bbolt (etcd's fork of bolt) by melekes · Pull Request #3610 · tendermint/tendermint

melekes · 2019-05-01T09:52:17Z

Original description:

add boltdb implement for db interface.

The boltdb is safe and high performence embedded KV database. It is based on B+tree and Mmap.
Now it is maintained by etcd-io org. https://github.com/etcd-io/bbolt
It is much better than LSM tree (levelDB) when RANDOM and SCAN read.

Replaced #3604
Refs #1835

Updated all relevant documentation in docs
Updated all code comments where relevant
Wrote tests
Updated CHANGELOG_PENDING.md

libs/db/boltdb.go

libs/db/boltdb_test.go

libs/db/common_test.go

Lawliet-Chan · 2019-05-01T11:45:05Z

It seems that go_leveldb is wrong when you run the TestIterator() :-p

BY THE WAY.
Am I going to be a contributor of yours when this PR merged ? 😂

melekes · 2019-05-01T11:49:36Z

libs/db/boltdb.go

+
+func (bdb *boltDBBatch) Close() {}
+
+// WARNING: Any concurrent writes (Set, SetSync) will block until the Iterator


this is concerning. should we rewrite Iterator to execute transaction for each Next() call rather then holding a lock?

Do you mean that *boltDBBatch.Iterator(start,end) will block the concurrent writes？
But why ？ *boltDBBatch.Iterator(start,end) only creates an read-only transaction. Why do you think that concurrent writes will block?

Do you mean that *boltDBBatch.Iterator(start,end) will block the concurrent writes？

yes. to verify comment out if backend = BoltDBBackend condition in TestPrefixIteratorNoMatch1

Yes, BoltDB does not support concurrent transactions. This code does not work, as the transactions created are never closed, and the next write will deadlock. The tx needs to be included in the iterator struct and closed.

Wait. Didn't I do that?

Oh no. I will fix. Thank you so much for pointing this out 💚

melekes · 2019-05-01T11:51:04Z

libs/db/boltdb.go

+}
+
+// nonEmptyKey returns a []byte("nil") if key is empty.
+// WARNING: this may collude with "nil" user key!


bolt does not support empty keys!

I think that we should judge if the key is empty.
If the key is empty, we should return an error (key must not be empty)
In fact, many embedded KVDBs do not allow key to be empty.

We should modify the nonEmptyKey() that return an error when key is empty.

Are we using non-empty keys anywhere (the sdk)? If not, returning an error makes sense. Otherwise, we would need to support existing use-cases nonetheless.

Are we using non-empty keys anywhere (the sdk)?

This logic was explicitly added by Jae. Not sure what for. Maybe for SDK?

OK, then let's keep it like you've implemented it (for now).

I want to know where to use empty-key in cosmos-sdk.
[]byte("nil") is not a good idea because you probably judge the key in other places.
And if you let the empty-key keep it , it will be incompatible with other better KVDBs.

@alexanderbez @jaekwon --> #3610 (comment)

Ethan: also how do we handle the empty key (non nil) on the fsdb?
Jae: mmm lets panic for fsdb.

created an issue https://github.com/tendermint/tendermint/issues/3614

codecov-io · 2019-05-01T11:52:13Z

Codecov Report

Merging #3610 into develop will increase coverage by 0.05%.
The diff coverage is 63.9%.

@@             Coverage Diff             @@
##           develop    #3610      +/-   ##
===========================================
+ Coverage    64.18%   64.23%   +0.05%     
===========================================
  Files          213      214       +1     
  Lines        17490    17669     +179     
===========================================
+ Hits         11226    11350     +124     
- Misses        5339     5385      +46     
- Partials       925      934       +9

Impacted Files	Coverage Δ
libs/db/db.go	`38.88% <ø> (ø)`	⬆️
libs/db/mem_db.go	`82.9% <100%> (ø)`	⬆️
libs/db/fsdb.go	`69.78% <100%> (ø)`	⬆️
libs/db/boltdb.go	`63.47% <63.47%> (ø)`
privval/signer_validator_endpoint.go	`75.55% <0%> (-10%)`	⬇️
privval/socket_listeners.go	`86.2% <0%> (-3.45%)`	⬇️
libs/db/mem_batch.go	`92.59% <0%> (-0.75%)`	⬇️
consensus/reactor.go	`70.6% <0%> (-0.71%)`	⬇️
p2p/pex/pex_reactor.go	`83.38% <0%> (+1.78%)`	⬆️
... and 4 more

melekes · 2019-05-01T11:53:12Z

It seems that go_leveldb is wrong when you run the TestIterator() :-p

what do you mean?

Am I going to be a contributor of yours when this PR merged ?

yes

libs/db/boltdb.go

libs/db/boltdb_test.go

liamsi · 2019-05-01T16:44:43Z

libs/db/boltdb_test.go

+	db.Close()
+}
+
+func BenchmarkBoltDBRandomReadsWrites(b *testing.B) {


BTW, on my mbp:

BenchmarkBoltDBRandomReadsWrites-12 100 13983447 ns/op BenchmarkGoLevelDBRandomReadsWrites-12 100000 13278 ns/op

Isn't this supposed to be faster?

BenchmarkBoltDBRandomReadsWrites does not reflect our load

I'll double check. If bolt is slower for our load, I'll be 😢 because I spent a good portion of the day working on top of add boltdb for storage #3604

It's not fair to compare goleveldb and bolt in this case (BenchmarkBoltDBRandomReadsWrites) because Set is synchronous in bolt! We can turn fsync off for this benchmark by using bolt.NoSync option.

Sounds great. By the way, the bolt is better than leveldb in random read because it's based on B+TREE.
I will find some authority benchmark reports for you tomorrow. Now it's too late in China I will go for sleep.
HAPPY MAY DAY 😁😁

Co-Authored-By: melekes <anton.kalyaev@gmail.com>

plus specify bucket in the top comment

liamsi

The changes look pretty straight forward. Great work @melekes and @CrocdileChan 🚀
I would wait for the benchmarks (as per https://github.com/tendermint/tendermint/pull/3610/files#r280132399) before we merge this. Also, I didn't test this in a real setting yet. Other than that we should probably highlight this in the changelog, and use all channels to encourage more people to experiment with and test this backend.

melekes · 2019-05-02T06:05:00Z

I would wait for the benchmarks (as per https://github.com/tendermint/tendermint/pull/3610/files#r280132399) before we merge this

benchmarks should not hold us from merging this.

Lawliet-Chan · 2019-05-02T14:25:04Z

I would wait for the benchmarks (as per https://github.com/tendermint/tendermint/pull/3610/files#r280132399) before we merge this

benchmarks should not hold us from merging this.

So now what's blocking merging this ? The NIL key?

liamsi

Let's merge this 👍 Thank you both!

Lawliet-Chan · 2019-05-06T09:54:32Z

I have a question 😂 why am not the contributor of yours now? The number of contributors is still only 133. You promise that I will be the contributor of you when this PR is merged.

melekes · 2019-05-06T11:51:29Z

why am not the contributor of yours now?

please wait till this gets merged to master (0.31.6 release)

Lawliet-Chan · 2019-05-06T13:01:35Z

ok! Thank you very much.

leoluk

I replayed cosmoshub-2 using cosmos-sdk v0.34.3 on this Tendermint branch.

Required fixes:

diff --git a/libs/db/boltdb.go b/libs/db/boltdb.go
index 6a31f11a9..12ef806ae 100644
--- a/libs/db/boltdb.go
+++ b/libs/db/boltdb.go
@@ -161,11 +161,11 @@ func (bdb *BoltDB) NewBatch() Batch {
 }
 
 func (bdb *boltDBBatch) Set(key, value []byte) {
-	bdb.buffer.Store(key, value)
+	bdb.buffer.Store(string(key), string(value))
 }
 
 func (bdb *boltDBBatch) Delete(key []byte) {
-	bdb.buffer.Delete(key)
+	bdb.buffer.Delete(string(key))
 }
 
 // NOTE: the operation is synchronous (see BoltDB for reasons)
@@ -174,7 +174,7 @@ func (bdb *boltDBBatch) Write() {
 		b := tx.Bucket(bucket)
 		var putErr error
 		bdb.buffer.Range(func(key, value interface{}) bool {
-			putErr = b.Put(key.([]byte), value.([]byte))
+			putErr = b.Put([]byte(key.(string)), []byte(value.(string)))
 			return putErr == nil // stop if putErr is not nil
 		})
 		return putErr
@@ -198,7 +198,7 @@ func (bdb *BoltDB) Iterator(start, end []byte) Iterator {
 		panic(err)
 	}
 	c := tx.Bucket(bucket).Cursor()
-	return newBoltDBIterator(c, start, end, false)
+	return newBoltDBIterator(tx, c, start, end, false)
 }
 
 // WARNING: Any concurrent writes (Set, SetSync) will block until the Iterator
@@ -209,12 +209,14 @@ func (bdb *BoltDB) ReverseIterator(start, end []byte) Iterator {
 		panic(err)
 	}
 	c := tx.Bucket(bucket).Cursor()
-	return newBoltDBIterator(c, start, end, true)
+	return newBoltDBIterator(tx, c, start, end, true)
 }
 
 // boltDBIterator allows you to iterate on range of keys/values given some
 // start / end keys (nil & nil will result in doing full scan).
 type boltDBIterator struct {
+	tx *bbolt.Tx
+
 	itr   *bbolt.Cursor
 	start []byte
 	end   []byte
@@ -226,7 +228,7 @@ type boltDBIterator struct {
 	isReverse bool
 }
 
-func newBoltDBIterator(itr *bbolt.Cursor, start, end []byte, isReverse bool) *boltDBIterator {
+func newBoltDBIterator(tx *bbolt.Tx, itr *bbolt.Cursor, start, end []byte, isReverse bool) *boltDBIterator {
 	var ck, cv []byte
 	if isReverse {
 		if end == nil {
@@ -244,6 +246,7 @@ func newBoltDBIterator(itr *bbolt.Cursor, start, end []byte, isReverse bool) *bo
 	}
 
 	return &boltDBIterator{
+		tx:          tx,
 		itr:          itr,
 		start:        start,
 		end:          end,
@@ -305,7 +308,12 @@ func (itr *boltDBIterator) Value() []byte {
 }
 
 // boltdb cursor has no close op.
-func (itr *boltDBIterator) Close() {}
+func (itr *boltDBIterator) Close() {
+	err := itr.tx.Rollback()
+	if err != nil {
+		panic(err)
+	}
+}
 
 func (itr *boltDBIterator) assertIsValid() {
 	if !itr.Valid() {

Benchmark results:

Backend	Result
goleveldb	34 blocks/s
boltdb	5 blocks/s
memdb	1.5 blocks/s

In all cases, the database was stored on a tmpfs, with fsync disabled.

Replaying/syncing the chain is very write-heavy, which is the opposite of what B+trees are optimized for, so it's unsurprising that leveldb performance is much better.

This should not be merged.

leoluk · 2019-05-04T21:16:47Z

libs/db/boltdb.go

+}
+
+func (bdb *boltDBBatch) Set(key, value []byte) {
+	bdb.buffer.Store(key, value)


This cannot possibly work, since []byte is unhashable, and panics with hash of unhashable type []uint8. Strings are hashable so the fix is to cast to a string.

It also implies that this code path lacks tests.

leoluk · 2019-05-06T14:09:16Z

libs/db/boltdb.go

+
+func (bdb *boltDBBatch) Close() {}
+
+// WARNING: Any concurrent writes (Set, SetSync) will block until the Iterator


Yes, BoltDB does not support concurrent transactions. This code does not work, as the transactions created are never closed, and the next write will deadlock. The tx needs to be included in the iterator struct and closed.

liamsi · 2019-05-06T14:37:19Z

Thanks a lot for the extensive testing and feedback @leoluk!
Would you argue that there is absolutely to reason to add boltdb support? Remember that tendermint is not only used by the cosmos-hub.

Lawliet-Chan · 2019-05-06T14:43:29Z

@leoluk thanks for your benchmark and test. Is it possible that tendermint will be used in read-more-an-write-less ? b+tree will performs better than lsm-tree in read-heavy. I think that we should show more storage implementions in tendermint.

Refs #3610 (comment) If we do not close, other txs will be stuck forever.

leoluk · 2019-05-06T15:20:38Z

Demonstrating a specific use case where boltdb actually outperforms goleveldb would be good to justify the expense of maintaining it. The most common use-case - syncing a chain - is write-heavy due to how the IAVL tree works, which is not specific to cosmos-sdk.

Refs #3610 (comment) If we do not close, other txs will be stuck forever.

melekes · 2019-05-06T19:05:13Z

The most common use-case - syncing a chain - is write-heavy due to how the IAVL tree works, which is not specific to cosmos-sdk.

most of the users will use state-sync once it's implemented.

`[]byte` is unhashable and needs to be casted to a string. See tendermint#3610 (comment) Ref https://github.com/tendermint/tendermint/issues/3626

Description: add boltdb implement for db interface. The boltdb is safe and high performence embedded KV database. It is based on B+tree and Mmap. Now it is maintained by etcd-io org. https://github.com/etcd-io/bbolt It is much better than LSM tree (levelDB) when RANDOM and SCAN read. Replaced tendermint#3604 Refs tendermint#1835 Commits: * add boltdb for storage * update boltdb in gopkg.toml * update bbolt in Gopkg.lock * dep update Gopkg.lock * add boltdb'bucket when create Boltdb * some modifies * address my own comments * fix most of the Iterator tests for boltdb * bolt does not support concurrent writes while iterating * add WARNING word * note that ReadOnly option is not supported * fixes after Ismail's review Co-Authored-By: melekes <anton.kalyaev@gmail.com> * panic if View returns error plus specify bucket in the top comment

Refs tendermint#3610 (comment) If we do not close, other txs will be stuck forever.

`[]byte` is unhashable and needs to be casted to a string. See tendermint#3610 (comment) Ref https://github.com/tendermint/tendermint/issues/3626

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melekes requested review from ebuchman and xla as code owners May 1, 2019 09:52

melekes mentioned this pull request May 1, 2019

add boltdb for storage #3604

Closed

golangcibot reviewed May 1, 2019

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CrocdileChan and others added 7 commits May 1, 2019 14:04

add boltdb for storage

ada2cb2

update boltdb in gopkg.toml

f578d01

update bbolt in Gopkg.lock

fa0ea1a

dep update Gopkg.lock

9ac020a

add boltdb'bucket when create Boltdb

27a3540

some modifies

5f3c052

address my own comments

f6648a7

melekes force-pushed the anton/bbolt branch from 1f39126 to f6648a7 Compare May 1, 2019 10:05

melekes changed the title ~~add boltdb for storage~~ bbolt (etcd's fork of bolt) May 1, 2019

melekes added 3 commits May 1, 2019 15:26

fix most of the Iterator tests for boltdb

2c5e785

bolt does not support concurrent writes while iterating

60ed018

add WARNING word

a888211

melekes commented May 1, 2019

View reviewed changes

note that ReadOnly option is not supported

8749dfd