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Implement addBatchInDisk for big trees

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Implement addBatchInDisk for big trees, which does not puts the tree in
memory, and works directly over the db data, parallelizing for each CPU.
This commit is contained in:
arnaucube
2021-10-14 16:59:26 +02:00
parent 3f7e769974
commit 6cf1e58d9f
10 changed files with 660 additions and 105 deletions
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177
addbatch_test.go
View File

@@ -11,7 +11,9 @@ import (
"time"
qt "github.com/frankban/quicktest"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
"go.vocdoni.io/dvote/db/pebbledb"
)
var debug = true
@@ -37,12 +39,12 @@ func debugTime(descr string, time1, time2 time.Duration) {
}
func testInit(c *qt.C, n int) (*Tree, *Tree) {
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -68,7 +70,7 @@ func TestAddBatchTreeEmpty(t *testing.T) {
nLeafs := 1024
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -91,7 +93,7 @@ func TestAddBatchTreeEmpty(t *testing.T) {
}
time1 := time.Since(start)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -99,7 +101,7 @@ func TestAddBatchTreeEmpty(t *testing.T) {
tree2.dbgInit()
start = time.Now()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
time2 := time.Since(start)
if debug {
@@ -107,7 +109,7 @@ func TestAddBatchTreeEmpty(t *testing.T) {
printTestContext(" ", nLeafs, "Poseidon", "memory")
tree2.dbg.print(" ")
}
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree, tree2)
@@ -118,7 +120,7 @@ func TestAddBatchTreeEmptyNotPowerOf2(t *testing.T) {
nLeafs := 1027
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -133,7 +135,7 @@ func TestAddBatchTreeEmptyNotPowerOf2(t *testing.T) {
}
}
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -146,9 +148,9 @@ func TestAddBatchTreeEmptyNotPowerOf2(t *testing.T) {
keys = append(keys, k)
values = append(values, v)
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree, tree2)
@@ -165,13 +167,13 @@ func randomBytes(n int) []byte {
func TestAddBatchTestVector1(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -198,20 +200,20 @@ func TestAddBatchTestVector1(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
// 2nd test vectors
database1, err = badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err = badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err = NewTree(database1, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err = badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err = badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err = NewTree(database2, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -242,9 +244,9 @@ func TestAddBatchTestVector1(t *testing.T) {
}
}
indexes, err = tree2.AddBatch(keys, values)
invalids, err = tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
}
@@ -253,13 +255,13 @@ func TestAddBatchTestVector2(t *testing.T) {
// test vector with unbalanced tree
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -286,9 +288,9 @@ func TestAddBatchTestVector2(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
@@ -298,13 +300,13 @@ func TestAddBatchTestVector3(t *testing.T) {
// test vector with unbalanced tree
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -331,9 +333,9 @@ func TestAddBatchTestVector3(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
@@ -347,13 +349,13 @@ func TestAddBatchTreeEmptyRandomKeys(t *testing.T) {
nLeafs := 8
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -371,9 +373,9 @@ func TestAddBatchTreeEmptyRandomKeys(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
}
@@ -407,7 +409,7 @@ func TestAddBatchTreeNotEmptyFewLeafs(t *testing.T) {
values = append(values, v)
}
start = time.Now()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
time2 := time.Since(start)
if debug {
@@ -415,7 +417,7 @@ func TestAddBatchTreeNotEmptyFewLeafs(t *testing.T) {
printTestContext(" ", nLeafs, "Poseidon", "memory")
tree2.dbg.print(" ")
}
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
@@ -450,7 +452,7 @@ func TestAddBatchTreeNotEmptyEnoughLeafs(t *testing.T) {
values = append(values, v)
}
start = time.Now()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
time2 := time.Since(start)
if debug {
@@ -458,7 +460,7 @@ func TestAddBatchTreeNotEmptyEnoughLeafs(t *testing.T) {
printTestContext(" ", nLeafs, "Poseidon", "memory")
tree2.dbg.print(" ")
}
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
}
@@ -495,9 +497,9 @@ func TestAddBatchTreeEmptyRepeatedLeafs(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, nRepeatedKeys)
c.Check(len(invalids), qt.Equals, nRepeatedKeys)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
}
@@ -527,9 +529,9 @@ func TestAddBatchTreeNotEmptyFewLeafsRepeatedLeafs(t *testing.T) {
}
}
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, initialNLeafs)
c.Assert(len(invalids), qt.Equals, initialNLeafs)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
}
@@ -664,7 +666,7 @@ func TestAddBatchTreeNotEmpty(t *testing.T) {
values = append(values, v)
}
start = time.Now()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
time2 := time.Since(start)
if debug {
@@ -672,7 +674,7 @@ func TestAddBatchTreeNotEmpty(t *testing.T) {
printTestContext(" ", nLeafs, "Poseidon", "memory")
tree2.dbg.print(" ")
}
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
@@ -697,7 +699,7 @@ func TestAddBatchNotEmptyUnbalanced(t *testing.T) {
}
time1 := time.Since(start)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -729,7 +731,7 @@ func TestAddBatchNotEmptyUnbalanced(t *testing.T) {
values = append(values, v)
}
start = time.Now()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
time2 := time.Since(start)
if debug {
@@ -737,7 +739,7 @@ func TestAddBatchNotEmptyUnbalanced(t *testing.T) {
printTestContext(" ", nLeafs, "Poseidon", "memory")
tree2.dbg.print(" ")
}
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
@@ -774,7 +776,7 @@ func TestAddBatchBench(t *testing.T) {
func benchAdd(t *testing.T, ks, vs [][]byte) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -794,7 +796,7 @@ func benchAdd(t *testing.T, ks, vs [][]byte) {
func benchAddBatch(t *testing.T, ks, vs [][]byte) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -827,7 +829,7 @@ func TestDbgStats(t *testing.T) {
}
// 1
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -841,7 +843,7 @@ func TestDbgStats(t *testing.T) {
}
// 2
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -854,7 +856,7 @@ func TestDbgStats(t *testing.T) {
c.Assert(len(invalids), qt.Equals, 0)
// 3
database3, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database3, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree3, err := NewTree(database3, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -889,7 +891,7 @@ func TestLoadVT(t *testing.T) {
nLeafs := 1024
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -902,9 +904,9 @@ func TestLoadVT(t *testing.T) {
keys = append(keys, k)
values = append(values, v)
}
indexes, err := tree.AddBatch(keys, values)
invalids, err := tree.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
rTx := tree.db.ReadTx()
defer rTx.Discard()
@@ -925,7 +927,7 @@ func TestAddKeysWithEmptyValues(t *testing.T) {
nLeafs := 1024
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -946,29 +948,29 @@ func TestAddKeysWithEmptyValues(t *testing.T) {
}
}
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
defer tree2.db.Close() //nolint:errcheck
tree2.dbgInit()
indexes, err := tree2.AddBatch(keys, values)
invalids, err := tree2.AddBatch(keys, values)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree, tree2)
// use tree3 to add nil value array
database3, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database3, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree3, err := NewTree(database3, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
defer tree3.db.Close() //nolint:errcheck
indexes, err = tree3.AddBatch(keys, nil)
invalids, err = tree3.AddBatch(keys, nil)
c.Assert(err, qt.IsNil)
c.Check(len(indexes), qt.Equals, 0)
c.Check(len(invalids), qt.Equals, 0)
checkRoots(c, tree, tree3)
kAux, proofV, siblings, existence, err := tree2.GenProof(keys[9])
@@ -1003,6 +1005,65 @@ func TestAddKeysWithEmptyValues(t *testing.T) {
c.Check(verif, qt.IsFalse)
}
func TestAddBatchThresholdInDisk(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree1.db.Close() //nolint:errcheck
database2, err := pebbledb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree2.db.Close() //nolint:errcheck
database3, err := pebbledb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree3, err := NewTree(database3, 256, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
defer tree3.db.Close() //nolint:errcheck
// customize thresholdNLeafs for the test
thresholdNLeafs = 1024
var keys, values [][]byte
for i := 0; i < 3*thresholdNLeafs; i++ {
k := randomBytes(32)
v := randomBytes(32)
if err := tree1.Add(k, v); err != nil {
t.Fatal(err)
}
if i < thresholdNLeafs+1 {
if err := tree2.Add(k, v); err != nil {
t.Fatal(err)
}
}
// store for later addition through AddBatch
keys = append(keys, k)
values = append(values, v)
}
invalids, err := tree2.AddBatch(keys[thresholdNLeafs+1:], values[thresholdNLeafs+1:])
c.Assert(err, qt.IsNil)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree2)
// call directly the tree3.addBatchInDisk to ensure that is tested
wTx := tree3.db.WriteTx()
defer wTx.Discard()
invalids, err = tree3.addBatchInDisk(wTx, keys, values)
c.Assert(err, qt.IsNil)
err = wTx.Commit()
c.Assert(err, qt.IsNil)
c.Check(len(invalids), qt.Equals, 0)
// check that both trees roots are equal
checkRoots(c, tree1, tree3)
}
// TODO test adding batch with multiple invalid keys
// TODO for tests of AddBatch, if the root does not match the Add root, bulk
// all the leafs of both trees into a log file to later be able to debug and

3
circomproofs_test.go
View File

@@ -6,12 +6,13 @@ import (
"testing"
qt "github.com/frankban/quicktest"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
)
func TestCircomVerifierProof(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 4, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)

4
go.mod
View File

@@ -5,6 +5,6 @@ go 1.16
require (
github.com/frankban/quicktest v1.13.0
github.com/iden3/go-iden3-crypto v0.0.6-0.20210308142348-8f85683b2cef
go.vocdoni.io/dvote v1.0.4-0.20210806163627-9494efbc5382
golang.org/x/crypto v0.0.0-20210711020723-a769d52b0f97
go.vocdoni.io/dvote v1.0.4-0.20211025120558-83c64f440044
golang.org/x/crypto v0.0.0-20210920023735-84f357641f63
)

293
go.sum
View File

File diff suppressed because it is too large Load Diff

5
helpers_test.go
View File

@@ -9,6 +9,7 @@ import (
"time"
qt "github.com/frankban/quicktest"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
)
@@ -87,12 +88,12 @@ func TestReadTreeDBG(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 100, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 100, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)

3
testvectors/circom/go-data-generator/generator_test.go
View File

@@ -8,12 +8,13 @@ import (
qt "github.com/frankban/quicktest"
"github.com/vocdoni/arbo"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
)
func TestGenerator(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := arbo.NewTree(database, 4, arbo.HashFunctionPoseidon)
c.Assert(err, qt.IsNil)

207
tree.go
View File

@@ -17,6 +17,7 @@ import (
"fmt"
"io"
"math"
"runtime"
"sync"
"go.vocdoni.io/dvote/db"
@@ -45,6 +46,12 @@ const (
)
var (
// thresholdNLeafs defines the threshold number of leafs in the tree
// that determines if AddBatch will work in memory or in disk. Is
// defined as a var in order to have the ability to modify it for
// testing purposes.
thresholdNLeafs = 1024 // TODO define a reasonable value
dbKeyRoot = []byte("root")
dbKeyNLeafs = []byte("nleafs")
emptyValue = []byte{0}
@@ -197,11 +204,6 @@ func (t *Tree) AddBatchWithTx(wTx db.WriteTx, keys, values [][]byte) ([]Invalid,
return nil, ErrSnapshotNotEditable
}
vt, err := t.loadVT(wTx)
if err != nil {
return nil, err
}
e := []byte{}
// equal the number of keys & values
if len(keys) > len(values) {
@@ -214,6 +216,201 @@ func (t *Tree) AddBatchWithTx(wTx db.WriteTx, keys, values [][]byte) ([]Invalid,
values = values[:len(keys)]
}
nLeafs, err := t.GetNLeafsWithTx(wTx)
if err != nil {
return nil, err
}
if nLeafs > thresholdNLeafs {
return t.addBatchInDisk(wTx, keys, values)
}
return t.addBatchInMemory(wTx, keys, values)
}
func (t *Tree) addBatchInDisk(wTx db.WriteTx, keys, values [][]byte) ([]Invalid, error) {
nCPU := flp2(runtime.NumCPU())
if nCPU == 1 || len(keys) < nCPU {
var invalids []Invalid
for i := 0; i < len(keys); i++ {
if err := t.AddWithTx(wTx, keys[i], values[i]); err != nil {
invalids = append(invalids, Invalid{i, err})
}
}
return invalids, nil
}
kvs, invalids, err := keysValuesToKvs(t.maxLevels, keys, values)
if err != nil {
return nil, err
}
buckets := splitInBuckets(kvs, nCPU)
root, err := t.RootWithTx(wTx)
if err != nil {
return nil, err
}
l := int(math.Log2(float64(nCPU)))
subRoots, err := t.getSubRootsAtLevel(wTx, root, l+1)
if err != nil {
return nil, err
}
if len(subRoots) != nCPU {
// Already populated Tree but Unbalanced.
// add one key at each bucket, and then continue with the flow
for i := 0; i < len(buckets); i++ {
// add one leaf of the bucket, if there is an error when
// adding the k-v, try to add the next one of the bucket
// (until one is added)
inserted := -1
for j := 0; j < len(buckets[i]); j++ {
if newRoot, err := t.add(wTx, root, 0, buckets[i][j].k, buckets[i][j].v); err == nil {
inserted = j
root = newRoot
break
}
}
// remove the inserted element from buckets[i]
if inserted != -1 {
buckets[i] = append(buckets[i][:inserted], buckets[i][inserted+1:]...)
}
}
subRoots, err = t.getSubRootsAtLevel(wTx, root, l+1)
if err != nil {
return nil, err
}
}
if len(subRoots) != nCPU {
return nil, fmt.Errorf("This error should not be reached."+
" len(subRoots) != nCPU, len(subRoots)=%d, nCPU=%d."+
" Please report it in a new issue:"+
" https://github.com/vocdoni/arbo/issues/new", len(subRoots), nCPU)
}
invalidsInBucket := make([][]Invalid, nCPU)
txs := make([]db.WriteTx, nCPU)
for i := 0; i < nCPU; i++ {
txs[i] = t.db.WriteTx()
err := txs[i].Apply(wTx)
if err != nil {
return nil, err
}
}
var wg sync.WaitGroup
wg.Add(nCPU)
for i := 0; i < nCPU; i++ {
go func(cpu int) {
// use different wTx for each cpu, after once all
// are done, iter over the cpuWTxs and copy their
// content into the main wTx
for j := 0; j < len(buckets[cpu]); j++ {
subRoots[cpu], err = t.add(txs[cpu], subRoots[cpu], l, buckets[cpu][j].k, buckets[cpu][j].v)
if err != nil {
invalidsInBucket[cpu] = append(invalidsInBucket[cpu], Invalid{buckets[cpu][j].pos, err})
}
}
wg.Done()
}(i)
}
wg.Wait()
for i := 0; i < nCPU; i++ {
if err := wTx.Apply(txs[i]); err != nil {
return nil, err
}
txs[i].Discard()
}
for i := 0; i < len(invalidsInBucket); i++ {
invalids = append(invalids, invalidsInBucket[i]...)
}
newRoot, err := t.upFromSubRoots(wTx, subRoots)
if err != nil {
return nil, err
}
// update dbKeyNLeafs
if err := t.SetRootWithTx(wTx, newRoot); err != nil {
return nil, err
}
// update nLeafs
if err := t.incNLeafs(wTx, len(keys)-len(invalids)); err != nil {
return nil, err
}
return invalids, nil
}
func (t *Tree) upFromSubRoots(wTx db.WriteTx, subRoots [][]byte) ([]byte, error) {
// is a method of Tree just to get access to t.hashFunction and
// t.emptyHash.
// go up from subRoots to up, storing nodes in the given WriteTx
// once up at the root, store it in the WriteTx using the dbKeyRoot
if len(subRoots) == 1 {
return subRoots[0], nil
}
var newSubRoots [][]byte
// TODO store the nodes key-values into the wTx
for i := 0; i < len(subRoots); i += 2 {
if bytes.Equal(subRoots[i], t.emptyHash) && bytes.Equal(subRoots[i+1], t.emptyHash) {
// TODO: || (ns[i].typ() == vtLeaf && ns[i+1].typ() == vtEmpty) {
// when both sub nodes are empty, the parent is also empty
// or
// (TODO WIP) when 1st sub node is a leaf but the 2nd is empty, the
// leaf is used as parent
newSubRoots = append(newSubRoots, subRoots[i])
continue
}
// TODO if ns[i].typ() == vtEmpty && ns[i+1].typ() == vtLeaf {
// when 2nd sub node is a leaf but the 1st is empty, the
// leaf is used as 'parent'
k, v, err := t.newIntermediate(subRoots[i], subRoots[i+1])
if err != nil {
return nil, err
}
// store k-v to db
if err = wTx.Set(k, v); err != nil {
return nil, err
}
newSubRoots = append(newSubRoots, k)
}
return t.upFromSubRoots(wTx, newSubRoots)
}
func (t *Tree) getSubRootsAtLevel(rTx db.ReadTx, root []byte, l int) ([][]byte, error) {
// go at level l and return each node key, where each node key is the
// subRoot of the subTree that starts there
var subRoots [][]byte
err := t.iterWithStop(rTx, root, 0, func(currLvl int, k, v []byte) bool {
if currLvl == l && !bytes.Equal(k, t.emptyHash) {
subRoots = append(subRoots, k)
}
if currLvl >= l {
return true // to stop the iter from going down
}
return false
})
return subRoots, err
}
func (t *Tree) addBatchInMemory(wTx db.WriteTx, keys, values [][]byte) ([]Invalid, error) {
vt, err := t.loadVT(wTx)
if err != nil {
return nil, err
}
invalids, err := vt.addBatch(keys, values)
if err != nil {
return nil, err

62
tree_test.go
View File

@@ -11,6 +11,7 @@ import (
qt "github.com/frankban/quicktest"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
"go.vocdoni.io/dvote/db/pebbledb"
)
func checkRootBIString(c *qt.C, tree *Tree, expected string) {
@@ -23,11 +24,20 @@ func checkRootBIString(c *qt.C, tree *Tree, expected string) {
func TestDBTx(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
dbBadger, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
wTx := database.WriteTx()
testDBTx(c, dbBadger)
_, err = wTx.Get([]byte("a"))
dbPebble, err := pebbledb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
testDBTx(c, dbPebble)
}
func testDBTx(c *qt.C, database db.Database) {
wTx := database.WriteTx()
defer wTx.Discard()
_, err := wTx.Get([]byte("a"))
c.Assert(err, qt.Equals, db.ErrKeyNotFound)
err = wTx.Set([]byte("a"), []byte("b"))
@@ -60,7 +70,7 @@ func TestAddTestVectors(t *testing.T) {
}
func testAdd(c *qt.C, hashFunc HashFunction, testVectors []string) {
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, hashFunc)
c.Assert(err, qt.IsNil)
@@ -92,7 +102,7 @@ func testAdd(c *qt.C, hashFunc HashFunction, testVectors []string) {
func TestAddBatch(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -110,7 +120,7 @@ func TestAddBatch(t *testing.T) {
checkRootBIString(c, tree,
"296519252211642170490407814696803112091039265640052570497930797516015811235")
database, err = badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err = badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -133,7 +143,7 @@ func TestAddBatch(t *testing.T) {
func TestAddDifferentOrder(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -148,7 +158,7 @@ func TestAddDifferentOrder(t *testing.T) {
}
}
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -173,7 +183,7 @@ func TestAddDifferentOrder(t *testing.T) {
func TestAddRepeatedIndex(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -191,7 +201,7 @@ func TestAddRepeatedIndex(t *testing.T) {
func TestUpdate(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -244,7 +254,7 @@ func TestUpdate(t *testing.T) {
func TestAux(t *testing.T) { // TODO split in proper tests
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -283,7 +293,7 @@ func TestAux(t *testing.T) { // TODO split in proper tests
func TestGet(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -307,7 +317,7 @@ func TestGet(t *testing.T) {
func TestGenProofAndVerify(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -339,7 +349,7 @@ func TestGenProofAndVerify(t *testing.T) {
func TestDumpAndImportDump(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -357,7 +367,7 @@ func TestDumpAndImportDump(t *testing.T) {
e, err := tree1.Dump(nil)
c.Assert(err, qt.IsNil)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -376,7 +386,7 @@ func TestDumpAndImportDump(t *testing.T) {
func TestRWMutex(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -408,7 +418,7 @@ func TestRWMutex(t *testing.T) {
// TODO UPDATE
// func TestSetGetNLeafs(t *testing.T) {
// c := qt.New(t)
// database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
// database, err := badgerdb.New(db.Options{Path: c.TempDir()})
// c.Assert(err, qt.IsNil)
// tree, err := NewTree(database, 100, HashFunctionPoseidon)
// c.Assert(err, qt.IsNil)
@@ -459,12 +469,12 @@ func TestRWMutex(t *testing.T) {
func TestAddBatchFullyUsed(t *testing.T) {
c := qt.New(t)
database1, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database1, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree1, err := NewTree(database1, 4, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
database2, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database2, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree2, err := NewTree(database2, 4, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -518,7 +528,7 @@ func TestAddBatchFullyUsed(t *testing.T) {
func TestSetRoot(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -574,7 +584,7 @@ func TestSetRoot(t *testing.T) {
func TestSnapshot(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -624,7 +634,7 @@ func TestSnapshot(t *testing.T) {
func TestGetFromSnapshotExpectArboErrKeyNotFound(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 256, HashFunctionPoseidon)
c.Assert(err, qt.IsNil)
@@ -644,7 +654,7 @@ func TestGetFromSnapshotExpectArboErrKeyNotFound(t *testing.T) {
func TestKeyLen(t *testing.T) {
c := qt.New(t)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
// maxLevels is 100, keyPath length = ceil(maxLevels/8) = 13
maxLevels := 100
@@ -678,7 +688,7 @@ func TestKeyLen(t *testing.T) {
// expect errors when adding a key bigger than maximum capacity of the
// tree: ceil(maxLevels/8)
maxLevels = 32
database, err = badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err = badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err = NewTree(database, maxLevels, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -748,7 +758,7 @@ func TestKeyLen(t *testing.T) {
func TestKeyLenBiggerThan32(t *testing.T) {
c := qt.New(t)
maxLevels := 264
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, maxLevels, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)
@@ -790,7 +800,7 @@ func BenchmarkAdd(b *testing.B) {
func benchmarkAdd(b *testing.B, hashFunc HashFunction, ks, vs [][]byte) {
c := qt.New(b)
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, 140, hashFunc)
c.Assert(err, qt.IsNil)

6
vt.go
View File

@@ -37,7 +37,7 @@ type kv struct {
v []byte
}
func (p *params) keysValuesToKvs(ks, vs [][]byte) ([]kv, []Invalid, error) {
func keysValuesToKvs(maxLevels int, ks, vs [][]byte) ([]kv, []Invalid, error) {
if len(ks) != len(vs) {
return nil, nil, fmt.Errorf("len(keys)!=len(values) (%d!=%d)",
len(ks), len(vs))
@@ -45,7 +45,7 @@ func (p *params) keysValuesToKvs(ks, vs [][]byte) ([]kv, []Invalid, error) {
var invalids []Invalid
var kvs []kv
for i := 0; i < len(ks); i++ {
keyPath, err := keyPathFromKey(p.maxLevels, ks[i])
keyPath, err := keyPathFromKey(maxLevels, ks[i])
if err != nil {
invalids = append(invalids, Invalid{i, err})
continue
@@ -101,7 +101,7 @@ func (t *vt) addBatch(ks, vs [][]byte) ([]Invalid, error) {
l := int(math.Log2(float64(nCPU)))
kvs, invalids, err := t.params.keysValuesToKvs(ks, vs)
kvs, invalids, err := keysValuesToKvs(t.params.maxLevels, ks, vs)
if err != nil {
return invalids, err
}

5
vt_test.go
View File

@@ -7,6 +7,7 @@ import (
"testing"
qt "github.com/frankban/quicktest"
"go.vocdoni.io/dvote/db"
"go.vocdoni.io/dvote/db/badgerdb"
)
@@ -16,7 +17,7 @@ func testVirtualTree(c *qt.C, maxLevels int, keys, values [][]byte) {
c.Assert(len(keys), qt.Equals, len(values))
// normal tree, to have an expected root value
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, maxLevels, HashFunctionSha256)
c.Assert(err, qt.IsNil)
@@ -121,7 +122,7 @@ func TestVirtualTreeAddBatch(t *testing.T) {
}
// normal tree, to have an expected root value
database, err := badgerdb.New(badgerdb.Options{Path: c.TempDir()})
database, err := badgerdb.New(db.Options{Path: c.TempDir()})
c.Assert(err, qt.IsNil)
tree, err := NewTree(database, maxLevels, HashFunctionBlake2b)
c.Assert(err, qt.IsNil)