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Merge pull request #6475 from prometheus/constant-compaction 

Constant memory compaction
This commit is contained in:
Brian Brazil 2019-12-18 13:22:02 +00:00 committed by GitHub
parent 2d7c8069d0 2b653ee230
commit 92f31c3ec2
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 277 additions and 154 deletions
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4
tsdb/block.go
View File

@ -50,10 +50,6 @@ type IndexWriter interface {
// are added later.
AddSeries(ref uint64, l labels.Labels, chunks ...chunks.Meta) error
// WriteLabelIndex serializes an index from label names to values.
// The passed in values chained tuples of strings of the length of names.
WriteLabelIndex(names []string, values []string) error
// Close writes any finalization and closes the resources associated with
// the underlying writer.
Close() error

27
tsdb/compact.go
View File

@ -722,11 +722,6 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
symbols = newMergedStringIter(symbols, syms)
}
var (
values = map[string]stringset{}
ref = uint64(0)
)
for symbols.Next() {
if err := indexw.AddSymbol(symbols.At()); err != nil {
return errors.Wrap(err, "add symbol")
@ -737,6 +732,7 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
}
delIter := &deletedIterator{}
ref := uint64(0)
for set.Next() {
select {
case <-c.ctx.Done():
@ -836,33 +832,12 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
}
}
for _, l := range lset {
valset, ok := values[l.Name]
if !ok {
valset = stringset{}
values[l.Name] = valset
}
valset.set(l.Value)
}
ref++
}
if set.Err() != nil {
return errors.Wrap(set.Err(), "iterate compaction set")
}
s := make([]string, 0, 256)
for n, v := range values {
s = s[:0]
for x := range v {
s = append(s, x)
}
if err := indexw.WriteLabelIndex([]string{n}, s); err != nil {
return errors.Wrap(err, "write label index")
}
}
return nil
}

374
tsdb/index/index.go
View File

@ -15,6 +15,7 @@ package index
import (
"bufio"
"bytes"
"context"
"encoding/binary"
"hash"
@ -70,8 +71,6 @@ const (
idxStageNone indexWriterStage = iota
idxStageSymbols
idxStageSeries
idxStageLabelIndex
idxStagePostings
idxStageDone
)
@ -83,10 +82,6 @@ func (s indexWriterStage) String() string {
return "symbols"
case idxStageSeries:
return "series"
case idxStageLabelIndex:
return "label index"
case idxStagePostings:
return "postings"
case idxStageDone:
return "done"
}
@ -111,13 +106,20 @@ func newCRC32() hash.Hash32 {
// Writer implements the IndexWriter interface for the standard
// serialization format.
type Writer struct {
ctx context.Context
f *os.File
fbuf *bufio.Writer
pos uint64
ctx context.Context
toc TOC
stage indexWriterStage
// For the main index file.
f *fileWriter
// Temporary file for postings.
fP *fileWriter
// Temporary file for posting offsets table.
fPO *fileWriter
cntPO uint64
toc TOC
stage indexWriterStage
postingsStart uint64 // Due to padding, can differ from TOC entry.
// Reusable memory.
buf1 encoding.Encbuf
@ -128,9 +130,8 @@ type Writer struct {
symbolFile *fileutil.MmapFile
lastSymbol string
labelIndexes []labelIndexHashEntry // label index offsets
postings []postingsHashEntry // postings lists offsets
labelNames map[string]uint64 // label names, and their usage
labelIndexes []labelIndexHashEntry // Label index offsets.
labelNames map[string]uint64 // Label names, and their usage.
// Hold last series to validate that clients insert new series in order.
lastSeries labels.Labels
@ -193,7 +194,18 @@ func NewWriter(ctx context.Context, fn string) (*Writer, error) {
return nil, errors.Wrap(err, "remove any existing index at path")
}
f, err := os.OpenFile(fn, os.O_CREATE|os.O_WRONLY, 0666)
// Main index file we are building.
f, err := newFileWriter(fn)
if err != nil {
return nil, err
}
// Temporary file for postings.
fP, err := newFileWriter(fn + "_tmp_p")
if err != nil {
return nil, err
}
// Temporary file for posting offset table.
fPO, err := newFileWriter(fn + "_tmp_po")
if err != nil {
return nil, err
}
@ -204,15 +216,14 @@ func NewWriter(ctx context.Context, fn string) (*Writer, error) {
iw := &Writer{
ctx: ctx,
f: f,
fbuf: bufio.NewWriterSize(f, 1<<22),
pos: 0,
fP: fP,
fPO: fPO,
stage: idxStageNone,
// Reusable memory.
buf1: encoding.Encbuf{B: make([]byte, 0, 1<<22)},
buf2: encoding.Encbuf{B: make([]byte, 0, 1<<22)},
// Caches.
labelNames: make(map[string]uint64, 1<<8),
crc32: newCRC32(),
}
@ -223,9 +234,41 @@ func NewWriter(ctx context.Context, fn string) (*Writer, error) {
}
func (w *Writer) write(bufs ...[]byte) error {
return w.f.write(bufs...)
}
func (w *Writer) writeAt(buf []byte, pos uint64) error {
return w.f.writeAt(buf, pos)
}
func (w *Writer) addPadding(size int) error {
return w.f.addPadding(size)
}
type fileWriter struct {
f *os.File
fbuf *bufio.Writer
pos uint64
name string
}
func newFileWriter(name string) (*fileWriter, error) {
f, err := os.OpenFile(name, os.O_CREATE|os.O_RDWR, 0666)
if err != nil {
return nil, err
}
return &fileWriter{
f: f,
fbuf: bufio.NewWriterSize(f, 1<<22),
pos: 0,
name: name,
}, nil
}
func (fw *fileWriter) write(bufs ...[]byte) error {
for _, b := range bufs {
n, err := w.fbuf.Write(b)
w.pos += uint64(n)
n, err := fw.fbuf.Write(b)
fw.pos += uint64(n)
if err != nil {
return err
}
@ -233,29 +276,47 @@ func (w *Writer) write(bufs ...[]byte) error {
// offset references in v1 are only 4 bytes large.
// Once we move to compressed/varint representations in those areas, this limitation
// can be lifted.
if w.pos > 16*math.MaxUint32 {
return errors.Errorf("exceeding max size of 64GiB")
if fw.pos > 16*math.MaxUint32 {
return errors.Errorf("%q exceeding max size of 64GiB", fw.name)
}
}
return nil
}
func (w *Writer) writeAt(buf []byte, pos uint64) error {
if err := w.fbuf.Flush(); err != nil {
func (fw *fileWriter) flush() error {
return fw.fbuf.Flush()
}
func (fw *fileWriter) writeAt(buf []byte, pos uint64) error {
if err := fw.flush(); err != nil {
return err
}
_, err := w.f.WriteAt(buf, int64(pos))
_, err := fw.f.WriteAt(buf, int64(pos))
return err
}
// 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)
func (fw *fileWriter) addPadding(size int) error {
p := fw.pos % uint64(size)
if p == 0 {
return nil
}
p = uint64(size) - p
return errors.Wrap(w.write(make([]byte, p)), "add padding")
return errors.Wrap(fw.write(make([]byte, p)), "add padding")
}
func (fw *fileWriter) close() error {
if err := fw.flush(); err != nil {
return err
}
if err := fw.f.Sync(); err != nil {
return err
}
return fw.f.Close()
}
func (fw *fileWriter) remove() error {
return os.Remove(fw.name)
}
// ensureStage handles transitions between write stages and ensures that IndexWriter
@ -270,6 +331,12 @@ func (w *Writer) ensureStage(s indexWriterStage) error {
if w.stage == s {
return nil
}
if w.stage < s-1 {
// A stage has been skipped.
if err := w.ensureStage(s - 1); err != nil {
return err
}
}
if w.stage > s {
return errors.Errorf("invalid stage %q, currently at %q", s, w.stage)
}
@ -277,7 +344,7 @@ func (w *Writer) ensureStage(s indexWriterStage) error {
// Mark start of sections in table of contents.
switch s {
case idxStageSymbols:
w.toc.Symbols = w.pos
w.toc.Symbols = w.f.pos
if err := w.startSymbols(); err != nil {
return err
}
@ -285,22 +352,30 @@ func (w *Writer) ensureStage(s indexWriterStage) error {
if err := w.finishSymbols(); err != nil {
return err
}
w.toc.Series = w.pos
case idxStageLabelIndex:
w.toc.LabelIndices = w.pos
w.toc.Series = w.f.pos
case idxStageDone:
w.toc.Postings = w.pos
w.toc.LabelIndices = w.f.pos
// LabelIndices generation depends on the posting offset
// table produced at this stage.
if err := w.writePostingsToTmpFiles(); err != nil {
return err
}
if err := w.writeLabelIndices(); err != nil {
return err
}
w.toc.Postings = w.f.pos
if err := w.writePostings(); err != nil {
return err
}
w.toc.LabelIndicesTable = w.pos
w.toc.LabelIndicesTable = w.f.pos
if err := w.writeLabelIndexesOffsetTable(); err != nil {
return err
}
w.toc.PostingsTable = w.pos
w.toc.PostingsTable = w.f.pos
if err := w.writePostingsOffsetTable(); err != nil {
return err
}
@ -339,15 +414,14 @@ func (w *Writer) AddSeries(ref uint64, lset labels.Labels, chunks ...chunks.Meta
return errors.Errorf("failed to write padding bytes: %v", err)
}
if w.pos%16 != 0 {
return errors.Errorf("series write not 16-byte aligned at %d", w.pos)
if w.f.pos%16 != 0 {
return errors.Errorf("series write not 16-byte aligned at %d", w.f.pos)
}
w.buf2.Reset()
w.buf2.PutUvarint(len(lset))
for _, l := range lset {
// here we have an index for the symbol file if v2, otherwise it's an offset
index, err := w.symbols.ReverseLookup(l.Name)
if err != nil {
return errors.Errorf("symbol entry for %q does not exist, %v", l.Name, err)
@ -421,24 +495,24 @@ func (w *Writer) AddSymbol(sym string) error {
func (w *Writer) finishSymbols() error {
// Write out the length and symbol count.
w.buf1.Reset()
w.buf1.PutBE32int(int(w.pos - w.toc.Symbols - 4))
w.buf1.PutBE32int(int(w.f.pos - w.toc.Symbols - 4))
w.buf1.PutBE32int(int(w.numSymbols))
if err := w.writeAt(w.buf1.Get(), w.toc.Symbols); err != nil {
return err
}
hashPos := w.pos
hashPos := w.f.pos
// Leave space for the hash. We can only calculate it
// now that the number of symbols is known, so mmap and do it from there.
if err := w.write([]byte("hash")); err != nil {
return err
}
if err := w.fbuf.Flush(); err != nil {
if err := w.f.flush(); err != nil {
return err
}
var err error
w.symbolFile, err = fileutil.OpenMmapFile(w.f.Name())
w.symbolFile, err = fileutil.OpenMmapFile(w.f.name)
if err != nil {
return err
}
@ -457,31 +531,71 @@ func (w *Writer) finishSymbols() error {
return nil
}
func (w *Writer) WriteLabelIndex(names []string, values []string) error {
if len(values)%len(names) != 0 {
return errors.Errorf("invalid value list length %d for %d names", len(values), len(names))
}
if err := w.ensureStage(idxStageLabelIndex); err != nil {
return errors.Wrap(err, "ensure stage")
func (w *Writer) writeLabelIndices() error {
if err := w.fPO.flush(); err != nil {
return err
}
valt, err := NewStringTuples(values, len(names))
// Find all the label values in the tmp posting offset table.
f, err := fileutil.OpenMmapFile(w.fPO.name)
if err != nil {
return err
}
sort.Sort(valt)
defer f.Close()
d := encoding.NewDecbufRaw(realByteSlice(f.Bytes()), int(w.fPO.pos))
cnt := w.cntPO
current := []byte{}
values := []uint32{}
for d.Err() == nil && cnt > 0 {
cnt--
d.Uvarint() // Keycount.
name := d.UvarintBytes() // Label name.
value := yoloString(d.UvarintBytes()) // Label value.
d.Uvarint64() // Offset.
if len(name) == 0 {
continue // All index is ignored.
}
if !bytes.Equal(name, current) && len(values) > 0 {
// We've reached a new label name.
if err := w.writeLabelIndex(string(current), values); err != nil {
return err
}
values = values[:0]
}
current = name
sid, err := w.symbols.ReverseLookup(value)
if err != nil {
return err
}
values = append(values, sid)
}
if d.Err() != nil {
return d.Err()
}
// Handle the last label.
if len(values) > 0 {
if err := w.writeLabelIndex(string(current), values); err != nil {
return err
}
}
return nil
}
func (w *Writer) writeLabelIndex(name string, values []uint32) error {
// Align beginning to 4 bytes for more efficient index list scans.
if err := w.addPadding(4); err != nil {
return err
}
w.labelIndexes = append(w.labelIndexes, labelIndexHashEntry{
keys: names,
offset: w.pos,
keys: []string{name},
offset: w.f.pos,
})
startPos := w.pos
startPos := w.f.pos
// Leave 4 bytes of space for the length, which will be calculated later.
if err := w.write([]byte("alen")); err != nil {
return err
@ -489,21 +603,16 @@ func (w *Writer) WriteLabelIndex(names []string, values []string) error {
w.crc32.Reset()
w.buf1.Reset()
w.buf1.PutBE32int(len(names))
w.buf1.PutBE32int(valt.Len())
w.buf1.PutBE32int(1) // Number of names.
w.buf1.PutBE32int(len(values))
w.buf1.WriteToHash(w.crc32)
if err := w.write(w.buf1.Get()); err != nil {
return err
}
// here we have an index for the symbol file if v2, otherwise it's an offset
for _, v := range valt.entries {
sid, err := w.symbols.ReverseLookup(v)
if err != nil {
return errors.Errorf("symbol entry for %q does not exist: %v", v, err)
}
for _, v := range values {
w.buf1.Reset()
w.buf1.PutBE32(sid)
w.buf1.PutBE32(v)
w.buf1.WriteToHash(w.crc32)
if err := w.write(w.buf1.Get()); err != nil {
return err
@ -512,7 +621,7 @@ func (w *Writer) WriteLabelIndex(names []string, values []string) error {
// Write out the length.
w.buf1.Reset()
w.buf1.PutBE32int(int(w.pos - startPos - 4))
w.buf1.PutBE32int(int(w.f.pos - startPos - 4))
if err := w.writeAt(w.buf1.Get(), startPos); err != nil {
return err
}
@ -524,7 +633,7 @@ func (w *Writer) WriteLabelIndex(names []string, values []string) error {
// writeLabelIndexesOffsetTable writes the label indices offset table.
func (w *Writer) writeLabelIndexesOffsetTable() error {
startPos := w.pos
startPos := w.f.pos
// Leave 4 bytes of space for the length, which will be calculated later.
if err := w.write([]byte("alen")); err != nil {
return err
@ -552,7 +661,7 @@ func (w *Writer) writeLabelIndexesOffsetTable() error {
}
// Write out the length.
w.buf1.Reset()
w.buf1.PutBE32int(int(w.pos - startPos - 4))
w.buf1.PutBE32int(int(w.f.pos - startPos - 4))
if err := w.writeAt(w.buf1.Get(), startPos); err != nil {
return err
}
@ -564,39 +673,69 @@ func (w *Writer) writeLabelIndexesOffsetTable() error {
// writePostingsOffsetTable writes the postings offset table.
func (w *Writer) writePostingsOffsetTable() error {
startPos := w.pos
// Ensure everything is in the temporary file.
if err := w.fPO.flush(); err != nil {
return err
}
startPos := w.f.pos
// Leave 4 bytes of space for the length, which will be calculated later.
if err := w.write([]byte("alen")); err != nil {
return err
}
w.crc32.Reset()
// Copy over the tmp posting offset table, however we need to
// adjust the offsets.
adjustment := w.postingsStart
w.buf1.Reset()
w.buf1.PutBE32int(len(w.postings))
w.crc32.Reset()
w.buf1.PutBE32int(int(w.cntPO)) // Count.
w.buf1.WriteToHash(w.crc32)
if err := w.write(w.buf1.Get()); err != nil {
return err
}
for _, e := range w.postings {
f, err := fileutil.OpenMmapFile(w.fPO.name)
if err != nil {
return err
}
defer f.Close()
d := encoding.NewDecbufRaw(realByteSlice(f.Bytes()), int(w.fPO.pos))
cnt := w.cntPO
for d.Err() == nil && cnt > 0 {
w.buf1.Reset()
w.buf1.PutUvarint(2)
w.buf1.PutUvarintStr(e.name)
w.buf1.PutUvarintStr(e.value)
w.buf1.PutUvarint64(e.offset)
w.buf1.PutUvarint(d.Uvarint()) // Keycount.
w.buf1.PutUvarintStr(yoloString(d.UvarintBytes())) // Label name.
w.buf1.PutUvarintStr(yoloString(d.UvarintBytes())) // Label value.
w.buf1.PutUvarint64(d.Uvarint64() + adjustment) // Offset.
w.buf1.WriteToHash(w.crc32)
if err := w.write(w.buf1.Get()); err != nil {
return err
}
cnt--
}
if d.Err() != nil {
return d.Err()
}
// Cleanup temporary file.
if err := w.fPO.close(); err != nil {
return err
}
if err := w.fPO.remove(); err != nil {
return err
}
w.fPO = nil
// Write out the length.
w.buf1.Reset()
w.buf1.PutBE32int(int(w.pos - startPos - 4))
w.buf1.PutBE32int(int(w.f.pos - startPos - 4))
if err := w.writeAt(w.buf1.Get(), startPos); err != nil {
return err
}
// Finally write the hash.
w.buf1.Reset()
w.buf1.PutHashSum(w.crc32)
return w.write(w.buf1.Get())
@ -619,17 +758,17 @@ func (w *Writer) writeTOC() error {
return w.write(w.buf1.Get())
}
func (w *Writer) writePostings() error {
func (w *Writer) writePostingsToTmpFiles() error {
names := make([]string, 0, len(w.labelNames))
for n := range w.labelNames {
names = append(names, n)
}
sort.Strings(names)
if err := w.fbuf.Flush(); err != nil {
if err := w.f.flush(); err != nil {
return err
}
f, err := fileutil.OpenMmapFile(w.f.Name())
f, err := fileutil.OpenMmapFile(w.f.name)
if err != nil {
return err
}
@ -647,9 +786,10 @@ func (w *Writer) writePostings() error {
}
offsets = append(offsets, uint32(startPos/16))
// Skip to next series.
d.Skip(d.Uvarint() + crc32.Size)
x := d.Uvarint()
d.Skip(x + crc32.Size)
if err := d.Err(); err != nil {
return nil
return err
}
}
if err := w.writePosting("", "", offsets); err != nil {
@ -745,15 +885,20 @@ func (w *Writer) writePostings() error {
func (w *Writer) writePosting(name, value string, offs []uint32) error {
// Align beginning to 4 bytes for more efficient postings list scans.
if err := w.addPadding(4); err != nil {
if err := w.fP.addPadding(4); err != nil {
return err
}
w.postings = append(w.postings, postingsHashEntry{
name: name,
value: value,
offset: w.pos,
})
// Write out postings offset table to temporary file as we go.
w.buf1.Reset()
w.buf1.PutUvarint(2)
w.buf1.PutUvarintStr(name)
w.buf1.PutUvarintStr(value)
w.buf1.PutUvarint64(w.fP.pos) // This is relative to the postings tmp file, not the final index file.
if err := w.fPO.write(w.buf1.Get()); err != nil {
return err
}
w.cntPO++
w.buf1.Reset()
w.buf1.PutBE32int(len(offs))
@ -768,7 +913,41 @@ func (w *Writer) writePosting(name, value string, offs []uint32) error {
w.buf2.Reset()
w.buf2.PutBE32int(w.buf1.Len())
w.buf1.PutHash(w.crc32)
return w.write(w.buf2.Get(), w.buf1.Get())
return w.fP.write(w.buf2.Get(), w.buf1.Get())
}
func (w *Writer) writePostings() error {
// There's padding in the tmp file, make sure it actually works.
if err := w.f.addPadding(4); err != nil {
return err
}
w.postingsStart = w.f.pos
// Copy temporary file into main index.
if err := w.fP.flush(); err != nil {
return err
}
if _, err := w.fP.f.Seek(0, 0); err != nil {
return err
}
// Don't need to calculate a checksum, so can copy directly.
n, err := io.CopyBuffer(w.f.fbuf, w.fP.f, make([]byte, 1<<20))
if err != nil {
return err
}
if uint64(n) != w.fP.pos {
return errors.Errorf("wrote %d bytes to posting temporary file, but only read back %d", w.fP.pos, n)
}
w.f.pos += uint64(n)
if err := w.fP.close(); err != nil {
return err
}
if err := w.fP.remove(); err != nil {
return err
}
w.fP = nil
return nil
}
type uint32slice []uint32
@ -782,11 +961,6 @@ type labelIndexHashEntry struct {
offset uint64
}
type postingsHashEntry struct {
name, value string
offset uint64
}
func (w *Writer) Close() error {
if err := w.ensureStage(idxStageDone); err != nil {
return err
@ -796,13 +970,17 @@ func (w *Writer) Close() error {
return err
}
}
if err := w.fbuf.Flush(); err != nil {
return err
if w.fP != nil {
if err := w.fP.close(); err != nil {
return err
}
}
if err := w.f.Sync(); err != nil {
return err
if w.fPO != nil {
if err := w.fPO.close(); err != nil {
return err
}
}
return w.f.Close()
return w.f.close()
}
// StringTuples provides access to a sorted list of string tuples.

26
tsdb/index/index_test.go
View File

@ -83,16 +83,6 @@ func (m mockIndex) AddSeries(ref uint64, l labels.Labels, chunks ...chunks.Meta)
return nil
}
func (m mockIndex) WriteLabelIndex(names []string, values []string) error {
// TODO support composite indexes
if len(names) != 1 {
return errors.New("composite indexes not supported yet")
}
sort.Strings(values)
m.labelIndex[names[0]] = values
return nil
}
func (m mockIndex) Close() error {
return nil
}
@ -200,9 +190,6 @@ func TestIndexRW_Postings(t *testing.T) {
testutil.Ok(t, iw.AddSeries(3, series[2]))
testutil.Ok(t, iw.AddSeries(4, series[3]))
testutil.Ok(t, iw.WriteLabelIndex([]string{"a"}, []string{"1"}))
testutil.Ok(t, iw.WriteLabelIndex([]string{"b"}, []string{"1", "2", "3", "4"}))
testutil.Ok(t, iw.Close())
ir, err := NewFileReader(fn)
@ -289,8 +276,6 @@ func TestPostingsMany(t *testing.T) {
for i, s := range series {
testutil.Ok(t, iw.AddSeries(uint64(i), s))
}
err = iw.WriteLabelIndex([]string{"foo"}, []string{"bar"})
testutil.Ok(t, err)
testutil.Ok(t, iw.Close())
ir, err := NewFileReader(fn)
@ -427,17 +412,6 @@ func TestPersistence_index_e2e(t *testing.T) {
postings.Add(uint64(i), s.labels)
}
for k, v := range values {
var vals []string
for e := range v {
vals = append(vals, e)
}
sort.Strings(vals)
testutil.Ok(t, iw.WriteLabelIndex([]string{k}, vals))
testutil.Ok(t, mi.WriteLabelIndex([]string{k}, vals))
}
err = iw.Close()
testutil.Ok(t, err)