst []byte, capacity int64, segments []*SeriesSegment, key []byte, offset int64, id uint64) error {