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Use pre-allocated protobufs during backups. (hypermodeinc#5404)
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Backups convert the values stored in disk into an intermediate format
(for backwards compatibility reasons). This creates a lot of
pb.PostingList and pb.BackupPostingList objects that are discarded
almost immediatly. Using preallocated protobufs (one per thread used by
the stream object) should avoid these allocations altogether.

Fixes DGRAPH-1312
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@martinmr @dna2github
martinmr authored and dna2github committed Jul 18, 2020
1 parent 79b2754 commit 50d8310
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Showing 5 changed files with 55 additions and 23 deletions.
2 changes: 1 addition & 1 deletion go.mod
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Expand Up @@ -16,7 +16,7 @@ require (
github.com/blevesearch/segment v0.0.0-20160915185041-762005e7a34f // indirect
github.com/blevesearch/snowballstem v0.0.0-20180110192139-26b06a2c243d // indirect
github.com/codahale/hdrhistogram v0.0.0-20161010025455-3a0bb77429bd
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515210839-ef28ef36b592
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200522174526-6eaa5009af27
github.com/dgraph-io/dgo/v200 v200.0.0-20200401175452-e463f9234453
github.com/dgraph-io/ristretto v0.0.2
github.com/dgrijalva/jwt-go v3.2.0+incompatible
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18 changes: 8 additions & 10 deletions go.sum
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Original file line number Diff line number Diff line change
Expand Up @@ -78,15 +78,16 @@ github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c
github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/dgraph-io/badger v1.6.0 h1:DshxFxZWXUcO0xX476VJC07Xsr6ZCBVRHKZ93Oh7Evo=
github.com/dgraph-io/badger v1.6.0/go.mod h1:zwt7syl517jmP8s94KqSxTlM6IMsdhYy6psNgSztDR4=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515084818-8ee988574454 h1:xxDt2YtzZ2tVCWVk4tcYyKtZVtWRcScAcsbNhHcE/Qg=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515084818-8ee988574454/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515182826-fafb627b4ce4 h1:0hhuliB6NlxxmqQdrl0MkZi+qjibu69uPKtckRn8E0I=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515182826-fafb627b4ce4/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515210839-ef28ef36b592 h1:j6j3yunDbktI4H3tbj3grt2enO4EPbhstU6Tb8HwqdQ=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200515210839-ef28ef36b592/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200512223356-b7913a671128 h1:S0f6h0t9A3Y+5e7VGMKS/1KVFkAYeNFu3eSpIKHwoQY=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200512223356-b7913a671128/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200518184454-adeff4ecf354 h1:yh6VBtOVenGM/trAufglMpXcTolsFkDa7RZnv5pVqrU=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200518184454-adeff4ecf354/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200518195549-7d06ee67fa2a h1:NixEXAVZF7ik777mj6EKrCCjTxgQ0jWQEHThs09NwFw=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200518195549-7d06ee67fa2a/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200522174526-6eaa5009af27 h1:2oSyH418QYuj2IhW5XWvSJqu5S2wT6czY2ZmPcLhgB4=
github.com/dgraph-io/badger/v2 v2.0.1-rc1.0.20200522174526-6eaa5009af27/go.mod h1:3KY8+bsP8wI0OEnQJAKpd4wIJW/Mm32yw2j/9FUVnIM=
github.com/dgraph-io/dgo/v200 v200.0.0-20200401175452-e463f9234453 h1:DTgOrw91nMIukDm/WEvdobPLl0LgeDd/JE66+24jBks=
github.com/dgraph-io/dgo/v200 v200.0.0-20200401175452-e463f9234453/go.mod h1:Co+FwJrnndSrPORO8Gdn20dR7FPTfmXr0W/su0Ve/Ig=
github.com/dgraph-io/ristretto v0.0.2-0.20200115201040-8f368f2f2ab3 h1:MQLRM35Pp0yAyBYksjbj1nZI/w6eyRY/mWoM1sFf4kU=
github.com/dgraph-io/ristretto v0.0.2-0.20200115201040-8f368f2f2ab3/go.mod h1:KPxhHT9ZxKefz+PCeOGsrHpl1qZ7i70dGTu2u+Ahh6E=
github.com/dgraph-io/ristretto v0.0.2 h1:a5WaUrDa0qm0YrAAS1tUykT5El3kt62KNZZeMxQn3po=
github.com/dgraph-io/ristretto v0.0.2/go.mod h1:KPxhHT9ZxKefz+PCeOGsrHpl1qZ7i70dGTu2u+Ahh6E=
Expand Down Expand Up @@ -335,7 +336,6 @@ github.com/pierrec/lz4 v2.0.5+incompatible/go.mod h1:pdkljMzZIN41W+lC3N2tnIh5sFi
github.com/pingcap/errors v0.11.4 h1:lFuQV/oaUMGcD2tqt+01ROSmJs75VG1ToEOkZIZ4nE4=
github.com/pingcap/errors v0.11.4/go.mod h1:Oi8TUi2kEtXXLMJk9l1cGmz20kV3TaQ0usTwv5KuLY8=
github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
github.com/pkg/errors v0.8.1 h1:iURUrRGxPUNPdy5/HRSm+Yj6okJ6UtLINN0Q9M4+h3I=
github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
Expand Down Expand Up @@ -405,7 +405,6 @@ github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnIn
github.com/spf13/viper v1.3.2 h1:VUFqw5KcqRf7i70GOzW7N+Q7+gxVBkSSqiXB12+JQ4M=
github.com/spf13/viper v1.3.2/go.mod h1:ZiWeW+zYFKm7srdB9IoDzzZXaJaI5eL9QjNiN/DMA2s=
github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
github.com/stretchr/objx v0.1.1 h1:2vfRuCMp5sSVIDSqO8oNnWJq7mPa6KVP3iPIwFBuy8A=
github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
github.com/stretchr/testify v1.2.1/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
Expand Down Expand Up @@ -510,7 +509,6 @@ golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7w
golang.org/x/sys v0.0.0-20190422165155-953cdadca894/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20190626221950-04f50cda93cb/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20190813064441-fde4db37ae7a/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200116001909-b77594299b42 h1:vEOn+mP2zCOVzKckCZy6YsCtDblrpj/w7B9nxGNELpg=
golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200323222414-85ca7c5b95cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200420163511-1957bb5e6d1f h1:gWF768j/LaZugp8dyS4UwsslYCYz9XgFxvlgsn0n9H8=
Expand Down
8 changes: 3 additions & 5 deletions posting/list.go
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Original file line number Diff line number Diff line change
Expand Up @@ -1490,17 +1490,15 @@ func (l *List) PartSplits() []uint64 {
}

// ToBackupPostingList converts a posting list into its representation used for storing backups.
func ToBackupPostingList(l *pb.PostingList) *pb.BackupPostingList {
bl := pb.BackupPostingList{}
if l == nil {
return &bl
func ToBackupPostingList(l *pb.PostingList, bl *pb.BackupPostingList) {
if l == nil || bl == nil {
return
}

bl.Uids = codec.Decode(l.Pack, 0)
bl.Postings = l.Postings
bl.CommitTs = l.CommitTs
bl.Splits = l.Splits
return &bl
}

// FromBackupPostingList converts a posting list in the format used for backups to a
Expand Down
4 changes: 2 additions & 2 deletions worker/backup_ee.go
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ func backupCurrentGroup(ctx context.Context, req *pb.BackupRequest) (*pb.Status,
return nil, err
}

bp := &BackupProcessor{DB: pstore, Request: req}
bp := NewBackupProcessor(pstore, req)
return bp.WriteBackup(ctx)
}

Expand Down Expand Up @@ -185,7 +185,7 @@ func ProcessBackupRequest(ctx context.Context, req *pb.BackupRequest, forceFull
}
m.Encrypted = (x.WorkerConfig.EncryptionKey != nil)

bp := &BackupProcessor{Request: req}
bp := NewBackupProcessor(nil, req)
return bp.CompleteBackup(ctx, &m)
}

Expand Down
46 changes: 41 additions & 5 deletions worker/backup_processor.go
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Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,40 @@ import (
"github.com/dgraph-io/dgraph/x"
)

const (
// backupNumGo is the number of go routines used by the backup stream writer.
backupNumGo = 16
)

// BackupProcessor handles the different stages of the backup process.
type BackupProcessor struct {
// DB is the Badger pstore managed by this node.
DB *badger.DB
// Request stores the backup request containing the parameters for this backup.
Request *pb.BackupRequest

// plList is an array of pre-allocated pb.PostingList objects.
plList []*pb.PostingList
// bplList is an array of pre-allocated pb.BackupPostingList objects.
bplList []*pb.BackupPostingList
}

func NewBackupProcessor(db *badger.DB, req *pb.BackupRequest) *BackupProcessor {
bp := &BackupProcessor{
DB: db,
Request: req,
plList: make([]*pb.PostingList, backupNumGo),
bplList: make([]*pb.BackupPostingList, backupNumGo),
}

for i := range bp.plList {
bp.plList[i] = &pb.PostingList{}
}
for i := range bp.bplList {
bp.bplList[i] = &pb.BackupPostingList{}
}

return bp
}

// LoadResult holds the output of a Load operation.
Expand Down Expand Up @@ -94,6 +122,7 @@ func (pr *BackupProcessor) WriteBackup(ctx context.Context) (*pb.Status, error)

stream := pr.DB.NewStreamAt(pr.Request.ReadTs)
stream.LogPrefix = "Dgraph.Backup"
stream.NumGo = backupNumGo
stream.KeyToList = pr.toBackupList
stream.ChooseKey = func(item *badger.Item) bool {
parsedKey, err := x.Parse(item.Key())
Expand Down Expand Up @@ -187,7 +216,8 @@ func (m *Manifest) GoString() string {
m.Since, m.Groups, m.Encrypted)
}

func (pr *BackupProcessor) toBackupList(key []byte, itr *badger.Iterator) (*bpb.KVList, error) {
func (pr *BackupProcessor) toBackupList(key []byte, itr *badger.Iterator) (
*bpb.KVList, error) {
list := &bpb.KVList{}

item := itr.Item()
Expand Down Expand Up @@ -218,7 +248,7 @@ func (pr *BackupProcessor) toBackupList(key []byte, itr *badger.Iterator) (*bpb.
}
kv.Key = backupKey

backupPl, err := toBackupPostingList(kv.Value)
backupPl, err := pr.toBackupPostingList(kv.Value, itr.ThreadId)
if err != nil {
return nil, err
}
Expand Down Expand Up @@ -262,12 +292,18 @@ func toBackupKey(key []byte) ([]byte, error) {
return backupKey, nil
}

func toBackupPostingList(val []byte) ([]byte, error) {
pl := &pb.PostingList{}
func (pr *BackupProcessor) toBackupPostingList(val []byte, threadNum int) ([]byte, error) {
pl := pr.plList[threadNum]
bpl := pr.bplList[threadNum]
pl.Reset()
bpl.Reset()

if err := pl.Unmarshal(val); err != nil {
return nil, errors.Wrapf(err, "while reading posting list")
}
backupVal, err := posting.ToBackupPostingList(pl).Marshal()
posting.ToBackupPostingList(pl, bpl)
backupVal, err := bpl.Marshal()

if err != nil {
return nil, errors.Wrapf(err, "while converting posting list for backup")
}
Expand Down

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