prometheus/tsdb/chunks/chunks.go

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// Copyright 2017 The Prometheus Authors
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
package chunks
import (
"bufio"
"bytes"
"encoding/binary"
"fmt"
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"hash"
"hash/crc32"
"io"
"os"
"path/filepath"
"strconv"
"github.com/pkg/errors"
"github.com/prometheus/prometheus/tsdb/chunkenc"
tsdb_errors "github.com/prometheus/prometheus/tsdb/errors"
"github.com/prometheus/prometheus/tsdb/fileutil"
)
// Segment header fields constants.
const (
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// MagicChunks is 4 bytes at the head of a series file.
MagicChunks = 0x85BD40DD
// MagicChunksSize is the size in bytes of MagicChunks.
MagicChunksSize = 4
chunksFormatV1 = 1
ChunksFormatVersionSize = 1
segmentHeaderPaddingSize = 3
// SegmentHeaderSize defines the total size of the header part.
SegmentHeaderSize = MagicChunksSize + ChunksFormatVersionSize + segmentHeaderPaddingSize
)
// Chunk fields constants.
const (
// MaxChunkLengthFieldSize defines the maximum size of the data length part.
MaxChunkLengthFieldSize = binary.MaxVarintLen32
// ChunkEncodingSize defines the size of the chunk encoding part.
ChunkEncodingSize = 1
)
// ChunkRef is a generic reference for reading chunk data. In prometheus it
// is either a HeadChunkRef or BlockChunkRef, though other implementations
// may have their own reference types.
type ChunkRef uint64
// HeadSeriesRef refers to in-memory series.
type HeadSeriesRef uint64
// HeadChunkRef packs a HeadSeriesRef and a ChunkID into a global 8 Byte ID.
// The HeadSeriesRef and ChunkID may not exceed 5 and 3 bytes respectively.
type HeadChunkRef uint64
func NewHeadChunkRef(hsr HeadSeriesRef, chunkID HeadChunkID) HeadChunkRef {
if hsr > (1<<40)-1 {
panic("series ID exceeds 5 bytes")
}
if chunkID > (1<<24)-1 {
panic("chunk ID exceeds 3 bytes")
}
return HeadChunkRef(uint64(hsr<<24) | uint64(chunkID))
}
func (p HeadChunkRef) Unpack() (HeadSeriesRef, HeadChunkID) {
return HeadSeriesRef(p >> 24), HeadChunkID(p<<40) >> 40
}
// HeadChunkID refers to a specific chunk in a series (memSeries) in the Head.
// Each memSeries has its own monotonically increasing number to refer to its chunks.
// If the HeadChunkID value is...
// * memSeries.firstChunkID+len(memSeries.mmappedChunks), it's the head chunk.
// * less than the above, but >= memSeries.firstID, then it's
// memSeries.mmappedChunks[i] where i = HeadChunkID - memSeries.firstID.
// Example:
// assume a memSeries.firstChunkID=7 and memSeries.mmappedChunks=[p5,p6,p7,p8,p9].
// | HeadChunkID value | refers to ... |
// |-------------------|----------------------------------------------------------------------------------------|
// | 0-6 | chunks that have been compacted to blocks, these won't return data for queries in Head |
// | 7-11 | memSeries.mmappedChunks[i] where i is 0 to 4. |
// | 12 | memSeries.headChunk |
type HeadChunkID uint64
// BlockChunkRef refers to a chunk within a persisted block.
// The upper 4 bytes are for the segment index and
// the lower 4 bytes are for the segment offset where the data starts for this chunk.
type BlockChunkRef uint64
// NewBlockChunkRef packs the file index and byte offset into a BlockChunkRef.
func NewBlockChunkRef(fileIndex, fileOffset uint64) BlockChunkRef {
return BlockChunkRef(fileIndex<<32 | fileOffset)
}
func (b BlockChunkRef) Unpack() (int, int) {
sgmIndex := int(b >> 32)
chkStart := int((b << 32) >> 32)
return sgmIndex, chkStart
}
// Meta holds information about a chunk of data.
type Meta struct {
// Ref and Chunk hold either a reference that can be used to retrieve
// chunk data or the data itself.
// If Chunk is nil, call ChunkReader.Chunk(Meta.Ref) to get the chunk and assign it to the Chunk field
Ref ChunkRef
Chunk chunkenc.Chunk
// Time range the data covers.
// When MaxTime == math.MaxInt64 the chunk is still open and being appended to.
MinTime, MaxTime int64
}
Add basic initial developer docs for TSDB (#9451) * Add basic initial developer docs for TSDB There's a decent amount of content already out there (blog posts, conference talks, etc), but: * when they get stale, they don't tend to get updated * they still leave me with questions that I'ld like to answer for developers (like me) who want to use, or work with, TSDB What I propose is developer docs inside the prometheus repository. Easy to find and harness the power of the community to expand it and keep it up to date. * perfect is the enemy of good. Let's have a base and incrementally improve * Markdown docs should be broad but not too deep. Source code comments can complement them, and are the ideal place for implementation details. Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * use example code that works out of the box Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * Apply suggestions from code review Co-authored-by: Ganesh Vernekar <15064823+codesome@users.noreply.github.com> Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * PR feedback Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * more docs Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * PR feedback Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * Apply suggestions from code review Signed-off-by: Dieter Plaetinck <dieter@grafana.com> Co-authored-by: Bartlomiej Plotka <bwplotka@gmail.com> * Apply suggestions from code review Signed-off-by: Dieter Plaetinck <dieter@grafana.com> Co-authored-by: Ganesh Vernekar <15064823+codesome@users.noreply.github.com> * feedback Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * Update tsdb/docs/usage.md Signed-off-by: Dieter Plaetinck <dieter@grafana.com> Co-authored-by: Ganesh Vernekar <15064823+codesome@users.noreply.github.com> * final tweaks Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * workaround docs versioning issue Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * Move example code to real executable, testable example. Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * cleanup example test and make sure it always reproduces Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * obtain temp dir in a way that works with older Go versions Signed-off-by: Dieter Plaetinck <dieter@grafana.com> * Fix Ganesh's comments Signed-off-by: Ganesh Vernekar <ganeshvern@gmail.com> Co-authored-by: Ganesh Vernekar <15064823+codesome@users.noreply.github.com> Co-authored-by: Bartlomiej Plotka <bwplotka@gmail.com> Co-authored-by: Ganesh Vernekar <ganeshvern@gmail.com>
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// Iterator iterates over the chunks of a single time series.
storage: Added Chunks{Queryable/Querier/SeriesSet/Series/Iteratable. Added generic Merge{SeriesSet/Querier} implementation. (#7005) * storage: Added Chunks{Queryable/Querier/SeriesSet/Series/Iteratable. Added generic Merge{SeriesSet/Querier} implementation. ## Rationales: In many places (e.g. chunk Remote read, Thanos Receive fetching chunk from TSDB), we operate on encoded chunks not samples. This means that we unnecessary decode/encode, wasting CPU, time and memory. This PR adds chunk iterator interfaces and makes the merge code to be reused between both seriesSets I will make the use of it in following PR inside tsdb itself. For now fanout implements it and mergers. All merges now also allows passing series mergers. This opens doors for custom deduplications other than TSDB vertical ones (e.g. offline one we have in Thanos). ## Changes * Added Chunk versions of all iterating methods. It all starts in Querier/ChunkQuerier. The plan is that Storage will implement both chunked and samples. * Added Seek to chunks.Iterator interface for iterating over chunks. * NewMergeChunkQuerier was added; Both this and NewMergeQuerier are now using generigMergeQuerier to share the code. Generic code was added. * Improved tests. * Added some TODO for further simplifications in next PRs. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com> * Addressed Brian's comments. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com> * Moved s/Labeled/SeriesLabels as per Krasi suggestion. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com> * Addressed Krasi's comments. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com> * Second iteration of Krasi comments. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com> * Another round of comments. Signed-off-by: Bartlomiej Plotka <bwplotka@gmail.com>
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type Iterator interface {
// At returns the current meta.
// It depends on implementation if the chunk is populated or not.
At() Meta
// Next advances the iterator by one.
Next() bool
// Err returns optional error if Next is false.
Err() error
}
// writeHash writes the chunk encoding and raw data into the provided hash.
func (cm *Meta) writeHash(h hash.Hash, buf []byte) error {
buf = append(buf[:0], byte(cm.Chunk.Encoding()))
if _, err := h.Write(buf[:1]); err != nil {
return err
}
if _, err := h.Write(cm.Chunk.Bytes()); err != nil {
return err
}
return nil
}
// OverlapsClosedInterval Returns true if the chunk overlaps [mint, maxt].
func (cm *Meta) OverlapsClosedInterval(mint, maxt int64) bool {
// The chunk itself is a closed interval [cm.MinTime, cm.MaxTime].
return cm.MinTime <= maxt && mint <= cm.MaxTime
}
var errInvalidSize = fmt.Errorf("invalid size")
var castagnoliTable *crc32.Table
func init() {
castagnoliTable = crc32.MakeTable(crc32.Castagnoli)
}
// newCRC32 initializes a CRC32 hash with a preconfigured polynomial, so the
// polynomial may be easily changed in one location at a later time, if necessary.
func newCRC32() hash.Hash32 {
return crc32.New(castagnoliTable)
}
// Writer implements the ChunkWriter interface for the standard
// serialization format.
type Writer struct {
dirFile *os.File
files []*os.File
wbuf *bufio.Writer
n int64
crc32 hash.Hash
buf [binary.MaxVarintLen32]byte
segmentSize int64
}
const (
// DefaultChunkSegmentSize is the default chunks segment size.
DefaultChunkSegmentSize = 512 * 1024 * 1024
)
// NewWriterWithSegSize returns a new writer against the given directory
// and allows setting a custom size for the segments.
func NewWriterWithSegSize(dir string, segmentSize int64) (*Writer, error) {
return newWriter(dir, segmentSize)
}
// NewWriter returns a new writer against the given directory
// using the default segment size.
func NewWriter(dir string) (*Writer, error) {
return newWriter(dir, DefaultChunkSegmentSize)
}
func newWriter(dir string, segmentSize int64) (*Writer, error) {
if segmentSize <= 0 {
segmentSize = DefaultChunkSegmentSize
}
if err := os.MkdirAll(dir, 0o777); err != nil {
return nil, err
}
dirFile, err := fileutil.OpenDir(dir)
if err != nil {
return nil, err
}
return &Writer{
dirFile: dirFile,
n: 0,
crc32: newCRC32(),
segmentSize: segmentSize,
}, nil
}
func (w *Writer) tail() *os.File {
if len(w.files) == 0 {
return nil
}
return w.files[len(w.files)-1]
}
// finalizeTail writes all pending data to the current tail file,
// truncates its size, and closes it.
func (w *Writer) finalizeTail() error {
tf := w.tail()
if tf == nil {
return nil
}
if err := w.wbuf.Flush(); err != nil {
return err
}
if err := tf.Sync(); err != nil {
return err
}
// As the file was pre-allocated, we truncate any superfluous zero bytes.
off, err := tf.Seek(0, io.SeekCurrent)
if err != nil {
return err
}
if err := tf.Truncate(off); err != nil {
return err
}
return tf.Close()
}
func (w *Writer) cut() error {
// Sync current tail to disk and close.
if err := w.finalizeTail(); err != nil {
return err
}
n, f, _, err := cutSegmentFile(w.dirFile, MagicChunks, chunksFormatV1, w.segmentSize)
if err != nil {
return err
}
w.n = int64(n)
w.files = append(w.files, f)
if w.wbuf != nil {
w.wbuf.Reset(f)
} else {
w.wbuf = bufio.NewWriterSize(f, 8*1024*1024)
}
return nil
}
func cutSegmentFile(dirFile *os.File, magicNumber uint32, chunksFormat byte, allocSize int64) (headerSize int, newFile *os.File, seq int, returnErr error) {
p, seq, err := nextSequenceFile(dirFile.Name())
if err != nil {
return 0, nil, 0, errors.Wrap(err, "next sequence file")
}
ptmp := p + ".tmp"
f, err := os.OpenFile(ptmp, os.O_WRONLY|os.O_CREATE, 0o666)
if err != nil {
return 0, nil, 0, errors.Wrap(err, "open temp file")
}
defer func() {
if returnErr != nil {
errs := tsdb_errors.NewMulti(returnErr)
if f != nil {
errs.Add(f.Close())
}
// Calling RemoveAll on a non-existent file does not return error.
errs.Add(os.RemoveAll(ptmp))
returnErr = errs.Err()
}
}()
if allocSize > 0 {
if err = fileutil.Preallocate(f, allocSize, true); err != nil {
return 0, nil, 0, errors.Wrap(err, "preallocate")
}
}
if err = dirFile.Sync(); err != nil {
return 0, nil, 0, errors.Wrap(err, "sync directory")
}
// Write header metadata for new file.
metab := make([]byte, SegmentHeaderSize)
binary.BigEndian.PutUint32(metab[:MagicChunksSize], magicNumber)
metab[4] = chunksFormat
n, err := f.Write(metab)
if err != nil {
return 0, nil, 0, errors.Wrap(err, "write header")
}
if err := f.Close(); err != nil {
return 0, nil, 0, errors.Wrap(err, "close temp file")
}
f = nil
if err := fileutil.Rename(ptmp, p); err != nil {
return 0, nil, 0, errors.Wrap(err, "replace file")
}
f, err = os.OpenFile(p, os.O_WRONLY, 0o666)
if err != nil {
return 0, nil, 0, errors.Wrap(err, "open final file")
}
// Skip header for further writes.
if _, err := f.Seek(int64(n), 0); err != nil {
return 0, nil, 0, errors.Wrap(err, "seek in final file")
}
return n, f, seq, nil
}
func (w *Writer) write(b []byte) error {
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n, err := w.wbuf.Write(b)
w.n += int64(n)
return err
}
// WriteChunks writes as many chunks as possible to the current segment,
// cuts a new segment when the current segment is full and
// writes the rest of the chunks in the new segment.
func (w *Writer) WriteChunks(chks ...Meta) error {
var (
batchSize = int64(0)
batchStart = 0
batches = make([][]Meta, 1)
batchID = 0
firstBatch = true
)
for i, chk := range chks {
// Each chunk contains: data length + encoding + the data itself + crc32
chkSize := int64(MaxChunkLengthFieldSize) // The data length is a variable length field so use the maximum possible value.
chkSize += ChunkEncodingSize // The chunk encoding.
chkSize += int64(len(chk.Chunk.Bytes())) // The data itself.
chkSize += crc32.Size // The 4 bytes of crc32.
batchSize += chkSize
// Cut a new batch when it is not the first chunk(to avoid empty segments) and
// the batch is too large to fit in the current segment.
cutNewBatch := (i != 0) && (batchSize+SegmentHeaderSize > w.segmentSize)
// When the segment already has some data than
// the first batch size calculation should account for that.
if firstBatch && w.n > SegmentHeaderSize {
cutNewBatch = batchSize+w.n > w.segmentSize
if cutNewBatch {
firstBatch = false
}
}
if cutNewBatch {
batchStart = i
batches = append(batches, []Meta{})
batchID++
batchSize = chkSize
}
batches[batchID] = chks[batchStart : i+1]
}
// Create a new segment when one doesn't already exist.
if w.n == 0 {
if err := w.cut(); err != nil {
return err
}
}
for i, chks := range batches {
if err := w.writeChunks(chks); err != nil {
return err
}
// Cut a new segment only when there are more chunks to write.
// Avoid creating a new empty segment at the end of the write.
if i < len(batches)-1 {
if err := w.cut(); err != nil {
return err
}
}
}
return nil
}
// writeChunks writes the chunks into the current segment irrespective
// of the configured segment size limit. A segment should have been already
// started before calling this.
func (w *Writer) writeChunks(chks []Meta) error {
if len(chks) == 0 {
return nil
}
seq := uint64(w.seq())
for i := range chks {
chk := &chks[i]
chk.Ref = ChunkRef(NewBlockChunkRef(seq, uint64(w.n)))
n := binary.PutUvarint(w.buf[:], uint64(len(chk.Chunk.Bytes())))
if err := w.write(w.buf[:n]); err != nil {
return err
}
w.buf[0] = byte(chk.Chunk.Encoding())
if err := w.write(w.buf[:1]); err != nil {
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return err
}
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if err := w.write(chk.Chunk.Bytes()); err != nil {
return err
}
w.crc32.Reset()
if err := chk.writeHash(w.crc32, w.buf[:]); err != nil {
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return err
}
if err := w.write(w.crc32.Sum(w.buf[:0])); err != nil {
return err
}
}
return nil
}
func (w *Writer) seq() int {
return len(w.files) - 1
}
func (w *Writer) Close() error {
if err := w.finalizeTail(); err != nil {
return err
}
// close dir file (if not windows platform will fail on rename)
return w.dirFile.Close()
}
// ByteSlice abstracts a byte slice.
type ByteSlice interface {
Len() int
Range(start, end int) []byte
}
type realByteSlice []byte
func (b realByteSlice) Len() int {
return len(b)
}
func (b realByteSlice) Range(start, end int) []byte {
return b[start:end]
}
// Reader implements a ChunkReader for a serialized byte stream
// of series data.
type Reader struct {
// The underlying bytes holding the encoded series data.
// Each slice holds the data for a different segment.
bs []ByteSlice
cs []io.Closer // Closers for resources behind the byte slices.
size int64 // The total size of bytes in the reader.
pool chunkenc.Pool
}
func newReader(bs []ByteSlice, cs []io.Closer, pool chunkenc.Pool) (*Reader, error) {
cr := Reader{pool: pool, bs: bs, cs: cs}
for i, b := range cr.bs {
if b.Len() < SegmentHeaderSize {
return nil, errors.Wrapf(errInvalidSize, "invalid segment header in segment %d", i)
}
// Verify magic number.
if m := binary.BigEndian.Uint32(b.Range(0, MagicChunksSize)); m != MagicChunks {
return nil, errors.Errorf("invalid magic number %x", m)
}
// Verify chunk format version.
if v := int(b.Range(MagicChunksSize, MagicChunksSize+ChunksFormatVersionSize)[0]); v != chunksFormatV1 {
return nil, errors.Errorf("invalid chunk format version %d", v)
}
cr.size += int64(b.Len())
}
return &cr, nil
}
// NewDirReader returns a new Reader against sequentially numbered files in the
// given directory.
func NewDirReader(dir string, pool chunkenc.Pool) (*Reader, error) {
files, err := sequenceFiles(dir)
if err != nil {
return nil, err
}
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if pool == nil {
pool = chunkenc.NewPool()
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}
var (
bs []ByteSlice
cs []io.Closer
)
for _, fn := range files {
f, err := fileutil.OpenMmapFile(fn)
if err != nil {
return nil, tsdb_errors.NewMulti(
errors.Wrap(err, "mmap files"),
tsdb_errors.CloseAll(cs),
).Err()
}
cs = append(cs, f)
bs = append(bs, realByteSlice(f.Bytes()))
}
reader, err := newReader(bs, cs, pool)
if err != nil {
return nil, tsdb_errors.NewMulti(
err,
tsdb_errors.CloseAll(cs),
).Err()
}
return reader, nil
}
func (s *Reader) Close() error {
return tsdb_errors.CloseAll(s.cs)
}
// Size returns the size of the chunks.
func (s *Reader) Size() int64 {
return s.size
}
// Chunk returns a chunk from a given reference.
func (s *Reader) Chunk(ref ChunkRef) (chunkenc.Chunk, error) {
sgmIndex, chkStart := BlockChunkRef(ref).Unpack()
chkCRC32 := newCRC32()
if sgmIndex >= len(s.bs) {
return nil, errors.Errorf("segment index %d out of range", sgmIndex)
}
sgmBytes := s.bs[sgmIndex]
if chkStart+MaxChunkLengthFieldSize > sgmBytes.Len() {
return nil, errors.Errorf("segment doesn't include enough bytes to read the chunk size data field - required:%v, available:%v", chkStart+MaxChunkLengthFieldSize, sgmBytes.Len())
}
// With the minimum chunk length this should never cause us reading
// over the end of the slice.
c := sgmBytes.Range(chkStart, chkStart+MaxChunkLengthFieldSize)
chkDataLen, n := binary.Uvarint(c)
if n <= 0 {
return nil, errors.Errorf("reading chunk length failed with %d", n)
}
chkEncStart := chkStart + n
chkEnd := chkEncStart + ChunkEncodingSize + int(chkDataLen) + crc32.Size
chkDataStart := chkEncStart + ChunkEncodingSize
chkDataEnd := chkEnd - crc32.Size
if chkEnd > sgmBytes.Len() {
return nil, errors.Errorf("segment doesn't include enough bytes to read the chunk - required:%v, available:%v", chkEnd, sgmBytes.Len())
}
sum := sgmBytes.Range(chkDataEnd, chkEnd)
if _, err := chkCRC32.Write(sgmBytes.Range(chkEncStart, chkDataEnd)); err != nil {
return nil, err
}
if act := chkCRC32.Sum(nil); !bytes.Equal(act, sum) {
return nil, errors.Errorf("checksum mismatch expected:%x, actual:%x", sum, act)
}
chkData := sgmBytes.Range(chkDataStart, chkDataEnd)
chkEnc := sgmBytes.Range(chkEncStart, chkEncStart+ChunkEncodingSize)[0]
return s.pool.Get(chunkenc.Encoding(chkEnc), chkData)
}
func nextSequenceFile(dir string) (string, int, error) {
files, err := os.ReadDir(dir)
if err != nil {
return "", 0, err
}
i := uint64(0)
for _, f := range files {
j, err := strconv.ParseUint(f.Name(), 10, 64)
if err != nil {
continue
}
// It is not necessary that we find the files in number order,
// for example with '1000000' and '200000', '1000000' would come first.
// Though this is a very very race case, we check anyway for the max id.
if j > i {
i = j
}
}
return segmentFile(dir, int(i+1)), int(i + 1), nil
}
func segmentFile(baseDir string, index int) string {
return filepath.Join(baseDir, fmt.Sprintf("%0.6d", index))
}
func sequenceFiles(dir string) ([]string, error) {
files, err := os.ReadDir(dir)
if err != nil {
return nil, err
}
var res []string
for _, fi := range files {
if _, err := strconv.ParseUint(fi.Name(), 10, 64); err != nil {
continue
}
res = append(res, filepath.Join(dir, fi.Name()))
}
return res, nil
}