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[EN Performance] Optimize checkpoint serialization for -37GB operational RAM, -2.7 minutes duration, -19.6 million allocs (50% fewer allocs) #3050

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merged 7 commits into from
Aug 23, 2022
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[EN Performance] Optimize checkpoint serialization for -37GB operational RAM, -2.7 minutes duration, -19.6 million allocs (50% fewer allocs) #3050

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3be56c5
Modify NodeIterator to enable subtrie iteration
fxamacker Aug 22, 2022
9bc441c
Use subtries to optimize checkpoint serialization
fxamacker Aug 22, 2022
28331ac
Merge branch 'master' into fxamacker/reduce-checkpoint-serialization-…
fxamacker Aug 22, 2022
b88da42
Merge branch 'master' into fxamacker/reduce-checkpoint-serialization-…
fxamacker Aug 23, 2022
14b7303
Merge branch 'master' into fxamacker/reduce-checkpoint-serialization-…
fxamacker Aug 23, 2022
d136a3e
Merge branch 'master' into fxamacker/reduce-checkpoint-serialization-…
fxamacker Aug 23, 2022
20f3022
Merge branch 'master' into fxamacker/reduce-checkpoint-serialization-…
fxamacker Aug 23, 2022
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11 changes: 5 additions & 6 deletions ledger/complete/mtrie/flattener/iterator.go
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ package flattener
import (
"github.com/onflow/flow-go/ledger"
"github.com/onflow/flow-go/ledger/complete/mtrie/node"
"github.com/onflow/flow-go/ledger/complete/mtrie/trie"
)

// NodeIterator is an iterator over the nodes in a trie.
Expand Down Expand Up @@ -76,13 +75,13 @@ type NodeIterator struct {
// as for each node, the children have been previously encountered.
// NodeIterator created by NewNodeIterator is safe for concurrent use
// because visitedNodes is always nil in this case.
func NewNodeIterator(mTrie *trie.MTrie) *NodeIterator {
func NewNodeIterator(n *node.Node) *NodeIterator {
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thanks for fixing this node iterator to be a proper node iterator.

// for a Trie with height H (measured by number of edges), the longest possible path contains H+1 vertices
stackSize := ledger.NodeMaxHeight + 1
i := &NodeIterator{
stack: make([]*node.Node, 0, stackSize),
}
i.unprocessedRoot = mTrie.RootNode()
i.unprocessedRoot = n
return i
}

Expand All @@ -98,15 +97,15 @@ func NewNodeIterator(mTrie *trie.MTrie) *NodeIterator {
// When re-building the Trie from the sequence of nodes, one can build the trie on the fly,
// as for each node, the children have been previously encountered.
// WARNING: visitedNodes is not safe for concurrent use.
func NewUniqueNodeIterator(mTrie *trie.MTrie, visitedNodes map[*node.Node]uint64) *NodeIterator {
func NewUniqueNodeIterator(n *node.Node, visitedNodes map[*node.Node]uint64) *NodeIterator {
// For a Trie with height H (measured by number of edges), the longest possible path
// contains H+1 vertices.
stackSize := ledger.NodeMaxHeight + 1
i := &NodeIterator{
stack: make([]*node.Node, 0, stackSize),
visitedNodes: visitedNodes,
}
i.unprocessedRoot = mTrie.RootNode()
i.unprocessedRoot = n
return i
}

Expand All @@ -115,7 +114,7 @@ func (i *NodeIterator) Next() bool {
// initial call to Next() for a non-empty trie
i.dig(i.unprocessedRoot)
i.unprocessedRoot = nil
return true
return len(i.stack) > 0
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Why did we change this? It seems like an important change, but I don't see why we would

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This is a bug fix for a problem that didn't surface yet because of the way node iterator was used.

The bug is unique node iterator's Next() returns true when i.unprocessedRoot is visited already and i.stack is empty.

This bug doesn't happen when we iterate nodes of an entire trie (root nodes are always unique). In this PR, we iterate nodes of subtries and subtries can be shared and visited already. So instead of always returning true assuming there's at least one unique node when digging i.unprocessedRoot, we only return true when there are unique nodes in the internal stack after calling dig(i.unprocessedRoot).

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Thanks for the explanation! It does make sense.
Would it be possible to maybe add a test catching this particular bug, and showing how the fix helps?

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Would it be possible to maybe add a test catching this particular bug, and showing how the fix helps?

Test for this bug is already in iterator_test.go#L269-L396.

The test iterates 3 left substries and 3 right subtries (some subtries are shared). The test verifies that:

  • order of iterated nodes is descendents first
  • shared subtries/nodes are not iterated twice
  • non-nil node is returned (meaning as long as Next() returns true Value() returns a non-nil node)

}

// the current head of the stack, `n`, has been recalled
Expand Down
151 changes: 140 additions & 11 deletions ledger/complete/mtrie/flattener/iterator_test.go
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ import (
func TestEmptyTrie(t *testing.T) {
emptyTrie := trie.NewEmptyMTrie()

itr := flattener.NewNodeIterator(emptyTrie)
itr := flattener.NewNodeIterator(emptyTrie.RootNode())
require.True(t, nil == itr.Value()) // initial iterator should return nil

require.False(t, itr.Next())
Expand All @@ -30,7 +30,7 @@ func TestPopulatedTrie(t *testing.T) {
emptyTrie := trie.NewEmptyMTrie()

// key: 0000...
p1 := testutils.PathByUint8(1)
p1 := testutils.PathByUint8(0)
v1 := testutils.LightPayload8('A', 'a')

// key: 0100....
Expand All @@ -43,12 +43,12 @@ func TestPopulatedTrie(t *testing.T) {
testTrie, _, err := trie.NewTrieWithUpdatedRegisters(emptyTrie, paths, payloads, true)
require.NoError(t, err)

for itr := flattener.NewNodeIterator(testTrie); itr.Next(); {
for itr := flattener.NewNodeIterator(testTrie.RootNode()); itr.Next(); {
fmt.Println(itr.Value().FmtStr("", ""))
fmt.Println()
}

itr := flattener.NewNodeIterator(testTrie)
itr := flattener.NewNodeIterator(testTrie.RootNode())

require.True(t, itr.Next())
p1_leaf := itr.Value()
Expand Down Expand Up @@ -80,13 +80,13 @@ func TestUniqueNodeIterator(t *testing.T) {
emptyTrie := trie.NewEmptyMTrie()

// visitedNodes is nil
itr := flattener.NewUniqueNodeIterator(emptyTrie, nil)
itr := flattener.NewUniqueNodeIterator(emptyTrie.RootNode(), nil)
require.False(t, itr.Next())
require.True(t, nil == itr.Value()) // initial iterator should return nil

// visitedNodes is empty map
visitedNodes := make(map[*node.Node]uint64)
itr = flattener.NewUniqueNodeIterator(emptyTrie, visitedNodes)
itr = flattener.NewUniqueNodeIterator(emptyTrie.RootNode(), visitedNodes)
require.False(t, itr.Next())
require.True(t, nil == itr.Value()) // initial iterator should return nil
})
Expand All @@ -95,7 +95,7 @@ func TestUniqueNodeIterator(t *testing.T) {
emptyTrie := trie.NewEmptyMTrie()

// key: 0000...
p1 := testutils.PathByUint8(1)
p1 := testutils.PathByUint8(0)
v1 := testutils.LightPayload8('A', 'a')

// key: 0100....
Expand Down Expand Up @@ -126,7 +126,7 @@ func TestUniqueNodeIterator(t *testing.T) {

// visitedNodes is nil
i := 0
for itr := flattener.NewUniqueNodeIterator(updatedTrie, nil); itr.Next(); {
for itr := flattener.NewUniqueNodeIterator(updatedTrie.RootNode(), nil); itr.Next(); {
n := itr.Value()
require.True(t, i < len(expectedNodes))
require.Equal(t, expectedNodes[i], n)
Expand All @@ -138,7 +138,7 @@ func TestUniqueNodeIterator(t *testing.T) {
// there isn't any shared sub-trie.
visitedNodes := make(map[*node.Node]uint64)
i = 0
for itr := flattener.NewUniqueNodeIterator(updatedTrie, visitedNodes); itr.Next(); {
for itr := flattener.NewUniqueNodeIterator(updatedTrie.RootNode(), visitedNodes); itr.Next(); {
n := itr.Value()
visitedNodes[n] = uint64(i)

Expand All @@ -157,7 +157,7 @@ func TestUniqueNodeIterator(t *testing.T) {
emptyTrie := trie.NewEmptyMTrie()

// key: 0000...
p1 := testutils.PathByUint8(1)
p1 := testutils.PathByUint8(0)
v1 := testutils.LightPayload8('A', 'a')

// key: 0100....
Expand Down Expand Up @@ -254,7 +254,7 @@ func TestUniqueNodeIterator(t *testing.T) {
visitedNodes := make(map[*node.Node]uint64)
i := 0
for _, trie := range tries {
for itr := flattener.NewUniqueNodeIterator(trie, visitedNodes); itr.Next(); {
for itr := flattener.NewUniqueNodeIterator(trie.RootNode(), visitedNodes); itr.Next(); {
n := itr.Value()
visitedNodes[n] = uint64(i)

Expand All @@ -265,4 +265,133 @@ func TestUniqueNodeIterator(t *testing.T) {
}
require.Equal(t, i, len(expectedNodes))
})

t.Run("subtries", func(t *testing.T) {

emptyTrie := trie.NewEmptyMTrie()

// key: 0000...
p1 := testutils.PathByUint8(0)
v1 := testutils.LightPayload8('A', 'a')

// key: 0100....
p2 := testutils.PathByUint8(64)
v2 := testutils.LightPayload8('B', 'b')

paths := []ledger.Path{p1, p2}
payloads := []ledger.Payload{*v1, *v2}

trie1, _, err := trie.NewTrieWithUpdatedRegisters(emptyTrie, paths, payloads, true)
require.NoError(t, err)

// trie1
// n4
// /
// /
// n3
// / \
// / \
// n1 (p1/v1) n2 (p2/v2)
//

// New trie reuses its parent's left sub-trie.

// key: 1000...
p3 := testutils.PathByUint8(128)
v3 := testutils.LightPayload8('C', 'c')

// key: 1100....
p4 := testutils.PathByUint8(192)
v4 := testutils.LightPayload8('D', 'd')

paths = []ledger.Path{p3, p4}
payloads = []ledger.Payload{*v3, *v4}

trie2, _, err := trie.NewTrieWithUpdatedRegisters(trie1, paths, payloads, true)
require.NoError(t, err)

// trie2
// n8
// / \
// / \
// n3 n7
// (shared) / \
// / \
// n5 n6
// (p3/v3) (p4/v4)

// New trie reuses its parent's right sub-trie, and left sub-trie's leaf node.

// key: 0000...
v5 := testutils.LightPayload8('E', 'e')

paths = []ledger.Path{p1}
payloads = []ledger.Payload{*v5}

trie3, _, err := trie.NewTrieWithUpdatedRegisters(trie2, paths, payloads, true)
require.NoError(t, err)

// trie3
// n11
// / \
// / \
// n10 n7
// / \ (shared)
// / \
// n9 n2
// (p1/v5) (shared)

leftSubtries := []*node.Node{
trie1.RootNode().LeftChild(),
trie2.RootNode().LeftChild(),
trie3.RootNode().LeftChild(),
}

expectedNodesInLeftSubtries := []*node.Node{
// unique nodes from trie1
trie1.RootNode().LeftChild().LeftChild(), // n1
trie1.RootNode().LeftChild().RightChild(), // n2
trie1.RootNode().LeftChild(), // n3
// unique nodes from trie3
trie3.RootNode().LeftChild().LeftChild(), // n9
trie3.RootNode().LeftChild(), // n10
}

rightSubtries := []*node.Node{
trie1.RootNode().RightChild(),
trie2.RootNode().RightChild(),
trie3.RootNode().RightChild(),
}

expectedNodesInRightSubtries := []*node.Node{
// unique nodes from trie2
trie2.RootNode().RightChild().LeftChild(), // n5
trie2.RootNode().RightChild().RightChild(), // n6
trie2.RootNode().RightChild(), // n7
}

testcases := []struct {
roots []*node.Node
expectedNodes []*node.Node
}{
{leftSubtries, expectedNodesInLeftSubtries},
{rightSubtries, expectedNodesInRightSubtries},
}

for _, tc := range testcases {
visitedNodes := make(map[*node.Node]uint64)
i := 0
for _, n := range tc.roots {
for itr := flattener.NewUniqueNodeIterator(n, visitedNodes); itr.Next(); {
n := itr.Value()
visitedNodes[n] = uint64(i)

require.True(t, i < len(tc.expectedNodes))
require.Equal(t, tc.expectedNodes[i], n)
i++
}
}
require.Equal(t, i, len(tc.expectedNodes))
}
})
}
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