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memdb: prevent iterator invalidation #1563

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memdb: prevent iterator invalidation #1563

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1a6d100
memdb: prevent iterator invalidation
ekexium Jan 23, 2025
c46d490
fix for snapshot iter
ekexium Jan 23, 2025
4c16a14
fix initKeysAndMutations
ekexium Jan 23, 2025
e1a3b5a
more checks
ekexium Jan 23, 2025
29fc98e
optimize batched iter
ekexium Jan 24, 2025
e906cd5
refine comment
ekexium Jan 24, 2025
e672ef4
minor improvements from comments
ekexium Feb 10, 2025
941d94b
fix: return error if the first fillBatch fails
ekexium Feb 10, 2025
de43ee4
revert snapshot check and minor improvements
ekexium Feb 11, 2025
b15c57a
comment: explain the sequence number and data race
ekexium Feb 12, 2025
9b45230
fix test
ekexium Feb 12, 2025
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4 changes: 2 additions & 2 deletions examples/gcworker/go.mod
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/rawkv/go.mod
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/1pc_txn/go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/async_commit/go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/delete_range/go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/pessimistic_txn/go.mod
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
4 changes: 2 additions & 2 deletions examples/txnkv/unsafedestoryrange/go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ require (
github.com/grpc-ecosystem/go-grpc-middleware v1.1.0 // indirect
github.com/opentracing/opentracing-go v1.2.0 // indirect
github.com/pingcap/errors v0.11.5-0.20211224045212-9687c2b0f87c // indirect
github.com/pingcap/failpoint v0.0.0-20220801062533-2eaa32854a6c // indirect
github.com/pingcap/failpoint v0.0.0-20240528011301-b51a646c7c86 // indirect
github.com/pingcap/kvproto v0.0.0-20241120071417-b5b7843d9037 // indirect
github.com/pingcap/log v1.1.1-0.20221110025148-ca232912c9f3 // indirect
github.com/pkg/errors v0.9.1 // indirect
Expand All @@ -30,7 +30,7 @@ require (
github.com/prometheus/procfs v0.15.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/tiancaiamao/gp v0.0.0-20221230034425-4025bc8a4d4a // indirect
github.com/tikv/pd/client v0.0.0-20241220053006-461b86adc78d // indirect
github.com/tikv/pd/client v0.0.0-20250107032658-5c4ab57d68de // indirect
github.com/twmb/murmur3 v1.1.3 // indirect
go.etcd.io/etcd/api/v3 v3.5.10 // indirect
go.etcd.io/etcd/client/pkg/v3 v3.5.10 // indirect
Expand Down
16 changes: 16 additions & 0 deletions internal/unionstore/arena/arena.go
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,10 @@ import (
"encoding/binary"
"math"

"github.com/tikv/client-go/v2/internal/logutil"
"github.com/tikv/client-go/v2/kv"
"go.uber.org/atomic"
"go.uber.org/zap"
)

const (
Expand Down Expand Up @@ -223,6 +225,20 @@ func (cp *MemDBCheckpoint) IsSamePosition(other *MemDBCheckpoint) bool {
return cp.blocks == other.blocks && cp.offsetInBlock == other.offsetInBlock
}

// LessThan compares two checkpoints.
func (cp *MemDBCheckpoint) LessThan(cp2 *MemDBCheckpoint) bool {
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if cp == nil || cp2 == nil {
logutil.BgLogger().Panic("unexpected nil checkpoint", zap.Any("cp", cp), zap.Any("cp2", cp2))
}
if cp.blocks < cp2.blocks {
return true
}
if cp.blocks == cp2.blocks && cp.offsetInBlock < cp2.offsetInBlock {
return true
}
return false
}

func (a *MemdbArena) Checkpoint() MemDBCheckpoint {
snap := MemDBCheckpoint{
blockSize: a.blockSize,
Expand Down
24 changes: 24 additions & 0 deletions internal/unionstore/art/art.go
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,16 @@ type ART struct {
lastTraversedNode atomic.Uint64
hitCount atomic.Uint64
missCount atomic.Uint64

// The counter of every write operation, used to invalidate iterators that were created before the write operation.
// The purpose of the counter is to check interleaving of write and read operations (via iterator).
// It does not protect against data race. If it happens, there must be a bug in the caller code.
// invariant: no concurrent access to it
WriteSeqNo int
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The WriteSeqNo seems not to have the concurrency invariance like SnapshotSeqNo below, should atomic variable be used for it?

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@ekexium ekexium Feb 12, 2025 •
edited
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The purpose of the sequence number is to check interleaving read and write operations, but not concurrent access. Even if we change it to an atomic variable, concurrent read and write can still corrupt the iterator.
If there exists data race on this variable, there must be a bug on the caller side.
I've updated the comment to explain the rationale.

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Trying to sort out the current issues:

  1. memdb has concurrent usage scenarios, such as pessimistic lock setting key flags while membuf read is performing a memdb snapshot read.
  2. The underlying implementation structure of memdb does not support concurrency and needs to be properly used by the upper layer with mutex protection. This is the issue being addressed by the PR at executor: in-txn statement read from MemBuffer's snapshot pingcap/tidb#59219.
  3. The situation where the memdb iterator is invalidated by interleaving writes, which is the purpose of introducing a mechanism like write sequence in this PR.

Implementation level:

  1. lastTraversedNode, hitCount, and missCount, several internal states of ART, are implemented as atomic variables. These states are modified by write operations, and the WriteSeqNo below will also be modified by write operations, requiring the upper layer to handle concurrency correctly.

This part of the code implementation is confusing, should we make the internal states of ART to be single-threaded, while allowing concurrent operations and protection to be handled at the upper layer of MemDB? So there is no need to consider data races or introduce atomic variables in the ART code.
/cc @you06

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@ekexium ekexium Feb 12, 2025 •
edited
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One difference between WriteSeqNo and lastTraversedNode is that the latter one is updated during read operations. Concurrent read operations are allowed (by design?). So even if we acquire an Rlock of memdb for every read operation lastTraversedNode still needs to be implemented by an atomic variable.

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If the traverse in snapshot-get do not cache the last-traversed node(maybe it's not worth cache for a snapshot-get), I think the art.lastTraversedNode can also be a non-atomic variable, but hitCount and missCount should be atomic.

client-go/internal/unionstore/art/art_snapshot.go

Line 79 in 456c3af

addr, lf := snap.tree.traverse(key, false)

// Increased by 1 when an operation that may affect the content returned by "snapshot" (i.e. stage[0]) happens.
// It's used to invalidate snapshot iterators.
// invariant: no concurrent access to it
SnapshotSeqNo int
}

func New() *ART {
Expand Down Expand Up @@ -115,6 +125,7 @@ func (t *ART) Set(key artKey, value []byte, ops ...kv.FlagsOp) error {
}
}

t.WriteSeqNo++
if len(t.stages) == 0 {
t.dirty = true
}
Expand Down Expand Up @@ -479,6 +490,10 @@ func (t *ART) RevertToCheckpoint(cp *arena.MemDBCheckpoint) {
t.allocator.vlogAllocator.RevertToCheckpoint(t, cp)
t.allocator.vlogAllocator.Truncate(cp)
t.allocator.vlogAllocator.OnMemChange()
t.WriteSeqNo++
if len(t.stages) == 0 || t.stages[0].LessThan(cp) {
t.SnapshotSeqNo++
}
}

func (t *ART) Stages() []arena.MemDBCheckpoint {
Expand All @@ -498,7 +513,9 @@ func (t *ART) Release(h int) {
if h != len(t.stages) {
panic("cannot release staging buffer")
}
t.WriteSeqNo++
if h == 1 {
t.SnapshotSeqNo++
tail := t.checkpoint()
if !t.stages[0].IsSamePosition(&tail) {
t.dirty = true
Expand All @@ -519,6 +536,11 @@ func (t *ART) Cleanup(h int) {
panic(fmt.Sprintf("cannot cleanup staging buffer, h=%v, len(tree.stages)=%v", h, len(t.stages)))
}

t.WriteSeqNo++
if h == 1 {
t.SnapshotSeqNo++
}

cp := &t.stages[h-1]
if !t.vlogInvalid {
curr := t.checkpoint()
Expand All @@ -542,6 +564,8 @@ func (t *ART) Reset() {
t.allocator.nodeAllocator.Reset()
t.allocator.vlogAllocator.Reset()
t.lastTraversedNode.Store(arena.NullU64Addr)
t.SnapshotSeqNo++
t.WriteSeqNo++
}

// DiscardValues releases the memory used by all values.
Expand Down
40 changes: 37 additions & 3 deletions internal/unionstore/art/art_iterator.go
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ import (
"fmt"
"sort"

"github.com/tikv/client-go/v2/internal/logutil"
"go.uber.org/zap"

"github.com/pkg/errors"
"github.com/tikv/client-go/v2/internal/unionstore/arena"
"github.com/tikv/client-go/v2/kv"
Expand Down Expand Up @@ -56,6 +59,7 @@ func (t *ART) iter(lowerBound, upperBound []byte, reverse, includeFlags bool) (*
// this avoids the initial value of currAddr equals to endAddr.
currAddr: arena.BadAddr,
endAddr: arena.NullAddr,
seqNo: t.WriteSeqNo,
}
it.init(lowerBound, upperBound)
if !it.valid {
Expand All @@ -76,12 +80,41 @@ type Iterator struct {
currLeaf *artLeaf
currAddr arena.MemdbArenaAddr
endAddr arena.MemdbArenaAddr

// only when seqNo == art.seqNo, the iterator is valid.
seqNo int
// ignoreSeqNo is used to ignore the seqNo check, used for snapshot iter before its full deprecation.
ignoreSeqNo bool
}

func (it *Iterator) checkSeqNo() {
if it.seqNo != it.tree.WriteSeqNo && !it.ignoreSeqNo {
logutil.BgLogger().Panic(
"seqNo mismatch",
zap.Int("it seqNo", it.seqNo),
zap.Int("art seqNo", it.tree.WriteSeqNo),
zap.Stack("stack"),
)
}
}

func (it *Iterator) Valid() bool {
it.checkSeqNo()
return it.valid
}

func (it *Iterator) Key() []byte {
it.checkSeqNo()
return it.currLeaf.GetKey()
}

func (it *Iterator) Flags() kv.KeyFlags {
it.checkSeqNo()
return it.currLeaf.GetKeyFlags()
}

func (it *Iterator) Valid() bool { return it.valid }
func (it *Iterator) Key() []byte { return it.currLeaf.GetKey() }
func (it *Iterator) Flags() kv.KeyFlags { return it.currLeaf.GetKeyFlags() }
func (it *Iterator) Value() []byte {
it.checkSeqNo()
if it.currLeaf.vLogAddr.IsNull() {
return nil
}
Expand All @@ -102,6 +135,7 @@ func (it *Iterator) Next() error {
// iterate is finished
return errors.New("Art: iterator is finished")
}
it.checkSeqNo()
if it.currAddr == it.endAddr {
it.valid = false
return nil
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3 changes: 3 additions & 0 deletions internal/unionstore/art/art_snapshot.go
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ import (
"github.com/tikv/client-go/v2/internal/unionstore/arena"
)

// getSnapshot returns the "snapshot" for snapshotGetter or snapshotIterator, which is usually the snapshot
// of stage[0]
func (t *ART) getSnapshot() arena.MemDBCheckpoint {
if len(t.stages) > 0 {
return t.stages[0]
Expand Down Expand Up @@ -49,6 +51,7 @@ func (t *ART) newSnapshotIterator(start, end []byte, desc bool) *SnapIter {
if err != nil {
panic(err)
}
inner.ignoreSeqNo = true
it := &SnapIter{
Iterator: inner,
cp: t.getSnapshot(),
Expand Down
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