vendor: bump TSDB

vendor/github.com/prometheus/tsdb/block.go

@@ -195,7 +195,7 @@ func readMetaFile(dir string) (*BlockMeta, error) {
 	if err := json.Unmarshal(b, &m); err != nil {
 		return nil, err
 	}
-	if m.Version != 1 && m.Version != 2 {
+	if m.Version != 1 {
 		return nil, errors.Errorf("unexpected meta file version %d", m.Version)
 	}
 
@@ -203,6 +203,8 @@ func readMetaFile(dir string) (*BlockMeta, error) {
 }
 
 func writeMetaFile(dir string, meta *BlockMeta) error {
+	meta.Version = 1
+
 	// Make any changes to the file appear atomic.
 	path := filepath.Join(dir, metaFilename)
 	tmp := path + ".tmp"
@@ -253,7 +255,7 @@ func OpenBlock(dir string, pool chunkenc.Pool) (*Block, error) {
 	if err != nil {
 		return nil, err
 	}
-	ir, err := index.NewFileReader(filepath.Join(dir, "index"), meta.Version)
+	ir, err := index.NewFileReader(filepath.Join(dir, "index"))
 	if err != nil {
 		return nil, err
 	}

vendor/github.com/prometheus/tsdb/chunkenc/xor.go

@@ -89,7 +89,6 @@ func (c *XORChunk) Appender() (Appender, error) {
 	}
 
 	a := &xorAppender{
-		c:        c,
 		b:        c.b,
 		t:        it.t,
 		v:        it.val,
@@ -119,7 +118,6 @@ func (c *XORChunk) Iterator() Iterator {
 }
 
 type xorAppender struct {
-	c *XORChunk
 	b *bstream
 
 	t      int64

vendor/github.com/prometheus/tsdb/compact.go

@@ -91,8 +91,8 @@ func newCompactorMetrics(r prometheus.Registerer) *compactorMetrics {
 		Help: "Total number of compactions that failed for the partition.",
 	})
 	m.duration = prometheus.NewHistogram(prometheus.HistogramOpts{
-		Name:    "prometheus_tsdb_compaction_duration",
-		Help:    "Duration of compaction runs.",
+		Name:    "prometheus_tsdb_compaction_duration_seconds",
+		Help:    "Duration of compaction runs",
 		Buckets: prometheus.ExponentialBuckets(1, 2, 10),
 	})
 	m.chunkSize = prometheus.NewHistogram(prometheus.HistogramOpts{
@@ -431,7 +431,6 @@ func (c *LeveledCompactor) write(dest string, meta *BlockMeta, blocks ...BlockRe
 	if err != nil {
 		return errors.Wrap(err, "open index writer")
 	}
-	meta.Version = indexw.Version
 
 	if err := c.populateBlock(blocks, meta, indexw, chunkw); err != nil {
 		return errors.Wrap(err, "write compaction")

vendor/github.com/prometheus/tsdb/db.go

@@ -122,6 +122,8 @@ type dbMetrics struct {
 	reloads              prometheus.Counter
 	reloadsFailed        prometheus.Counter
 	compactionsTriggered prometheus.Counter
+	cutoffs              prometheus.Counter
+	cutoffsFailed        prometheus.Counter
 	tombCleanTimer       prometheus.Histogram
 }
 
@@ -148,6 +150,14 @@ func newDBMetrics(db *DB, r prometheus.Registerer) *dbMetrics {
 		Name: "prometheus_tsdb_compactions_triggered_total",
 		Help: "Total number of triggered compactions for the partition.",
 	})
+	m.cutoffs = prometheus.NewCounter(prometheus.CounterOpts{
+		Name: "prometheus_tsdb_retention_cutoffs_total",
+		Help: "Number of times the database cut off block data from disk.",
+	})
+	m.cutoffsFailed = prometheus.NewCounter(prometheus.CounterOpts{
+		Name: "prometheus_tsdb_retention_cutoffs_failures_total",
+		Help: "Number of times the database failed to cut off block data from disk.",
+	})
 	m.tombCleanTimer = prometheus.NewHistogram(prometheus.HistogramOpts{
 		Name: "prometheus_tsdb_tombstone_cleanup_seconds",
 		Help: "The time taken to recompact blocks to remove tombstones.",
@@ -158,6 +168,8 @@ func newDBMetrics(db *DB, r prometheus.Registerer) *dbMetrics {
 			m.loadedBlocks,
 			m.reloads,
 			m.reloadsFailed,
+			m.cutoffs,
+			m.cutoffsFailed,
 			m.compactionsTriggered,
 			m.tombCleanTimer,
 		)
@@ -176,6 +188,10 @@ func Open(dir string, l log.Logger, r prometheus.Registerer, opts *Options) (db
 	if opts == nil {
 		opts = DefaultOptions
 	}
+	// Fixup bad format written by Prometheus 2.1.
+	if err := repairBadIndexVersion(l, dir); err != nil {
+		return nil, err
+	}
 
 	db = &DB{
 		dir:                dir,
@@ -277,7 +293,17 @@ func (db *DB) run() {
 	}
 }
 
-func (db *DB) retentionCutoff() (bool, error) {
+func (db *DB) retentionCutoff() (b bool, err error) {
+	defer func() {
+		if !b && err == nil {
+			// no data had to be cut off.
+			return
+		}
+		db.metrics.cutoffs.Inc()
+		if err != nil {
+			db.metrics.cutoffsFailed.Inc()
+		}
+	}()
 	if db.opts.RetentionDuration == 0 {
 		return false, nil
 	}

vendor/github.com/prometheus/tsdb/index/index.go

@@ -37,6 +37,7 @@ const (
 	MagicIndex = 0xBAAAD700
 
 	indexFormatV1 = 1
+	indexFormatV2 = 2
 )
 
 type indexWriterSeries struct {
@@ -135,7 +136,7 @@ type indexTOC struct {
 	postingsTable     uint64
 }
 
-// NewWriter returns a new Writer to the given filename.
+// NewWriter returns a new Writer to the given filename. It serializes data in format version 2.
 func NewWriter(fn string) (*Writer, error) {
 	dir := filepath.Dir(fn)
 
@@ -168,8 +169,6 @@ func NewWriter(fn string) (*Writer, error) {
 		symbols:       make(map[string]uint32, 1<<13),
 		seriesOffsets: make(map[uint64]uint64, 1<<16),
 		crc32:         newCRC32(),
-
-		Version: 2,
 	}
 	if err := iw.writeMeta(); err != nil {
 		return nil, err
@@ -195,7 +194,7 @@ func (w *Writer) write(bufs ...[]byte) error {
 	return nil
 }
 
-// addPadding adds zero byte padding until the file size is a multiple size_unit.
+// addPadding adds zero byte padding until the file size is a multiple size.
 func (w *Writer) addPadding(size int) error {
 	p := w.pos % uint64(size)
 	if p == 0 {
@@ -249,7 +248,7 @@ func (w *Writer) ensureStage(s indexWriterStage) error {
 func (w *Writer) writeMeta() error {
 	w.buf1.reset()
 	w.buf1.putBE32(MagicIndex)
-	w.buf1.putByte(indexFormatV1)
+	w.buf1.putByte(indexFormatV2)
 
 	return w.write(w.buf1.get())
 }
@@ -266,7 +265,13 @@ func (w *Writer) AddSeries(ref uint64, lset labels.Labels, chunks ...chunks.Meta
 	if _, ok := w.seriesOffsets[ref]; ok {
 		return errors.Errorf("series with reference %d already added", ref)
 	}
+	// We add padding to 16 bytes to increase the addressable space we get through 4 byte
+	// series references.
 	w.addPadding(16)
+
+	if w.pos%16 != 0 {
+		return errors.Errorf("series write not 16-byte aligned at %d", w.pos)
+	}
 	w.seriesOffsets[ref] = w.pos / 16
 
 	w.buf2.reset()
@@ -572,25 +577,22 @@ func (b realByteSlice) Sub(start, end int) ByteSlice {
 	return b[start:end]
 }
 
-// NewReader returns a new IndexReader on the given byte slice.
-func NewReader(b ByteSlice, version int) (*Reader, error) {
-	return newReader(b, nil, version)
+// NewReader returns a new IndexReader on the given byte slice. It automatically
+// handles different format versions.
+func NewReader(b ByteSlice) (*Reader, error) {
+	return newReader(b, nil)
 }
 
 // NewFileReader returns a new index reader against the given index file.
-func NewFileReader(path string, version int) (*Reader, error) {
+func NewFileReader(path string) (*Reader, error) {
 	f, err := fileutil.OpenMmapFile(path)
 	if err != nil {
 		return nil, err
 	}
-	return newReader(realByteSlice(f.Bytes()), f, version)
+	return newReader(realByteSlice(f.Bytes()), f)
 }
 
-func newReader(b ByteSlice, c io.Closer, version int) (*Reader, error) {
-	if version != 1 && version != 2 {
-		return nil, errors.Errorf("unexpected file version %d", version)
-	}
-
+func newReader(b ByteSlice, c io.Closer) (*Reader, error) {
 	r := &Reader{
 		b:        b,
 		c:        c,
@@ -598,16 +600,20 @@ func newReader(b ByteSlice, c io.Closer, version int) (*Reader, error) {
 		labels:   map[string]uint32{},
 		postings: map[labels.Label]uint32{},
 		crc32:    newCRC32(),
-		version:  version,
 	}
 
-	// Verify magic number.
-	if b.Len() < 4 {
+	// Verify header.
+	if b.Len() < 5 {
 		return nil, errors.Wrap(errInvalidSize, "index header")
 	}
 	if m := binary.BigEndian.Uint32(r.b.Range(0, 4)); m != MagicIndex {
 		return nil, errors.Errorf("invalid magic number %x", m)
 	}
+	r.version = int(r.b.Range(4, 5)[0])
+
+	if r.version != 1 && r.version != 2 {
+		return nil, errors.Errorf("unknown index file version %d", r.version)
+	}
 
 	if err := r.readTOC(); err != nil {
 		return nil, errors.Wrap(err, "read TOC")
@@ -880,8 +886,10 @@ func (r *Reader) LabelIndices() ([][]string, error) {
 // Series reads the series with the given ID and writes its labels and chunks into lbls and chks.
 func (r *Reader) Series(id uint64, lbls *labels.Labels, chks *[]chunks.Meta) error {
 	offset := id
+	// In version 2 series IDs are no longer exact references but series are 16-byte padded
+	// and the ID is the multiple of 16 of the actual position.
 	if r.version == 2 {
-		offset = 16 * id
+		offset = id * 16
 	}
 	d := r.decbufUvarintAt(int(offset))
 	if d.err() != nil {

vendor/github.com/prometheus/tsdb/repair.go

@@ -0,0 +1,90 @@
+package tsdb
+
+import (
+	"encoding/json"
+	"io"
+	"io/ioutil"
+	"os"
+	"path"
+	"path/filepath"
+
+	"github.com/go-kit/kit/log"
+	"github.com/go-kit/kit/log/level"
+	"github.com/oklog/ulid"
+	"github.com/pkg/errors"
+	"github.com/prometheus/tsdb/fileutil"
+)
+
+// repairBadIndexVersion repairs an issue in index and meta.json persistence introduced in
+// commit 129773b41a565fde5156301e37f9a87158030443.
+func repairBadIndexVersion(logger log.Logger, dir string) error {
+	// All blocks written by Prometheus 2.1 with a meta.json version of 2 are affected.
+	// We must actually set the index file version to 2 and revert the meta.json version back to 1.
+	subdirs, err := fileutil.ReadDir(dir)
+	if err != nil {
+		return err
+	}
+	for _, d := range subdirs {
+		// Skip non-block dirs.
+		if _, err := ulid.Parse(d); err != nil {
+			continue
+		}
+		d = path.Join(dir, d)
+
+		meta, err := readBogusMetaFile(d)
+		if err != nil {
+			return err
+		}
+		if meta.Version == 1 {
+			continue
+		}
+		level.Info(logger).Log("msg", "fixing broken block", "ulid", meta.ULID)
+
+		repl, err := os.Create(filepath.Join(d, "index.repaired"))
+		if err != nil {
+			return err
+		}
+		broken, err := os.Open(filepath.Join(d, "index"))
+		if err != nil {
+			return err
+		}
+		if _, err := io.Copy(repl, broken); err != nil {
+			return err
+		}
+		// Set the 5th byte to 2 to indiciate the correct file format version.
+		if _, err := repl.WriteAt([]byte{2}, 4); err != nil {
+			return err
+		}
+		if err := fileutil.Fsync(repl); err != nil {
+			return err
+		}
+		if err := repl.Close(); err != nil {
+			return err
+		}
+		if err := renameFile(repl.Name(), broken.Name()); err != nil {
+			return err
+		}
+		// Reset version of meta.json to 1.
+		meta.Version = 1
+		if err := writeMetaFile(d, meta); err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
+func readBogusMetaFile(dir string) (*BlockMeta, error) {
+	b, err := ioutil.ReadFile(filepath.Join(dir, metaFilename))
+	if err != nil {
+		return nil, err
+	}
+	var m BlockMeta
+
+	if err := json.Unmarshal(b, &m); err != nil {
+		return nil, err
+	}
+	if m.Version != 1 && m.Version != 2 {
+		return nil, errors.Errorf("unexpected meta file version %d", m.Version)
+	}
+	return &m, nil
+}

vendor/vendor.json

@@ -800,40 +800,40 @@
 			"revisionTime": "2016-04-11T19:08:41Z"
 		},
 		{
-			"checksumSHA1": "5mCM640B2xa7y+kRRUeVCglEk7o=",
+			"checksumSHA1": "CeD8QwiLL5CBkWMOfbaJxs4AFuM=",
 			"path": "github.com/prometheus/tsdb",
-			"revision": "44dd5e1202b7598d50c69ce3617ca6ae6503cf52",
-			"revisionTime": "2018-01-26T14:54:38Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
-			"checksumSHA1": "XTirmk6Pq5TBGIZEaN5VL4k3i1s=",
+			"checksumSHA1": "4X26TfLh8M4WuCFo/5a+Qk+ieSw=",
 			"path": "github.com/prometheus/tsdb/chunkenc",
-			"revision": "467948f3c3f2f6f4ed9881afba27dd3ae24393eb",
-			"revisionTime": "2018-01-18T08:32:54Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
 			"checksumSHA1": "+zsn1i8cqwgZXL8Bg6jDy32xjAo=",
 			"path": "github.com/prometheus/tsdb/chunks",
-			"revision": "467948f3c3f2f6f4ed9881afba27dd3ae24393eb",
-			"revisionTime": "2018-01-18T08:32:54Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
 			"checksumSHA1": "h49AAcJ5+iRBwCgbfQf+2T1E1ZE=",
 			"path": "github.com/prometheus/tsdb/fileutil",
-			"revision": "467948f3c3f2f6f4ed9881afba27dd3ae24393eb",
-			"revisionTime": "2018-01-18T08:32:54Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
-			"checksumSHA1": "yuiJaE3cAmZ/ws8NOfd56x36Sg4=",
+			"checksumSHA1": "Cpumd1FEx22Kz8I3HrhMPrSRPNA=",
 			"path": "github.com/prometheus/tsdb/index",
-			"revision": "467948f3c3f2f6f4ed9881afba27dd3ae24393eb",
-			"revisionTime": "2018-01-18T08:32:54Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
 			"checksumSHA1": "Va8HWvOFTwFeewZFadMAOzNGDps=",
 			"path": "github.com/prometheus/tsdb/labels",
-			"revision": "467948f3c3f2f6f4ed9881afba27dd3ae24393eb",
-			"revisionTime": "2018-01-18T08:32:54Z"
+			"revision": "bc49a665d16326ad6ad078b97e0f903d894f80f8",
+			"revisionTime": "2018-02-12T10:58:46Z"
 		},
 		{
 			"checksumSHA1": "5SYLEhADhdBVZAGPVHWggQl7H8k=",