Use LRU to cache MPT nodes. (#227)

* Add trait.

* Update merkle tree trait.

* Use NodeManager.

* fix.

* Use LRU for cache.

* fix clippy.

* Save layer size.

* Initialize LogManager with NodeManager.

* Fix.

* Fix test.

* fix.

Cargo.lock

@@ -223,7 +223,9 @@ dependencies = [
  "eth2_ssz",
  "eth2_ssz_derive",
  "ethereum-types 0.14.1",
+ "itertools 0.13.0",
  "lazy_static",
+ "lru 0.12.5",
  "once_cell",
  "serde",
  "tiny-keccak",
@@ -1673,7 +1675,7 @@ dependencies = [
  "hkdf",
  "lazy_static",
  "libp2p-core 0.30.2",
- "lru",
+ "lru 0.7.8",
  "parking_lot 0.11.2",
  "rand 0.8.5",
  "rlp",
@@ -2514,6 +2516,12 @@ version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
 
+[[package]]
+name = "foldhash"
+version = "0.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f81ec6369c545a7d40e4589b5597581fa1c441fe1cce96dd1de43159910a36a2"
+
 [[package]]
 name = "foreign-types"
 version = "0.3.2"
@@ -2946,6 +2954,17 @@ dependencies = [
  "allocator-api2",
 ]
 
+[[package]]
+name = "hashbrown"
+version = "0.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e087f84d4f86bf4b218b927129862374b72199ae7d8657835f1e89000eea4fb"
+dependencies = [
+ "allocator-api2",
+ "equivalent",
+ "foldhash",
+]
+
 [[package]]
 name = "hashers"
 version = "1.0.1"
@@ -4117,7 +4136,7 @@ dependencies = [
  "libp2p-core 0.33.0",
  "libp2p-swarm",
  "log",
- "lru",
+ "lru 0.7.8",
  "prost 0.10.4",
  "prost-build 0.10.4",
  "prost-codec",
@@ -4650,6 +4669,15 @@ dependencies = [
  "hashbrown 0.12.3",
 ]
 
+[[package]]
+name = "lru"
+version = "0.12.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "234cf4f4a04dc1f57e24b96cc0cd600cf2af460d4161ac5ecdd0af8e1f3b2a38"
+dependencies = [
+ "hashbrown 0.15.0",
+]
+
 [[package]]
 name = "lru-cache"
 version = "0.1.2"
@@ -5019,7 +5047,7 @@ dependencies = [
  "lazy_static",
  "libp2p",
  "lighthouse_metrics",
- "lru",
+ "lru 0.7.8",
  "parking_lot 0.12.3",
  "rand 0.8.5",
  "regex",

Cargo.toml

@@ -36,4 +36,8 @@ eth2_ssz = { path = "version-meld/eth2_ssz" }
 enr = { path = "version-meld/enr" }
 
 [profile.bench.package.'storage']
-debug = true
+debug = true
+
+[profile.dev]
+# enabling debug_assertions will make node fail to start because of checks in `clap`.
+debug-assertions = false

common/append_merkle/Cargo.toml

@@ -12,4 +12,6 @@ eth2_ssz_derive = "0.3.0"
 serde = { version = "1.0.137", features = ["derive"] }
 lazy_static = "1.4.0"
 tracing = "0.1.36"
-once_cell = "1.19.0"
+once_cell = "1.19.0"
+itertools = "0.13.0"
+lru = "0.12.5"

common/append_merkle/src/lib.rs

@@ -1,23 +1,28 @@
 mod merkle_tree;
+mod node_manager;
 mod proof;
 mod sha3;
 
 use anyhow::{anyhow, bail, Result};
+use itertools::Itertools;
 use std::cmp::Ordering;
 use std::collections::{BTreeMap, HashMap};
 use std::fmt::Debug;
 use std::marker::PhantomData;
+use std::sync::Arc;
 use tracing::{trace, warn};
 
+use crate::merkle_tree::MerkleTreeWrite;
 pub use crate::merkle_tree::{
     Algorithm, HashElement, MerkleTreeInitialData, MerkleTreeRead, ZERO_HASHES,
 };
+pub use crate::node_manager::{EmptyNodeDatabase, NodeDatabase, NodeManager, NodeTransaction};
 pub use proof::{Proof, RangeProof};
 pub use sha3::Sha3Algorithm;
 
 pub struct AppendMerkleTree<E: HashElement, A: Algorithm<E>> {
     /// Keep all the nodes in the latest version. `layers[0]` is the layer of leaves.
-    layers: Vec<Vec<E>>,
+    node_manager: NodeManager<E>,
     /// Keep the delta nodes that can be used to construct a history tree.
     /// The key is the root node of that version.
     delta_nodes_map: BTreeMap<u64, DeltaNodes<E>>,
@@ -35,13 +40,16 @@ pub struct AppendMerkleTree<E: HashElement, A: Algorithm<E>> {
 impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     pub fn new(leaves: Vec<E>, leaf_height: usize, start_tx_seq: Option<u64>) -> Self {
         let mut merkle = Self {
-            layers: vec![leaves],
+            node_manager: NodeManager::new_dummy(),
             delta_nodes_map: BTreeMap::new(),
             root_to_tx_seq_map: HashMap::new(),
             min_depth: None,
             leaf_height,
             _a: Default::default(),
         };
+        merkle.node_manager.start_transaction();
+        merkle.node_manager.add_layer();
+        merkle.node_manager.append_nodes(0, &leaves);
         if merkle.leaves() == 0 {
             if let Some(seq) = start_tx_seq {
                 merkle.delta_nodes_map.insert(
@@ -51,10 +59,12 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
                     },
                 );
             }
+            merkle.node_manager.commit();
             return merkle;
         }
         // Reconstruct the whole tree.
         merkle.recompute(0, 0, None);
+        merkle.node_manager.commit();
         // Commit the first version in memory.
         // TODO(zz): Check when the roots become available.
         merkle.commit(start_tx_seq);
@@ -62,53 +72,44 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     }
 
     pub fn new_with_subtrees(
-        initial_data: MerkleTreeInitialData<E>,
+        node_db: Arc<dyn NodeDatabase<E>>,
+        node_cache_capacity: usize,
         leaf_height: usize,
-        start_tx_seq: Option<u64>,
     ) -> Result<Self> {
         let mut merkle = Self {
-            layers: vec![vec![]],
+            node_manager: NodeManager::new(node_db, node_cache_capacity)?,
             delta_nodes_map: BTreeMap::new(),
             root_to_tx_seq_map: HashMap::new(),
             min_depth: None,
             leaf_height,
             _a: Default::default(),
         };
-        if initial_data.subtree_list.is_empty() {
-            if let Some(seq) = start_tx_seq {
-                merkle.delta_nodes_map.insert(
-                    seq,
-                    DeltaNodes {
-                        right_most_nodes: vec![],
-                    },
-                );
-            }
-            return Ok(merkle);
-        }
-        merkle.append_subtree_list(initial_data.subtree_list)?;
-        merkle.commit(start_tx_seq);
-        for (index, h) in initial_data.known_leaves {
-            merkle.fill_leaf(index, h);
-        }
-        for (layer_index, position, h) in initial_data.extra_mpt_nodes {
-            // TODO: Delete duplicate nodes from DB.
-            merkle.layers[layer_index][position] = h;
+        if merkle.height() == 0 {
+            merkle.node_manager.start_transaction();
+            merkle.node_manager.add_layer();
+            merkle.node_manager.commit();
         }
         Ok(merkle)
     }
 
     /// This is only used for the last chunk, so `leaf_height` is always 0 so far.
     pub fn new_with_depth(leaves: Vec<E>, depth: usize, start_tx_seq: Option<u64>) -> Self {
+        let mut node_manager = NodeManager::new_dummy();
+        node_manager.start_transaction();
         if leaves.is_empty() {
             // Create an empty merkle tree with `depth`.
             let mut merkle = Self {
-                layers: vec![vec![]; depth],
+                // dummy node manager for the last chunk.
+                node_manager,
                 delta_nodes_map: BTreeMap::new(),
                 root_to_tx_seq_map: HashMap::new(),
                 min_depth: Some(depth),
                 leaf_height: 0,
                 _a: Default::default(),
             };
+            for _ in 0..depth {
+                merkle.node_manager.add_layer();
+            }
             if let Some(seq) = start_tx_seq {
                 merkle.delta_nodes_map.insert(
                     seq,
@@ -117,20 +118,26 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
                     },
                 );
             }
+            merkle.node_manager.commit();
             merkle
         } else {
-            let mut layers = vec![vec![]; depth];
-            layers[0] = leaves;
             let mut merkle = Self {
-                layers,
+                // dummy node manager for the last chunk.
+                node_manager,
                 delta_nodes_map: BTreeMap::new(),
                 root_to_tx_seq_map: HashMap::new(),
                 min_depth: Some(depth),
                 leaf_height: 0,
                 _a: Default::default(),
             };
+            merkle.node_manager.add_layer();
+            merkle.append_nodes(0, &leaves);
+            for _ in 1..depth {
+                merkle.node_manager.add_layer();
+            }
             // Reconstruct the whole tree.
             merkle.recompute(0, 0, None);
+            merkle.node_manager.commit();
             // Commit the first version in memory.
             merkle.commit(start_tx_seq);
             merkle
@@ -142,18 +149,22 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             // appending null is not allowed.
             return;
         }
-        self.layers[0].push(new_leaf);
+        self.node_manager.start_transaction();
+        self.node_manager.push_node(0, new_leaf);
         self.recompute_after_append_leaves(self.leaves() - 1);
+        self.node_manager.commit();
     }
 
-    pub fn append_list(&mut self, mut leaf_list: Vec<E>) {
+    pub fn append_list(&mut self, leaf_list: Vec<E>) {
         if leaf_list.contains(&E::null()) {
             // appending null is not allowed.
             return;
         }
+        self.node_manager.start_transaction();
         let start_index = self.leaves();
-        self.layers[0].append(&mut leaf_list);
+        self.node_manager.append_nodes(0, &leaf_list);
         self.recompute_after_append_leaves(start_index);
+        self.node_manager.commit();
     }
 
     /// Append a leaf list by providing their intermediate node hash.
@@ -166,9 +177,11 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             // appending null is not allowed.
             bail!("subtree_root is null");
         }
+        self.node_manager.start_transaction();
         let start_index = self.leaves();
         self.append_subtree_inner(subtree_depth, subtree_root)?;
         self.recompute_after_append_subtree(start_index, subtree_depth - 1);
+        self.node_manager.commit();
         Ok(())
     }
 
@@ -177,11 +190,13 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             // appending null is not allowed.
             bail!("subtree_list contains null");
         }
+        self.node_manager.start_transaction();
         for (subtree_depth, subtree_root) in subtree_list {
             let start_index = self.leaves();
             self.append_subtree_inner(subtree_depth, subtree_root)?;
             self.recompute_after_append_subtree(start_index, subtree_depth - 1);
         }
+        self.node_manager.commit();
         Ok(())
     }
 
@@ -192,13 +207,15 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             // updating to null is not allowed.
             return;
         }
-        if self.layers[0].is_empty() {
+        self.node_manager.start_transaction();
+        if self.layer_len(0) == 0 {
             // Special case for the first data.
-            self.layers[0].push(updated_leaf);
+            self.push_node(0, updated_leaf);
         } else {
-            *self.layers[0].last_mut().unwrap() = updated_leaf;
+            self.update_node(0, self.layer_len(0) - 1, updated_leaf);
         }
         self.recompute_after_append_leaves(self.leaves() - 1);
+        self.node_manager.commit();
     }
 
     /// Fill an unknown `null` leaf with its real value.
@@ -207,13 +224,17 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     pub fn fill_leaf(&mut self, index: usize, leaf: E) {
         if leaf == E::null() {
             // fill leaf with null is not allowed.
-        } else if self.layers[0][index] == E::null() {
-            self.layers[0][index] = leaf;
+        } else if self.node(0, index) == E::null() {
+            self.node_manager.start_transaction();
+            self.update_node(0, index, leaf);
             self.recompute_after_fill_leaves(index, index + 1);
-        } else if self.layers[0][index] != leaf {
+            self.node_manager.commit();
+        } else if self.node(0, index) != leaf {
             panic!(
                 "Fill with invalid leaf, index={} was={:?} get={:?}",
-                index, self.layers[0][index], leaf
+                index,
+                self.node(0, index),
+                leaf
             );
         }
     }
@@ -226,6 +247,7 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         &mut self,
         proof: RangeProof<E>,
     ) -> Result<Vec<(usize, usize, E)>> {
+        self.node_manager.start_transaction();
         let mut updated_nodes = Vec::new();
         let mut left_nodes = proof.left_proof.proof_nodes_in_tree();
         if left_nodes.len() >= self.leaf_height {
@@ -237,6 +259,7 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             updated_nodes
                 .append(&mut self.fill_with_proof(right_nodes.split_off(self.leaf_height))?);
         }
+        self.node_manager.commit();
         Ok(updated_nodes)
     }
 
@@ -262,13 +285,16 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         if tx_merkle_nodes.is_empty() {
             return Ok(Vec::new());
         }
+        self.node_manager.start_transaction();
         let mut position_and_data =
             proof.file_proof_nodes_in_tree(tx_merkle_nodes, tx_merkle_nodes_size);
         let start_index = (start_index >> self.leaf_height) as usize;
         for (i, (position, _)) in position_and_data.iter_mut().enumerate() {
             *position += start_index >> i;
         }
-        self.fill_with_proof(position_and_data)
+        let updated_nodes = self.fill_with_proof(position_and_data)?;
+        self.node_manager.commit();
+        Ok(updated_nodes)
     }
 
     /// This assumes that the proof leaf is no lower than the tree leaf. It holds for both SegmentProof and ChunkProof.
@@ -280,28 +306,27 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         let mut updated_nodes = Vec::new();
         // A valid proof should not fail the following checks.
         for (i, (position, data)) in position_and_data.into_iter().enumerate() {
-            let layer = &mut self.layers[i];
-            if position > layer.len() {
+            if position > self.layer_len(i) {
                 bail!(
                     "proof position out of range, position={} layer.len()={}",
                     position,
-                    layer.len()
+                    self.layer_len(i)
                 );
             }
-            if position == layer.len() {
+            if position == self.layer_len(i) {
                 // skip padding node.
                 continue;
             }
-            if layer[position] == E::null() {
-                layer[position] = data.clone();
+            if self.node(i, position) == E::null() {
+                self.update_node(i, position, data.clone());
                 updated_nodes.push((i, position, data))
-            } else if layer[position] != data {
+            } else if self.node(i, position) != data {
                 // The last node in each layer may have changed in the tree.
                 trace!(
                     "conflict data layer={} position={} tree_data={:?} proof_data={:?}",
                     i,
                     position,
-                    layer[position],
+                    self.node(i, position),
                     data
                 );
             }
@@ -317,8 +342,8 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         if position >= self.leaves() {
             bail!("Out of bound: position={} end={}", position, self.leaves());
         }
-        if self.layers[0][position] != E::null() {
-            Ok(Some(self.layers[0][position].clone()))
+        if self.node(0, position) != E::null() {
+            Ok(Some(self.node(0, position)))
         } else {
             // The leaf hash is unknown.
             Ok(None)
@@ -366,10 +391,11 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
                 return;
             }
             let mut right_most_nodes = Vec::new();
-            for layer in &self.layers {
-                right_most_nodes.push((layer.len() - 1, layer.last().unwrap().clone()));
+            for height in 0..self.height() {
+                let pos = self.layer_len(height) - 1;
+                right_most_nodes.push((pos, self.node(height, pos)));
             }
-            let root = self.root().clone();
+            let root = self.root();
             self.delta_nodes_map
                 .insert(tx_seq, DeltaNodes::new(right_most_nodes));
             self.root_to_tx_seq_map.insert(root, tx_seq);
@@ -377,8 +403,8 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     }
 
     fn before_extend_layer(&mut self, height: usize) {
-        if height == self.layers.len() {
-            self.layers.push(Vec::new());
+        if height == self.height() {
+            self.node_manager.add_layer()
         }
     }
 
@@ -395,7 +421,6 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     }
 
     /// Given a range of changed leaf nodes and recompute the tree.
-    /// Since this tree is append-only, we always compute to the end.
     fn recompute(
         &mut self,
         mut start_index: usize,
@@ -405,42 +430,51 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         start_index >>= height;
         maybe_end_index = maybe_end_index.map(|end| end >> height);
         // Loop until we compute the new root and reach `tree_depth`.
-        while self.layers[height].len() > 1 || height < self.layers.len() - 1 {
+        while self.layer_len(height) > 1 || height < self.height() - 1 {
             let next_layer_start_index = start_index >> 1;
             if start_index % 2 == 1 {
                 start_index -= 1;
             }
 
-            let mut end_index = maybe_end_index.unwrap_or(self.layers[height].len());
-            if end_index % 2 == 1 && end_index != self.layers[height].len() {
+            let mut end_index = maybe_end_index.unwrap_or(self.layer_len(height));
+            if end_index % 2 == 1 && end_index != self.layer_len(height) {
                 end_index += 1;
             }
             let mut i = 0;
-            let mut iter = self.layers[height][start_index..end_index].chunks_exact(2);
+            let iter = self
+                .node_manager
+                .get_nodes(height, start_index, end_index)
+                .chunks(2);
             // We cannot modify the parent layer while iterating the child layer,
             // so just keep the changes and update them later.
             let mut parent_update = Vec::new();
-            while let Some([left, right]) = iter.next() {
-                // If either left or right is null (unknown), we cannot compute the parent hash.
-                // Note that if we are recompute a range of an existing tree,
-                // we do not need to keep these possibly null parent. This is only saved
-                // for the case of constructing a new tree from the leaves.
-                let parent = if *left == E::null() || *right == E::null() {
-                    E::null()
+            for chunk_iter in &iter {
+                let chunk: Vec<_> = chunk_iter.collect();
+                if chunk.len() == 2 {
+                    let left = &chunk[0];
+                    let right = &chunk[1];
+                    // If either left or right is null (unknown), we cannot compute the parent hash.
+                    // Note that if we are recompute a range of an existing tree,
+                    // we do not need to keep these possibly null parent. This is only saved
+                    // for the case of constructing a new tree from the leaves.
+                    let parent = if *left == E::null() || *right == E::null() {
+                        E::null()
+                    } else {
+                        A::parent(left, right)
+                    };
+                    parent_update.push((next_layer_start_index + i, parent));
+                    i += 1;
                 } else {
-                    A::parent(left, right)
-                };
-                parent_update.push((next_layer_start_index + i, parent));
-                i += 1;
-            }
-            if let [r] = iter.remainder() {
-                // Same as above.
-                let parent = if *r == E::null() {
-                    E::null()
-                } else {
-                    A::parent_single(r, height + self.leaf_height)
-                };
-                parent_update.push((next_layer_start_index + i, parent));
+                    assert_eq!(chunk.len(), 1);
+                    let r = &chunk[0];
+                    // Same as above.
+                    let parent = if *r == E::null() {
+                        E::null()
+                    } else {
+                        A::parent_single(r, height + self.leaf_height)
+                    };
+                    parent_update.push((next_layer_start_index + i, parent));
+                }
             }
             if !parent_update.is_empty() {
                 self.before_extend_layer(height + 1);
@@ -449,27 +483,27 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             // we can just overwrite `last_changed_parent_index` with new values.
             let mut last_changed_parent_index = None;
             for (parent_index, parent) in parent_update {
-                match parent_index.cmp(&self.layers[height + 1].len()) {
+                match parent_index.cmp(&self.layer_len(height + 1)) {
                     Ordering::Less => {
                         // We do not overwrite with null.
                         if parent != E::null() {
-                            if self.layers[height + 1][parent_index] == E::null()
+                            if self.node(height + 1, parent_index) == E::null()
                                 // The last node in a layer can be updated.
-                                || (self.layers[height + 1][parent_index] != parent
-                                    && parent_index == self.layers[height + 1].len() - 1)
+                                || (self.node(height + 1, parent_index) != parent
+                                    && parent_index == self.layer_len(height + 1) - 1)
                             {
-                                self.layers[height + 1][parent_index] = parent;
+                                self.update_node(height + 1, parent_index, parent);
                                 last_changed_parent_index = Some(parent_index);
-                            } else if self.layers[height + 1][parent_index] != parent {
+                            } else if self.node(height + 1, parent_index) != parent {
                                 // Recompute changes a node in the middle. This should be impossible
                                 // if the inputs are valid.
                                 panic!("Invalid append merkle tree! height={} index={} expected={:?} get={:?}",
-                                       height + 1, parent_index, self.layers[height + 1][parent_index], parent);
+                                       height + 1, parent_index, self.node(height + 1, parent_index), parent);
                             }
                         }
                     }
                     Ordering::Equal => {
-                        self.layers[height + 1].push(parent);
+                        self.push_node(height + 1, parent);
                         last_changed_parent_index = Some(parent_index);
                     }
                     Ordering::Greater => {
@@ -500,10 +534,10 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
         for height in 0..(subtree_depth - 1) {
             self.before_extend_layer(height);
             let subtree_layer_size = 1 << (subtree_depth - 1 - height);
-            self.layers[height].append(&mut vec![E::null(); subtree_layer_size]);
+            self.append_nodes(height, &vec![E::null(); subtree_layer_size]);
         }
         self.before_extend_layer(subtree_depth - 1);
-        self.layers[subtree_depth - 1].push(subtree_root);
+        self.push_node(subtree_depth - 1, subtree_root);
         Ok(())
     }
 
@@ -514,23 +548,45 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     }
 
     pub fn revert_to(&mut self, tx_seq: u64) -> Result<()> {
-        if self.layers[0].is_empty() {
+        if self.layer_len(0) == 0 {
             // Any previous state of an empty tree is always empty.
             return Ok(());
         }
+        self.node_manager.start_transaction();
         let delta_nodes = self
             .delta_nodes_map
             .get(&tx_seq)
-            .ok_or_else(|| anyhow!("tx_seq unavailable, root={:?}", tx_seq))?;
+            .ok_or_else(|| anyhow!("tx_seq unavailable, root={:?}", tx_seq))?
+            .clone();
         // Dropping the upper layers that are not in the old merkle tree.
-        self.layers.truncate(delta_nodes.right_most_nodes.len());
+        for height in (delta_nodes.right_most_nodes.len()..self.height()).rev() {
+            self.node_manager.truncate_layer(height);
+        }
         for (height, (last_index, right_most_node)) in
             delta_nodes.right_most_nodes.iter().enumerate()
         {
-            self.layers[height].truncate(*last_index + 1);
-            self.layers[height][*last_index] = right_most_node.clone();
+            self.node_manager.truncate_nodes(height, *last_index + 1);
+            self.update_node(height, *last_index, right_most_node.clone())
         }
         self.clear_after(tx_seq);
+        self.node_manager.commit();
+        Ok(())
+    }
+
+    // Revert to a tx_seq not in `delta_nodes_map`.
+    // This is needed to revert the last unfinished tx after restart.
+    pub fn revert_to_leaves(&mut self, leaves: usize) -> Result<()> {
+        self.node_manager.start_transaction();
+        for height in (0..self.height()).rev() {
+            let kept_nodes = leaves >> height;
+            if kept_nodes == 0 {
+                self.node_manager.truncate_layer(height);
+            } else {
+                self.node_manager.truncate_nodes(height, kept_nodes + 1);
+            }
+        }
+        self.recompute_after_append_leaves(leaves);
+        self.node_manager.commit();
         Ok(())
     }
 
@@ -550,17 +606,25 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
             bail!("empty tree");
         }
         Ok(HistoryTree {
-            layers: &self.layers,
+            node_manager: &self.node_manager,
             delta_nodes,
             leaf_height: self.leaf_height,
         })
     }
 
     pub fn reset(&mut self) {
-        self.layers = match self.min_depth {
-            None => vec![vec![]],
-            Some(depth) => vec![vec![]; depth],
-        };
+        self.node_manager.start_transaction();
+        for height in (0..self.height()).rev() {
+            self.node_manager.truncate_layer(height);
+        }
+        if let Some(depth) = self.min_depth {
+            for _ in 0..depth {
+                self.node_manager.add_layer();
+            }
+        } else {
+            self.node_manager.add_layer();
+        }
+        self.node_manager.commit();
     }
 
     fn clear_after(&mut self, tx_seq: u64) {
@@ -580,10 +644,10 @@ impl<E: HashElement, A: Algorithm<E>> AppendMerkleTree<E, A> {
     fn first_known_root_at(&self, index: usize) -> (usize, E) {
         let mut height = 0;
         let mut index_in_layer = index;
-        while height < self.layers.len() {
+        while height < self.height() {
             let node = self.node(height, index_in_layer);
             if !node.is_null() {
-                return (height + 1, node.clone());
+                return (height + 1, node);
             }
             height += 1;
             index_in_layer /= 2;
@@ -628,7 +692,7 @@ impl<E: HashElement> DeltaNodes<E> {
 
 pub struct HistoryTree<'m, E: HashElement> {
     /// A reference to the global tree nodes.
-    layers: &'m Vec<Vec<E>>,
+    node_manager: &'m NodeManager<E>,
     /// The delta nodes that are difference from `layers`.
     /// This could be a reference, we just take ownership for convenience.
     delta_nodes: &'m DeltaNodes<E>,
@@ -639,16 +703,18 @@ pub struct HistoryTree<'m, E: HashElement> {
 impl<E: HashElement, A: Algorithm<E>> MerkleTreeRead for AppendMerkleTree<E, A> {
     type E = E;
 
-    fn node(&self, layer: usize, index: usize) -> &Self::E {
-        &self.layers[layer][index]
+    fn node(&self, layer: usize, index: usize) -> Self::E {
+        self.node_manager
+            .get_node(layer, index)
+            .expect("index checked")
     }
 
     fn height(&self) -> usize {
-        self.layers.len()
+        self.node_manager.num_layers()
     }
 
     fn layer_len(&self, layer_height: usize) -> usize {
-        self.layers[layer_height].len()
+        self.node_manager.layer_size(layer_height)
     }
 
     fn padding_node(&self, height: usize) -> Self::E {
@@ -658,10 +724,13 @@ impl<E: HashElement, A: Algorithm<E>> MerkleTreeRead for AppendMerkleTree<E, A>
 
 impl<'a, E: HashElement> MerkleTreeRead for HistoryTree<'a, E> {
     type E = E;
-    fn node(&self, layer: usize, index: usize) -> &Self::E {
+    fn node(&self, layer: usize, index: usize) -> Self::E {
         match self.delta_nodes.get(layer, index).expect("range checked") {
-            Some(node) if *node != E::null() => node,
-            _ => &self.layers[layer][index],
+            Some(node) if *node != E::null() => node.clone(),
+            _ => self
+                .node_manager
+                .get_node(layer, index)
+                .expect("index checked"),
         }
     }
 
@@ -678,6 +747,22 @@ impl<'a, E: HashElement> MerkleTreeRead for HistoryTree<'a, E> {
     }
 }
 
+impl<E: HashElement, A: Algorithm<E>> MerkleTreeWrite for AppendMerkleTree<E, A> {
+    type E = E;
+
+    fn push_node(&mut self, layer: usize, node: Self::E) {
+        self.node_manager.push_node(layer, node);
+    }
+
+    fn append_nodes(&mut self, layer: usize, nodes: &[Self::E]) {
+        self.node_manager.append_nodes(layer, nodes);
+    }
+
+    fn update_node(&mut self, layer: usize, pos: usize, node: Self::E) {
+        self.node_manager.add_node(layer, pos, node);
+    }
+}
+
 #[macro_export]
 macro_rules! ensure_eq {
     ($given:expr, $expected:expr) => {
@@ -699,6 +784,7 @@ macro_rules! ensure_eq {
 #[cfg(test)]
 mod tests {
     use crate::merkle_tree::MerkleTreeRead;
+
     use crate::sha3::Sha3Algorithm;
     use crate::AppendMerkleTree;
     use ethereum_types::H256;

common/append_merkle/src/merkle_tree.rs

@@ -49,7 +49,7 @@ pub trait Algorithm<E: HashElement> {
 
 pub trait MerkleTreeRead {
     type E: HashElement;
-    fn node(&self, layer: usize, index: usize) -> &Self::E;
+    fn node(&self, layer: usize, index: usize) -> Self::E;
     fn height(&self) -> usize;
     fn layer_len(&self, layer_height: usize) -> usize;
     fn padding_node(&self, height: usize) -> Self::E;
@@ -58,7 +58,7 @@ pub trait MerkleTreeRead {
         self.layer_len(0)
     }
 
-    fn root(&self) -> &Self::E {
+    fn root(&self) -> Self::E {
         self.node(self.height() - 1, 0)
     }
 
@@ -70,16 +70,16 @@ pub trait MerkleTreeRead {
                 self.leaves()
             );
         }
-        if self.node(0, leaf_index) == &Self::E::null() {
+        if self.node(0, leaf_index) == Self::E::null() {
             bail!("Not ready to generate proof for leaf_index={}", leaf_index);
         }
         if self.height() == 1 {
-            return Proof::new(vec![self.root().clone(), self.root().clone()], vec![]);
+            return Proof::new(vec![self.root(), self.root().clone()], vec![]);
         }
         let mut lemma: Vec<Self::E> = Vec::with_capacity(self.height()); // path + root
         let mut path: Vec<bool> = Vec::with_capacity(self.height() - 2); // path - 1
         let mut index_in_layer = leaf_index;
-        lemma.push(self.node(0, leaf_index).clone());
+        lemma.push(self.node(0, leaf_index));
         for height in 0..(self.height() - 1) {
             trace!(
                 "gen_proof: height={} index={} hash={:?}",
@@ -93,15 +93,15 @@ pub trait MerkleTreeRead {
                     // TODO: This can be skipped if the tree size is available in validation.
                     lemma.push(self.padding_node(height));
                 } else {
-                    lemma.push(self.node(height, index_in_layer + 1).clone());
+                    lemma.push(self.node(height, index_in_layer + 1));
                 }
             } else {
                 path.push(false);
-                lemma.push(self.node(height, index_in_layer - 1).clone());
+                lemma.push(self.node(height, index_in_layer - 1));
             }
             index_in_layer >>= 1;
         }
-        lemma.push(self.root().clone());
+        lemma.push(self.root());
         if lemma.contains(&Self::E::null()) {
             bail!(
                 "Not enough data to generate proof, lemma={:?} path={:?}",
@@ -130,6 +130,13 @@ pub trait MerkleTreeRead {
     }
 }
 
+pub trait MerkleTreeWrite {
+    type E: HashElement;
+    fn push_node(&mut self, layer: usize, node: Self::E);
+    fn append_nodes(&mut self, layer: usize, nodes: &[Self::E]);
+    fn update_node(&mut self, layer: usize, pos: usize, node: Self::E);
+}
+
 /// This includes the data to reconstruct an `AppendMerkleTree` root where some nodes
 /// are `null`. Other intermediate nodes will be computed based on these known nodes.
 pub struct MerkleTreeInitialData<E: HashElement> {

common/append_merkle/src/node_manager.rs

@@ -0,0 +1,219 @@
+use crate::HashElement;
+use anyhow::Result;
+use lru::LruCache;
+use std::any::Any;
+use std::num::NonZeroUsize;
+use std::sync::Arc;
+use tracing::error;
+
+pub struct NodeManager<E: HashElement> {
+    cache: LruCache<(usize, usize), E>,
+    layer_size: Vec<usize>,
+    db: Arc<dyn NodeDatabase<E>>,
+    db_tx: Option<Box<dyn NodeTransaction<E>>>,
+}
+
+impl<E: HashElement> NodeManager<E> {
+    pub fn new(db: Arc<dyn NodeDatabase<E>>, capacity: usize) -> Result<Self> {
+        let mut layer = 0;
+        let mut layer_size = Vec::new();
+        while let Some(size) = db.get_layer_size(layer)? {
+            layer_size.push(size);
+            layer += 1;
+        }
+        Ok(Self {
+            cache: LruCache::new(NonZeroUsize::new(capacity).expect("capacity should be non-zero")),
+            layer_size,
+            db,
+            db_tx: None,
+        })
+    }
+
+    pub fn new_dummy() -> Self {
+        Self {
+            cache: LruCache::unbounded(),
+            layer_size: vec![],
+            db: Arc::new(EmptyNodeDatabase {}),
+            db_tx: None,
+        }
+    }
+
+    pub fn push_node(&mut self, layer: usize, node: E) {
+        self.add_node(layer, self.layer_size[layer], node);
+        self.set_layer_size(layer, self.layer_size[layer] + 1);
+    }
+
+    pub fn append_nodes(&mut self, layer: usize, nodes: &[E]) {
+        let mut pos = self.layer_size[layer];
+        let mut saved_nodes = Vec::with_capacity(nodes.len());
+        for node in nodes {
+            self.cache.put((layer, pos), node.clone());
+            saved_nodes.push((layer, pos, node));
+            pos += 1;
+        }
+        self.set_layer_size(layer, pos);
+        self.db_tx().save_node_list(&saved_nodes);
+    }
+
+    pub fn get_node(&self, layer: usize, pos: usize) -> Option<E> {
+        match self.cache.peek(&(layer, pos)) {
+            Some(node) => Some(node.clone()),
+            None => self.db.get_node(layer, pos).unwrap_or_else(|e| {
+                error!("Failed to get node: {}", e);
+                None
+            }),
+        }
+    }
+
+    pub fn get_nodes(&self, layer: usize, start_pos: usize, end_pos: usize) -> NodeIterator<E> {
+        NodeIterator {
+            node_manager: self,
+            layer,
+            start_pos,
+            end_pos,
+        }
+    }
+
+    pub fn add_node(&mut self, layer: usize, pos: usize, node: E) {
+        // No need to insert if the value is unchanged.
+        if self.cache.get(&(layer, pos)) != Some(&node) {
+            self.db_tx().save_node(layer, pos, &node);
+            self.cache.put((layer, pos), node);
+        }
+    }
+
+    pub fn add_layer(&mut self) {
+        self.layer_size.push(0);
+        let layer = self.layer_size.len() - 1;
+        self.db_tx().save_layer_size(layer, 0);
+    }
+
+    pub fn layer_size(&self, layer: usize) -> usize {
+        self.layer_size[layer]
+    }
+
+    pub fn num_layers(&self) -> usize {
+        self.layer_size.len()
+    }
+
+    pub fn truncate_nodes(&mut self, layer: usize, pos_end: usize) {
+        let mut removed_nodes = Vec::new();
+        for pos in pos_end..self.layer_size[layer] {
+            self.cache.pop(&(layer, pos));
+            removed_nodes.push((layer, pos));
+        }
+        self.db_tx().remove_node_list(&removed_nodes);
+        self.set_layer_size(layer, pos_end);
+    }
+
+    pub fn truncate_layer(&mut self, layer: usize) {
+        self.truncate_nodes(layer, 0);
+        if layer == self.num_layers() - 1 {
+            self.layer_size.pop();
+            self.db_tx().remove_layer_size(layer);
+        }
+    }
+
+    pub fn start_transaction(&mut self) {
+        if self.db_tx.is_some() {
+            error!("start new tx before commit");
+            panic!("start new tx before commit");
+        }
+        self.db_tx = Some(self.db.start_transaction());
+    }
+
+    pub fn commit(&mut self) {
+        let tx = match self.db_tx.take() {
+            Some(tx) => tx,
+            None => {
+                error!("db_tx is None");
+                return;
+            }
+        };
+        if let Err(e) = self.db.commit(tx) {
+            error!("Failed to commit db transaction: {}", e);
+        }
+    }
+
+    fn db_tx(&mut self) -> &mut dyn NodeTransaction<E> {
+        (*self.db_tx.as_mut().expect("tx checked")).as_mut()
+    }
+
+    fn set_layer_size(&mut self, layer: usize, size: usize) {
+        self.layer_size[layer] = size;
+        self.db_tx().save_layer_size(layer, size);
+    }
+}
+
+pub struct NodeIterator<'a, E: HashElement> {
+    node_manager: &'a NodeManager<E>,
+    layer: usize,
+    start_pos: usize,
+    end_pos: usize,
+}
+
+impl<'a, E: HashElement> Iterator for NodeIterator<'a, E> {
+    type Item = E;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        if self.start_pos < self.end_pos {
+            let r = self.node_manager.get_node(self.layer, self.start_pos);
+            self.start_pos += 1;
+            r
+        } else {
+            None
+        }
+    }
+}
+
+pub trait NodeDatabase<E: HashElement>: Send + Sync {
+    fn get_node(&self, layer: usize, pos: usize) -> Result<Option<E>>;
+    fn get_layer_size(&self, layer: usize) -> Result<Option<usize>>;
+    fn start_transaction(&self) -> Box<dyn NodeTransaction<E>>;
+    fn commit(&self, tx: Box<dyn NodeTransaction<E>>) -> Result<()>;
+}
+
+pub trait NodeTransaction<E: HashElement>: Send + Sync {
+    fn save_node(&mut self, layer: usize, pos: usize, node: &E);
+    /// `nodes` are a list of tuples `(layer, pos, node)`.
+    fn save_node_list(&mut self, nodes: &[(usize, usize, &E)]);
+    fn remove_node_list(&mut self, nodes: &[(usize, usize)]);
+    fn save_layer_size(&mut self, layer: usize, size: usize);
+    fn remove_layer_size(&mut self, layer: usize);
+
+    fn into_any(self: Box<Self>) -> Box<dyn Any>;
+}
+
+/// A dummy database structure for in-memory merkle tree that will not read/write db.
+pub struct EmptyNodeDatabase {}
+pub struct EmptyNodeTransaction {}
+impl<E: HashElement> NodeDatabase<E> for EmptyNodeDatabase {
+    fn get_node(&self, _layer: usize, _pos: usize) -> Result<Option<E>> {
+        Ok(None)
+    }
+    fn get_layer_size(&self, _layer: usize) -> Result<Option<usize>> {
+        Ok(None)
+    }
+    fn start_transaction(&self) -> Box<dyn NodeTransaction<E>> {
+        Box::new(EmptyNodeTransaction {})
+    }
+    fn commit(&self, _tx: Box<dyn NodeTransaction<E>>) -> Result<()> {
+        Ok(())
+    }
+}
+
+impl<E: HashElement> NodeTransaction<E> for EmptyNodeTransaction {
+    fn save_node(&mut self, _layer: usize, _pos: usize, _node: &E) {}
+
+    fn save_node_list(&mut self, _nodes: &[(usize, usize, &E)]) {}
+
+    fn remove_node_list(&mut self, _nodes: &[(usize, usize)]) {}
+
+    fn save_layer_size(&mut self, _layer: usize, _size: usize) {}
+
+    fn remove_layer_size(&mut self, _layer: usize) {}
+
+    fn into_any(self: Box<Self>) -> Box<dyn Any> {
+        self
+    }
+}

node/src/client/builder.rs

@@ -112,7 +112,7 @@ impl ClientBuilder {
     pub fn with_rocksdb_store(mut self, config: &StorageConfig) -> Result<Self, String> {
         let executor = require!("sync", self, runtime_context).clone().executor;
         let store = Arc::new(
-            LogManager::rocksdb(LogConfig::default(), &config.db_dir, executor)
+            LogManager::rocksdb(config.log_config.clone(), &config.db_dir, executor)
                 .map_err(|e| format!("Unable to start RocksDB store: {:?}", e))?,
         );
 

node/src/config/convert.rs

@@ -11,6 +11,7 @@ use shared_types::{NetworkIdentity, ProtocolVersion};
 use std::net::IpAddr;
 use std::time::Duration;
 use storage::config::ShardConfig;
+use storage::log_store::log_manager::LogConfig;
 use storage::StorageConfig;
 
 impl ZgsConfig {
@@ -101,8 +102,11 @@ impl ZgsConfig {
     }
 
     pub fn storage_config(&self) -> Result<StorageConfig, String> {
+        let mut log_config = LogConfig::default();
+        log_config.flow.merkle_node_cache_capacity = self.merkle_node_cache_capacity;
         Ok(StorageConfig {
             db_dir: self.db_dir.clone().into(),
+            log_config,
         })
     }
 

node/src/config/mod.rs

@@ -60,6 +60,7 @@ build_config! {
     (prune_check_time_s, (u64), 60)
     (prune_batch_size, (usize), 16 * 1024)
     (prune_batch_wait_time_ms, (u64), 1000)
+    (merkle_node_cache_capacity, (usize), 32 * 1024 * 1024)
 
     // misc
     (log_config_file, (String), "log_config".to_string())

node/storage/src/config.rs

@@ -1,3 +1,4 @@
+use crate::log_store::log_manager::LogConfig;
 use serde::{Deserialize, Serialize};
 use ssz_derive::{Decode, Encode};
 use std::{cell::RefCell, path::PathBuf, rc::Rc, str::FromStr};
@@ -7,6 +8,7 @@ pub const SHARD_CONFIG_KEY: &str = "shard_config";
 #[derive(Clone)]
 pub struct Config {
     pub db_dir: PathBuf,
+    pub log_config: LogConfig,
 }
 
 #[derive(Clone, Copy, Debug, Decode, Encode, Serialize, Deserialize, Eq, PartialEq)]

node/storage/src/log_store/flow_store.rs

@@ -9,9 +9,11 @@ use crate::log_store::log_manager::{
 };
 use crate::log_store::{FlowRead, FlowSeal, FlowWrite};
 use crate::{try_option, ZgsKeyValueDB};
+use any::Any;
 use anyhow::{anyhow, bail, Result};
-use append_merkle::{MerkleTreeInitialData, MerkleTreeRead};
+use append_merkle::{MerkleTreeInitialData, MerkleTreeRead, NodeDatabase, NodeTransaction};
 use itertools::Itertools;
+use kvdb::DBTransaction;
 use parking_lot::RwLock;
 use shared_types::{ChunkArray, DataRoot, FlowProof, Merkle};
 use ssz::{Decode, Encode};
@@ -20,20 +22,20 @@ use std::cmp::Ordering;
 use std::collections::BTreeMap;
 use std::fmt::Debug;
 use std::sync::Arc;
-use std::{cmp, mem};
+use std::{any, cmp, mem};
 use tracing::{debug, error, trace};
 use zgs_spec::{BYTES_PER_SECTOR, SEALS_PER_LOAD, SECTORS_PER_LOAD, SECTORS_PER_SEAL};
 
 pub struct FlowStore {
-    db: FlowDBStore,
+    db: Arc<FlowDBStore>,
     seal_manager: SealTaskManager,
     config: FlowConfig,
 }
 
 impl FlowStore {
-    pub fn new(db: Arc<dyn ZgsKeyValueDB>, config: FlowConfig) -> Self {
+    pub fn new(db: Arc<FlowDBStore>, config: FlowConfig) -> Self {
         Self {
-            db: FlowDBStore::new(db),
+            db,
             seal_manager: Default::default(),
             config,
         }
@@ -93,6 +95,7 @@ impl FlowStore {
 #[derive(Clone, Debug)]
 pub struct FlowConfig {
     pub batch_size: usize,
+    pub merkle_node_cache_capacity: usize,
     pub shard_config: Arc<RwLock<ShardConfig>>,
 }
 
@@ -100,6 +103,8 @@ impl Default for FlowConfig {
     fn default() -> Self {
         Self {
             batch_size: SECTORS_PER_LOAD,
+            // Each node takes (8+8+32=)48 Bytes, so the default value is 1.5 GB memory size.
+            merkle_node_cache_capacity: 32 * 1024 * 1024,
             shard_config: Default::default(),
         }
     }
@@ -436,7 +441,7 @@ impl FlowDBStore {
         let mut expected_index = 0;
 
         let empty_data = vec![0; PORA_CHUNK_SIZE * ENTRY_SIZE];
-        let empty_root = *Merkle::new(data_to_merkle_leaves(&empty_data)?, 0, None).root();
+        let empty_root = Merkle::new(data_to_merkle_leaves(&empty_data)?, 0, None).root();
 
         for r in self.kvdb.iter(COL_ENTRY_BATCH_ROOT) {
             let (index_bytes, root_bytes) = r?;
@@ -666,3 +671,84 @@ fn decode_mpt_node_key(data: &[u8]) -> Result<(usize, usize)> {
     let position = try_decode_usize(&data[mem::size_of::<u64>()..])?;
     Ok((layer_index, position))
 }
+
+fn layer_size_key(layer: usize) -> Vec<u8> {
+    let mut key = "layer_size".as_bytes().to_vec();
+    key.extend_from_slice(&layer.to_be_bytes());
+    key
+}
+
+pub struct NodeDBTransaction(DBTransaction);
+
+impl NodeDatabase<DataRoot> for FlowDBStore {
+    fn get_node(&self, layer: usize, pos: usize) -> Result<Option<DataRoot>> {
+        Ok(self
+            .kvdb
+            .get(COL_FLOW_MPT_NODES, &encode_mpt_node_key(layer, pos))?
+            .map(|v| DataRoot::from_slice(&v)))
+    }
+
+    fn get_layer_size(&self, layer: usize) -> Result<Option<usize>> {
+        match self.kvdb.get(COL_FLOW_MPT_NODES, &layer_size_key(layer))? {
+            Some(v) => Ok(Some(try_decode_usize(&v)?)),
+            None => Ok(None),
+        }
+    }
+
+    fn start_transaction(&self) -> Box<dyn NodeTransaction<DataRoot>> {
+        Box::new(NodeDBTransaction(self.kvdb.transaction()))
+    }
+
+    fn commit(&self, tx: Box<dyn NodeTransaction<DataRoot>>) -> Result<()> {
+        let db_tx: Box<NodeDBTransaction> = tx
+            .into_any()
+            .downcast()
+            .map_err(|e| anyhow!("downcast failed, e={:?}", e))?;
+        self.kvdb.write(db_tx.0).map_err(Into::into)
+    }
+}
+
+impl NodeTransaction<DataRoot> for NodeDBTransaction {
+    fn save_node(&mut self, layer: usize, pos: usize, node: &DataRoot) {
+        self.0.put(
+            COL_FLOW_MPT_NODES,
+            &encode_mpt_node_key(layer, pos),
+            node.as_bytes(),
+        );
+    }
+
+    fn save_node_list(&mut self, nodes: &[(usize, usize, &DataRoot)]) {
+        for (layer_index, position, data) in nodes {
+            self.0.put(
+                COL_FLOW_MPT_NODES,
+                &encode_mpt_node_key(*layer_index, *position),
+                data.as_bytes(),
+            );
+        }
+    }
+
+    fn remove_node_list(&mut self, nodes: &[(usize, usize)]) {
+        for (layer_index, position) in nodes {
+            self.0.delete(
+                COL_FLOW_MPT_NODES,
+                &encode_mpt_node_key(*layer_index, *position),
+            );
+        }
+    }
+
+    fn save_layer_size(&mut self, layer: usize, size: usize) {
+        self.0.put(
+            COL_FLOW_MPT_NODES,
+            &layer_size_key(layer),
+            &size.to_be_bytes(),
+        );
+    }
+
+    fn remove_layer_size(&mut self, layer: usize) {
+        self.0.delete(COL_FLOW_MPT_NODES, &layer_size_key(layer));
+    }
+
+    fn into_any(self: Box<Self>) -> Box<dyn Any> {
+        self
+    }
+}

node/storage/src/log_store/load_chunk/mod.rs

@@ -4,11 +4,10 @@ mod seal;
 mod serde;
 
 use ::serde::{Deserialize, Serialize};
-use std::cmp::min;
-
 use anyhow::Result;
 use ethereum_types::H256;
 use ssz_derive::{Decode, Encode};
+use std::cmp::min;
 
 use crate::log_store::log_manager::data_to_merkle_leaves;
 use crate::try_option;
@@ -206,7 +205,7 @@ impl EntryBatch {
             }
         }
         Ok(Some(
-            *try_option!(self.to_merkle_tree(is_first_chunk)?).root(),
+            try_option!(self.to_merkle_tree(is_first_chunk)?).root(),
         ))
     }
 

node/storage/src/log_store/log_manager.rs

@@ -1,5 +1,5 @@
 use crate::config::ShardConfig;
-use crate::log_store::flow_store::{batch_iter_sharded, FlowConfig, FlowStore};
+use crate::log_store::flow_store::{batch_iter_sharded, FlowConfig, FlowDBStore, FlowStore};
 use crate::log_store::tx_store::TransactionStore;
 use crate::log_store::{
     FlowRead, FlowWrite, LogStoreChunkRead, LogStoreChunkWrite, LogStoreRead, LogStoreWrite,
@@ -94,6 +94,7 @@ impl MerkleManager {
     }
 
     fn revert_merkle_tree(&mut self, tx_seq: u64, tx_store: &TransactionStore) -> Result<()> {
+        debug!("revert merkle tree {}", tx_seq);
         // Special case for reverting tx_seq == 0
         if tx_seq == u64::MAX {
             self.pora_chunks_merkle.reset();
@@ -116,7 +117,7 @@ impl MerkleManager {
         if self.pora_chunks_merkle.leaves() == 0 && self.last_chunk_merkle.leaves() == 0 {
             self.last_chunk_merkle.append(H256::zero());
             self.pora_chunks_merkle
-                .update_last(*self.last_chunk_merkle.root());
+                .update_last(self.last_chunk_merkle.root());
         } else if self.last_chunk_merkle.leaves() != 0 {
             let last_chunk_start_index = self.last_chunk_start_index();
             let last_chunk_data = flow_store.get_available_entries(
@@ -355,7 +356,7 @@ impl LogStoreWrite for LogManager {
         merkle.revert_merkle_tree(tx_seq, &self.tx_store)?;
         merkle.try_initialize(&self.flow_store)?;
         assert_eq!(
-            Some(*merkle.last_chunk_merkle.root()),
+            Some(merkle.last_chunk_merkle.root()),
             merkle
                 .pora_chunks_merkle
                 .leaf_at(merkle.pora_chunks_merkle.leaves() - 1)?
@@ -577,7 +578,7 @@ impl LogStoreRead for LogManager {
     fn get_context(&self) -> crate::error::Result<(DataRoot, u64)> {
         let merkle = self.merkle.read_recursive();
         Ok((
-            *merkle.pora_chunks_merkle.root(),
+            merkle.pora_chunks_merkle.root(),
             merkle.last_chunk_start_index() + merkle.last_chunk_merkle.leaves() as u64,
         ))
     }
@@ -626,13 +627,10 @@ impl LogManager {
         executor: task_executor::TaskExecutor,
     ) -> Result<Self> {
         let tx_store = TransactionStore::new(db.clone())?;
-        let flow_store = Arc::new(FlowStore::new(db.clone(), config.flow));
-        let mut initial_data = flow_store.get_chunk_root_list()?;
-        // If the last tx `put_tx` does not complete, we will revert it in `initial_data.subtree_list`
-        // first and call `put_tx` later. The known leaves in its data will be saved in `extra_leaves`
-        // and inserted later.
-        let mut extra_leaves = Vec::new();
-
+        let flow_db = Arc::new(FlowDBStore::new(db.clone()));
+        let flow_store = Arc::new(FlowStore::new(flow_db.clone(), config.flow.clone()));
+        // If the last tx `put_tx` does not complete, we will revert it in `pora_chunks_merkle`
+        // first and call `put_tx` later.
         let next_tx_seq = tx_store.next_tx_seq();
         let mut start_tx_seq = if next_tx_seq > 0 {
             Some(next_tx_seq - 1)
@@ -640,15 +638,25 @@ impl LogManager {
             None
         };
         let mut last_tx_to_insert = None;
+
+        let mut pora_chunks_merkle = Merkle::new_with_subtrees(
+            flow_db,
+            config.flow.merkle_node_cache_capacity,
+            log2_pow2(PORA_CHUNK_SIZE),
+        )?;
         if let Some(last_tx_seq) = start_tx_seq {
             if !tx_store.check_tx_completed(last_tx_seq)? {
                 // Last tx not finalized, we need to check if its `put_tx` is completed.
                 let last_tx = tx_store
                     .get_tx_by_seq_number(last_tx_seq)?
                     .expect("tx missing");
-                let mut current_len = initial_data.leaves();
-                let expected_len =
-                    sector_to_segment(last_tx.start_entry_index + last_tx.num_entries() as u64);
+                let current_len = pora_chunks_merkle.leaves();
+                let expected_len = sector_to_segment(
+                    last_tx.start_entry_index
+                        + last_tx.num_entries() as u64
+                        + PORA_CHUNK_SIZE as u64
+                        - 1,
+                );
                 match expected_len.cmp(&(current_len)) {
                     Ordering::Less => {
                         bail!(
@@ -676,43 +684,33 @@ impl LogManager {
                                 previous_tx.start_entry_index + previous_tx.num_entries() as u64,
                             );
                             if current_len > expected_len {
-                                while let Some((subtree_depth, _)) = initial_data.subtree_list.pop()
-                                {
-                                    current_len -= 1 << (subtree_depth - 1);
-                                    if current_len == expected_len {
-                                        break;
-                                    }
-                                }
+                                pora_chunks_merkle.revert_to_leaves(expected_len)?;
                             } else {
-                                warn!(
-                                    "revert last tx with no-op: {} {}",
-                                    current_len, expected_len
-                                );
+                                assert_eq!(current_len, expected_len);
                             }
-                            assert_eq!(current_len, expected_len);
-                            while let Some((index, h)) = initial_data.known_leaves.pop() {
-                                if index < current_len {
-                                    initial_data.known_leaves.push((index, h));
-                                    break;
-                                } else {
-                                    extra_leaves.push((index, h));
-                                }
-                            }
-                            start_tx_seq = Some(last_tx_seq - 1);
+                            start_tx_seq = Some(previous_tx.seq);
                         };
                     }
                 }
             }
         }
 
-        let mut pora_chunks_merkle =
-            Merkle::new_with_subtrees(initial_data, log2_pow2(PORA_CHUNK_SIZE), start_tx_seq)?;
         let last_chunk_merkle = match start_tx_seq {
             Some(tx_seq) => {
-                tx_store.rebuild_last_chunk_merkle(pora_chunks_merkle.leaves(), tx_seq)?
+                let tx = tx_store.get_tx_by_seq_number(tx_seq)?.expect("tx missing");
+                if (tx.start_entry_index() + tx.num_entries() as u64) % PORA_CHUNK_SIZE as u64 == 0
+                {
+                    // The last chunk should be aligned, so it's empty.
+                    Merkle::new_with_depth(vec![], log2_pow2(PORA_CHUNK_SIZE) + 1, None)
+                } else {
+                    tx_store.rebuild_last_chunk_merkle(pora_chunks_merkle.leaves() - 1, tx_seq)?
+                }
             }
             // Initialize
-            None => Merkle::new_with_depth(vec![], 1, None),
+            None => {
+                pora_chunks_merkle.reset();
+                Merkle::new_with_depth(vec![], 1, None)
+            }
         };
 
         debug!(
@@ -722,10 +720,10 @@ impl LogManager {
             last_chunk_merkle.leaves(),
         );
         if last_chunk_merkle.leaves() != 0 {
-            pora_chunks_merkle.append(*last_chunk_merkle.root());
-            // update the merkle root
-            pora_chunks_merkle.commit(start_tx_seq);
+            pora_chunks_merkle.update_last(last_chunk_merkle.root());
         }
+        // update the merkle root
+        pora_chunks_merkle.commit(start_tx_seq);
         let merkle = RwLock::new(MerkleManager {
             pora_chunks_merkle,
             last_chunk_merkle,
@@ -744,18 +742,7 @@ impl LogManager {
         log_manager.start_receiver(receiver, executor);
 
         if let Some(tx) = last_tx_to_insert {
-            log_manager.revert_to(tx.seq - 1)?;
             log_manager.put_tx(tx)?;
-            let mut merkle = log_manager.merkle.write();
-            for (index, h) in extra_leaves {
-                if index < merkle.pora_chunks_merkle.leaves() {
-                    merkle.pora_chunks_merkle.fill_leaf(index, h);
-                } else {
-                    error!("out of range extra leaf: index={} hash={:?}", index, h);
-                }
-            }
-        } else {
-            assert!(extra_leaves.is_empty());
         }
         log_manager
             .merkle
@@ -894,16 +881,16 @@ impl LogManager {
                     // `last_chunk_merkle` was empty, so this is a new leaf in the top_tree.
                     merkle
                         .pora_chunks_merkle
-                        .append_subtree(1, *merkle.last_chunk_merkle.root())?;
+                        .append_subtree(1, merkle.last_chunk_merkle.root())?;
                 } else {
                     merkle
                         .pora_chunks_merkle
-                        .update_last(*merkle.last_chunk_merkle.root());
+                        .update_last(merkle.last_chunk_merkle.root());
                 }
                 if merkle.last_chunk_merkle.leaves() == PORA_CHUNK_SIZE {
                     batch_root_map.insert(
                         merkle.pora_chunks_merkle.leaves() - 1,
-                        (*merkle.last_chunk_merkle.root(), 1),
+                        (merkle.last_chunk_merkle.root(), 1),
                     );
                     self.complete_last_chunk_merkle(
                         merkle.pora_chunks_merkle.leaves() - 1,
@@ -959,7 +946,7 @@ impl LogManager {
                         .append_list(data_to_merkle_leaves(&pad_data)?);
                     merkle
                         .pora_chunks_merkle
-                        .update_last(*merkle.last_chunk_merkle.root());
+                        .update_last(merkle.last_chunk_merkle.root());
                 } else {
                     if last_chunk_pad != 0 {
                         is_full_empty = false;
@@ -969,10 +956,10 @@ impl LogManager {
                             .append_list(data_to_merkle_leaves(&pad_data[..last_chunk_pad])?);
                         merkle
                             .pora_chunks_merkle
-                            .update_last(*merkle.last_chunk_merkle.root());
+                            .update_last(merkle.last_chunk_merkle.root());
                         root_map.insert(
                             merkle.pora_chunks_merkle.leaves() - 1,
-                            (*merkle.last_chunk_merkle.root(), 1),
+                            (merkle.last_chunk_merkle.root(), 1),
                         );
                         completed_chunk_index = Some(merkle.pora_chunks_merkle.leaves() - 1);
                     }
@@ -983,7 +970,7 @@ impl LogManager {
                         let data = pad_data[start_index * ENTRY_SIZE
                             ..(start_index + PORA_CHUNK_SIZE) * ENTRY_SIZE]
                             .to_vec();
-                        let root = *Merkle::new(data_to_merkle_leaves(&data)?, 0, None).root();
+                        let root = Merkle::new(data_to_merkle_leaves(&data)?, 0, None).root();
                         merkle.pora_chunks_merkle.append(root);
                         root_map.insert(merkle.pora_chunks_merkle.leaves() - 1, (root, 1));
                         start_index += PORA_CHUNK_SIZE;
@@ -1061,7 +1048,7 @@ impl LogManager {
             }
             merkle
                 .pora_chunks_merkle
-                .update_last(*merkle.last_chunk_merkle.root());
+                .update_last(merkle.last_chunk_merkle.root());
         }
         let chunk_roots = self.flow_store.append_entries(flow_entry_array)?;
         for (chunk_index, chunk_root) in chunk_roots {

node/storage/src/log_store/tests.rs

@@ -8,6 +8,7 @@ use ethereum_types::H256;
 use rand::random;
 use shared_types::{compute_padded_chunk_size, ChunkArray, Transaction, CHUNK_SIZE};
 use std::cmp;
+
 use task_executor::test_utils::TestRuntime;
 
 #[test]

node/storage/src/log_store/tx_store.rs

@@ -292,6 +292,9 @@ impl TransactionStore {
             match tx.start_entry_index.cmp(&last_chunk_start_index) {
                 cmp::Ordering::Greater => {
                     tx_list.push((tx_seq, tx.merkle_nodes));
+                    if tx.start_entry_index >= last_chunk_start_index + PORA_CHUNK_SIZE as u64 {
+                        break;
+                    }
                 }
                 cmp::Ordering::Equal => {
                     tx_list.push((tx_seq, tx.merkle_nodes));

tests/node_cache_test.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+
+from test_framework.test_framework import TestFramework
+from utility.submission import create_submission, submit_data
+from utility.utils import wait_until
+
+
+class NodeCacheTest(TestFramework):
+    def setup_params(self):
+        self.zgs_node_configs[0] = {
+            "merkle_node_cache_capacity": 1024,
+        }
+
+    def run_test(self):
+        client = self.nodes[0]
+
+        chunk_data = b"\x02" * 256 * 1024 * 1024 * 3
+        submissions, data_root = create_submission(chunk_data)
+        self.contract.submit(submissions)
+        wait_until(lambda: self.contract.num_submissions() == 1)
+        wait_until(lambda: client.zgs_get_file_info(data_root) is not None)
+
+        segment = submit_data(client, chunk_data)
+        self.log.info("segment: %s", len(segment))
+        wait_until(lambda: client.zgs_get_file_info(data_root)["finalized"])
+
+        self.stop_storage_node(0)
+        self.start_storage_node(0)
+        self.nodes[0].wait_for_rpc_connection()
+
+        chunk_data = b"\x03" * 256 * (1024 * 765 + 5)
+        submissions, data_root = create_submission(chunk_data)
+        self.contract.submit(submissions)
+        wait_until(lambda: self.contract.num_submissions() == 2)
+        wait_until(lambda: client.zgs_get_file_info(data_root) is not None)
+
+        segment = submit_data(client, chunk_data)
+        self.log.info("segment: %s", len(segment))
+        wait_until(lambda: client.zgs_get_file_info(data_root)["finalized"])
+
+
+if __name__ == "__main__":
+    NodeCacheTest().main()