no overlapping on compaction when an existing block is not within default boundaries. (#461)

closes https://github.com/prometheus/prometheus/issues/4643

Signed-off-by: Krasi Georgiev <kgeorgie@redhat.com>

CHANGELOG.md

@@ -3,3 +3,5 @@
  - `LastCheckpoint` used to return just the segment name and now it returns the full relative path.
  - `NewSegmentsRangeReader` can now read over miltiple wal ranges by using the new `SegmentRange` struct.
  - `CorruptionErr` now also exposes the Segment `Dir` which is added when displaying any errors.
+ - `Head.Init()` is changed to `Head.Init(minValidTime int64)` where `minValidTime` is taken from the maxt of the last persisted block and any samples below `minValidTime` will not be loaded from the wal in the head. The same value is used when using the `Heah.Appender()` to disallow adding samples below the `minValidTime` timestamp. This change was nececary to fix a bug where a `Snapshot()` with the head included would create a block with custom time range(not bound to the default time ranges) and the next block population from the head would create an overlapping block.  
+    - https://github.com/prometheus/tsdb/issues/446

block_test.go

@@ -77,8 +77,9 @@ func createEmptyBlock(t *testing.T, dir string, meta *BlockMeta) *Block {
 	return b
 }
 
-// createPopulatedBlock creates a block with nSeries series, and nSamples samples.
+// createPopulatedBlock creates a block with nSeries series, filled with
-func createPopulatedBlock(tb testing.TB, dir string, nSeries, nSamples int) *Block {
+// samples of the given mint,maxt time range.
+func createPopulatedBlock(tb testing.TB, dir string, nSeries int, mint, maxt int64) *Block {
 	head, err := NewHead(nil, nil, nil, 2*60*60*1000)
 	testutil.Ok(tb, err)
 	defer head.Close()
@@ -87,12 +88,11 @@ func createPopulatedBlock(tb testing.TB, dir string, nSeries, nSamples int) *Blo
 	testutil.Ok(tb, err)
 	refs := make([]uint64, nSeries)
 
-	for n := 0; n < nSamples; n++ {
+	for ts := mint; ts <= maxt; ts++ {
 		app := head.Appender()
-		ts := n * 1000
 		for i, lbl := range lbls {
 			if refs[i] != 0 {
-				err := app.AddFast(refs[i], int64(ts), rand.Float64())
+				err := app.AddFast(refs[i], ts, rand.Float64())
 				if err == nil {
 					continue
 				}

compact_test.go

@@ -733,7 +733,7 @@ func TestDisableAutoCompactions(t *testing.T) {
 	case db.compactc <- struct{}{}:
 	default:
 	}
-	for x := 0; x < 10; x++ {
+	for x := 0; x < 20; x++ {
 		if len(db.Blocks()) > 0 {
 			break
 		}

db.go

@@ -271,12 +271,21 @@ func Open(dir string, l log.Logger, r prometheus.Registerer, opts *Options) (db
 	if err != nil {
 		return nil, err
 	}
-	if err := db.head.Init(); err != nil {
+
-		return nil, errors.Wrap(err, "read WAL")
-	}
 	if err := db.reload(); err != nil {
 		return nil, err
 	}
+	// Set the min valid time for the ingested samples
+	// to be no lower than the maxt of the last block.
+	blocks := db.Blocks()
+	minValidTime := int64(math.MinInt64)
+	if len(blocks) > 0 {
+		minValidTime = blocks[len(blocks)-1].Meta().MaxTime
+	}
+
+	if err := db.head.Init(minValidTime); err != nil {
+		return nil, errors.Wrap(err, "read WAL")
+	}
 
 	go db.run()
 
@@ -395,7 +404,8 @@ func (db *DB) compact() (err error) {
 		if db.head.MaxTime()-db.head.MinTime() <= db.opts.BlockRanges[0]/2*3 {
 			break
 		}
-		mint, maxt := rangeForTimestamp(db.head.MinTime(), db.opts.BlockRanges[0])
+		mint := db.head.MinTime()
+		maxt := rangeForTimestamp(mint, db.opts.BlockRanges[0])
 
 		// Wrap head into a range that bounds all reads to it.
 		head := &rangeHead{
@@ -826,9 +836,8 @@ func (db *DB) Querier(mint, maxt int64) (Querier, error) {
 	return sq, nil
 }
 
-func rangeForTimestamp(t int64, width int64) (mint, maxt int64) {
+func rangeForTimestamp(t int64, width int64) (maxt int64) {
-	mint = (t / width) * width
+	return (t/width)*width + width
-	return mint, mint + width
 }
 
 // Delete implements deletion of metrics. It only has atomicity guarantees on a per-block basis.

db_test.go

@@ -25,6 +25,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/go-kit/kit/log"
 	"github.com/oklog/ulid"
 	"github.com/pkg/errors"
 	"github.com/prometheus/client_golang/prometheus"
@@ -1199,6 +1200,11 @@ func TestQuerierWithBoundaryChunks(t *testing.T) {
 	testutil.Assert(t, count == 2, "expected 2 blocks in querier, got %d", count)
 }
 
+// TestInitializeHeadTimestamp ensures that the h.minTime is set properly.
+// 	- no blocks no WAL: set to the time of the first  appended sample
+// 	- no blocks with WAL: set to the smallest sample from the WAL
+//	- with blocks no WAL: set to the last block maxT
+// 	- with blocks with WAL: same as above
 func TestInitializeHeadTimestamp(t *testing.T) {
 	t.Run("clean", func(t *testing.T) {
 		dir, err := ioutil.TempDir("", "test_head_init")
@@ -1441,3 +1447,102 @@ func TestCorrectNumTombstones(t *testing.T) {
 	testutil.Ok(t, db.Delete(9, 11, labels.NewEqualMatcher("foo", "bar")))
 	testutil.Equals(t, uint64(3), db.blocks[0].meta.Stats.NumTombstones)
 }
+
+// TestBlockRanges checks the following use cases:
+//  - No samples can be added with timestamps lower than the last block maxt.
+//  - The compactor doesn't create overlaping blocks
+// even when the last blocks is not within the default boundaries.
+//	- Lower bondary is based on the smallest sample in the head and
+// upper boundary is rounded to the configured block range.
+//
+// This ensures that a snapshot that includes the head and creates a block with a custom time range
+// will not overlap with the first block created by the next compaction.
+func TestBlockRanges(t *testing.T) {
+	logger := log.NewLogfmtLogger(log.NewSyncWriter(os.Stderr))
+
+	dir, err := ioutil.TempDir("", "test_storage")
+	if err != nil {
+		t.Fatalf("Opening test dir failed: %s", err)
+	}
+
+	rangeToTriggercompaction := DefaultOptions.BlockRanges[0]/2*3 + 1
+
+	// Test that the compactor doesn't create overlapping blocks
+	// when a non standard block already exists.
+	firstBlockMaxT := int64(3)
+	createPopulatedBlock(t, dir, 1, 0, firstBlockMaxT)
+	db, err := Open(dir, logger, nil, DefaultOptions)
+	if err != nil {
+		t.Fatalf("Opening test storage failed: %s", err)
+	}
+	defer func() {
+		os.RemoveAll(dir)
+	}()
+	app := db.Appender()
+	lbl := labels.Labels{{"a", "b"}}
+	_, err = app.Add(lbl, firstBlockMaxT-1, rand.Float64())
+	if err == nil {
+		t.Fatalf("appending a sample with a timestamp covered by a previous block shouldn't be possible")
+	}
+	_, err = app.Add(lbl, firstBlockMaxT+1, rand.Float64())
+	testutil.Ok(t, err)
+	_, err = app.Add(lbl, firstBlockMaxT+2, rand.Float64())
+	testutil.Ok(t, err)
+	secondBlockMaxt := firstBlockMaxT + rangeToTriggercompaction
+	_, err = app.Add(lbl, secondBlockMaxt, rand.Float64()) // Add samples to trigger a new compaction
+
+	testutil.Ok(t, err)
+	testutil.Ok(t, app.Commit())
+	for x := 1; x < 10; x++ {
+		if len(db.Blocks()) == 2 {
+			break
+		}
+		time.Sleep(100 * time.Millisecond)
+	}
+	testutil.Equals(t, 2, len(db.Blocks()), "no new block created after the set timeout")
+
+	if db.Blocks()[0].Meta().MaxTime > db.Blocks()[1].Meta().MinTime {
+		t.Fatalf("new block overlaps  old:%v,new:%v", db.Blocks()[0].Meta(), db.Blocks()[1].Meta())
+	}
+
+	// Test that wal records are skipped when an existing block covers the same time ranges
+	// and compaction doesn't create an overlapping block.
+	db.DisableCompactions()
+	_, err = app.Add(lbl, secondBlockMaxt+1, rand.Float64())
+	testutil.Ok(t, err)
+	_, err = app.Add(lbl, secondBlockMaxt+2, rand.Float64())
+	testutil.Ok(t, err)
+	_, err = app.Add(lbl, secondBlockMaxt+3, rand.Float64())
+	testutil.Ok(t, err)
+	_, err = app.Add(lbl, secondBlockMaxt+4, rand.Float64())
+	testutil.Ok(t, app.Commit())
+	testutil.Ok(t, db.Close())
+
+	thirdBlockMaxt := secondBlockMaxt + 2
+	createPopulatedBlock(t, dir, 1, secondBlockMaxt+1, thirdBlockMaxt)
+
+	db, err = Open(dir, logger, nil, DefaultOptions)
+	if err != nil {
+		t.Fatalf("Opening test storage failed: %s", err)
+	}
+	defer db.Close()
+	testutil.Equals(t, 3, len(db.Blocks()), "db doesn't include expected number of blocks")
+	testutil.Equals(t, db.Blocks()[2].Meta().MaxTime, thirdBlockMaxt, "unexpected maxt of the last block")
+
+	app = db.Appender()
+	_, err = app.Add(lbl, thirdBlockMaxt+rangeToTriggercompaction, rand.Float64()) // Trigger a compaction
+	testutil.Ok(t, err)
+	testutil.Ok(t, app.Commit())
+	for x := 1; x < 10; x++ {
+		if len(db.Blocks()) == 4 {
+			break
+		}
+		time.Sleep(100 * time.Millisecond)
+	}
+
+	testutil.Equals(t, 4, len(db.Blocks()), "no new block created after the set timeout")
+
+	if db.Blocks()[2].Meta().MaxTime > db.Blocks()[3].Meta().MinTime {
+		t.Fatalf("new block overlaps  old:%v,new:%v", db.Blocks()[2].Meta(), db.Blocks()[3].Meta())
+	}
+}

head.go

@@ -59,7 +59,8 @@ type Head struct {
 	appendPool sync.Pool
 	bytesPool  sync.Pool
 
-	minTime, maxTime int64
+	minTime, maxTime int64 // Current min and max of the samples included in the head.
+	minValidTime     int64 // Mint allowed to be added to the head. It shouldn't be lower than the maxt of the last persisted block.
 	lastSeriesID     uint64
 
 	// All series addressable by their ID or hash.
@@ -300,13 +301,6 @@ func (h *Head) updateMinMaxTime(mint, maxt int64) {
 }
 
 func (h *Head) loadWAL(r *wal.Reader) error {
-	minValidTime := h.MinTime()
-	// If the min time is still uninitialized (no persisted blocks yet),
-	// we accept all sample timestamps from the WAL.
-	if minValidTime == math.MaxInt64 {
-		minValidTime = math.MinInt64
-	}
-
 	// Track number of samples that referenced a series we don't know about
 	// for error reporting.
 	var unknownRefs uint64
@@ -327,7 +321,7 @@ func (h *Head) loadWAL(r *wal.Reader) error {
 		inputs[i] = make(chan []RefSample, 300)
 
 		go func(input <-chan []RefSample, output chan<- []RefSample) {
-			unknown := h.processWALSamples(minValidTime, input, output)
+			unknown := h.processWALSamples(h.minValidTime, input, output)
 			atomic.AddUint64(&unknownRefs, unknown)
 			wg.Done()
 		}(inputs[i], outputs[i])
@@ -410,7 +404,7 @@ func (h *Head) loadWAL(r *wal.Reader) error {
 			}
 			for _, s := range tstones {
 				for _, itv := range s.intervals {
-					if itv.Maxt < minValidTime {
+					if itv.Maxt < h.minValidTime {
 						continue
 					}
 					h.tombstones.addInterval(s.ref, itv)
@@ -443,8 +437,12 @@ func (h *Head) loadWAL(r *wal.Reader) error {
 }
 
 // Init loads data from the write ahead log and prepares the head for writes.
-func (h *Head) Init() error {
+// It should be called before using an appender so that
+// limits the ingested samples to the head min valid time.
+func (h *Head) Init(minValidTime int64) error {
+	h.minValidTime = minValidTime
 	defer h.postings.EnsureOrder()
+	defer h.gc() // After loading the wal remove the obsolete data from the head.
 
 	if h.wal == nil {
 		return nil
@@ -486,6 +484,7 @@ func (h *Head) Init() error {
 	if err := h.wal.Repair(err); err != nil {
 		return errors.Wrap(err, "repair corrupted WAL")
 	}
+
 	return nil
 }
 
@@ -502,6 +501,7 @@ func (h *Head) Truncate(mint int64) (err error) {
 		return nil
 	}
 	atomic.StoreInt64(&h.minTime, mint)
+	h.minValidTime = mint
 
 	// Ensure that max time is at least as high as min time.
 	for h.MaxTime() < mint {
@@ -655,13 +655,22 @@ func (h *Head) Appender() Appender {
 func (h *Head) appender() *headAppender {
 	return &headAppender{
 		head: h,
-		minValidTime: h.MaxTime() - h.chunkRange/2,
+		// Set the minimum valid time to whichever is greater the head min valid time or the compaciton window.
+		// This ensures that no samples will be added within the compaction window to avoid races.
+		minValidTime: max(h.minValidTime, h.MaxTime()-h.chunkRange/2),
 		mint:         math.MaxInt64,
 		maxt:         math.MinInt64,
 		samples:      h.getAppendBuffer(),
 	}
 }
 
+func max(a, b int64) int64 {
+	if a > b {
+		return a
+	}
+	return b
+}
+
 func (h *Head) getAppendBuffer() []RefSample {
 	b := h.appendPool.Get()
 	if b == nil {
@@ -1411,7 +1420,7 @@ func (s *memSeries) cut(mint int64) *memChunk {
 
 	// Set upper bound on when the next chunk must be started. An earlier timestamp
 	// may be chosen dynamically at a later point.
-	_, s.nextAt = rangeForTimestamp(mint, s.chunkRange)
+	s.nextAt = rangeForTimestamp(mint, s.chunkRange)
 
 	app, err := c.chunk.Appender()
 	if err != nil {

head_test.go

@@ -15,6 +15,7 @@ package tsdb
 
 import (
 	"io/ioutil"
+	"math"
 	"math/rand"
 	"os"
 	"path/filepath"
@@ -123,7 +124,7 @@ func TestHead_ReadWAL(t *testing.T) {
 	testutil.Ok(t, err)
 	defer head.Close()
 
-	testutil.Ok(t, head.Init())
+	testutil.Ok(t, head.Init(math.MinInt64))
 	testutil.Equals(t, uint64(100), head.lastSeriesID)
 
 	s10 := head.series.getByID(10)
@@ -132,7 +133,7 @@ func TestHead_ReadWAL(t *testing.T) {
 	s100 := head.series.getByID(100)
 
 	testutil.Equals(t, labels.FromStrings("a", "1"), s10.lset)
-	testutil.Equals(t, labels.FromStrings("a", "2"), s11.lset)
+	testutil.Equals(t, (*memSeries)(nil), s11) // Series without samples should be garbage colected at head.Init().
 	testutil.Equals(t, labels.FromStrings("a", "4"), s50.lset)
 	testutil.Equals(t, labels.FromStrings("a", "3"), s100.lset)
 
@@ -146,7 +147,6 @@ func TestHead_ReadWAL(t *testing.T) {
 	}
 
 	testutil.Equals(t, []sample{{100, 2}, {101, 5}}, expandChunk(s10.iterator(0)))
-	testutil.Equals(t, 0, len(s11.chunks))
 	testutil.Equals(t, []sample{{101, 6}}, expandChunk(s50.iterator(0)))
 	testutil.Equals(t, []sample{{100, 3}}, expandChunk(s100.iterator(0)))
 }
@@ -288,7 +288,7 @@ func TestHeadDeleteSeriesWithoutSamples(t *testing.T) {
 	testutil.Ok(t, err)
 	defer head.Close()
 
-	testutil.Ok(t, head.Init())
+	testutil.Ok(t, head.Init(math.MinInt64))
 
 	testutil.Ok(t, head.Delete(0, 100, labels.NewEqualMatcher("a", "1")))
 }
@@ -923,7 +923,7 @@ func TestWalRepair(t *testing.T) {
 
 			h, err := NewHead(nil, nil, w, 1)
 			testutil.Ok(t, err)
-			testutil.Ok(t, h.Init())
+			testutil.Ok(t, h.Init(math.MinInt64))
 
 			sr, err := wal.NewSegmentsReader(dir)
 			testutil.Ok(t, err)

querier_test.go

@@ -1292,7 +1292,7 @@ func BenchmarkPersistedQueries(b *testing.B) {
 				dir, err := ioutil.TempDir("", "bench_persisted")
 				testutil.Ok(b, err)
 				defer os.RemoveAll(dir)
-				block := createPopulatedBlock(b, dir, nSeries, nSamples)
+				block := createPopulatedBlock(b, dir, nSeries, 1, int64(nSamples))
 				defer block.Close()
 
 				q, err := NewBlockQuerier(block, block.Meta().MinTime, block.Meta().MaxTime)