Checkpoint: add merkle tree in data table

src/table/lib.rs

@@ -7,6 +7,7 @@ pub mod crdt;
 pub mod schema;
 pub mod util;
 
+pub mod merkle;
 pub mod table;
 pub mod table_fullcopy;
 pub mod table_sharded;

src/table/merkle.rs

@@ -0,0 +1,352 @@
+use std::convert::TryInto;
+use std::sync::Arc;
+use std::time::Duration;
+
+use futures::select;
+use futures_util::future::*;
+use log::{info, warn};
+use serde::{Deserialize, Serialize};
+use sled::transaction::{
+	ConflictableTransactionError, ConflictableTransactionResult, TransactionalTree,
+};
+use tokio::sync::{watch, Notify};
+
+use garage_util::background::BackgroundRunner;
+use garage_util::data::*;
+use garage_util::error::Error;
+
+// This modules partitions the data in 2**16 partitions, based on the top
+// 16 bits (two bytes) of item's partition keys' hashes.
+// It builds one Merkle tree for each of these 2**16 partitions.
+
+pub(crate) struct MerkleUpdater {
+	table_name: String,
+	background: Arc<BackgroundRunner>,
+
+	// Content of the todo tree: items where
+	// - key = the key of an item in the main table, ie hash(partition_key)+sort_key
+	// - value = the hash of the full serialized item, if present,
+	//			 or an empty vec if item is absent (deleted)
+	pub(crate) todo: sled::Tree,
+	pub(crate) todo_notify: Notify,
+
+	// Content of the merkle tree: items where
+	// - key = .bytes() for MerkleNodeKey
+	// - value = serialization of a MerkleNode, assumed to be MerkleNode::empty if not found
+	pub(crate) merkle_tree: sled::Tree,
+	empty_node_hash: Hash,
+}
+
+#[derive(Clone)]
+pub struct MerkleNodeKey {
+	// partition: first 16 bits (two bytes) of the partition_key's hash
+	pub partition: [u8; 2],
+
+	// prefix: a prefix for the hash of full keys, i.e. hash(hash(partition_key)+sort_key)
+	pub prefix: Vec<u8>,
+}
+
+#[derive(PartialEq, Eq, Debug, Serialize, Deserialize)]
+pub enum MerkleNode {
+	// The empty Merkle node
+	Empty,
+
+	// An intermediate Merkle tree node for a prefix
+	// Contains the hashes of the 256 possible next prefixes
+	Intermediate(Vec<(u8, Hash)>),
+
+	// A final node for an item
+	// Contains the full key of the item and the hash of the value
+	Leaf(Vec<u8>, Hash),
+}
+
+impl MerkleUpdater {
+	pub(crate) fn new(
+		table_name: String,
+		background: Arc<BackgroundRunner>,
+		todo: sled::Tree,
+		merkle_tree: sled::Tree,
+	) -> Arc<Self> {
+		let empty_node_hash = blake2sum(&rmp_to_vec_all_named(&MerkleNode::Empty).unwrap()[..]);
+
+		Arc::new(Self {
+			table_name,
+			background,
+			todo,
+			todo_notify: Notify::new(),
+			merkle_tree,
+			empty_node_hash,
+		})
+	}
+
+	pub(crate) fn launch(self: &Arc<Self>) {
+		let self2 = self.clone();
+		self.background.spawn_worker(
+			format!("Merkle tree updater for {}", self.table_name),
+			|must_exit: watch::Receiver<bool>| self2.updater_loop(must_exit),
+		);
+	}
+
+	async fn updater_loop(
+		self: Arc<Self>,
+		mut must_exit: watch::Receiver<bool>,
+	) -> Result<(), Error> {
+		while !*must_exit.borrow() {
+			if let Some(x) = self.todo.iter().next() {
+				match x {
+					Ok((key, valhash)) => {
+						if let Err(e) = self.update_item(&key[..], &valhash[..]) {
+							warn!("Error while updating Merkle tree item: {}", e);
+						}
+					}
+					Err(e) => {
+						warn!("Error while iterating on Merkle todo tree: {}", e);
+						tokio::time::delay_for(Duration::from_secs(10)).await;
+					}
+				}
+			} else {
+				select! {
+					_ = self.todo_notify.notified().fuse() => (),
+					_ = must_exit.recv().fuse() => (),
+				}
+			}
+		}
+		Ok(())
+	}
+
+	fn update_item(&self, k: &[u8], vhash_by: &[u8]) -> Result<(), Error> {
+		let khash = blake2sum(k);
+
+		let new_vhash = if vhash_by.len() == 0 {
+			None
+		} else {
+			let vhash_by: [u8; 32] = vhash_by
+				.try_into()
+				.map_err(|_| Error::Message(format!("Invalid value in Merkle todo table")))?;
+			Some(Hash::from(vhash_by))
+		};
+
+		let key = MerkleNodeKey {
+			partition: k[0..2].try_into().unwrap(),
+			prefix: vec![],
+		};
+		self.merkle_tree
+			.transaction(|tx| self.update_item_rec(tx, k, khash, &key, new_vhash))?;
+
+		let deleted = self
+			.todo
+			.compare_and_swap::<_, _, Vec<u8>>(k, Some(vhash_by), None)?
+			.is_ok();
+
+		if !deleted {
+			info!(
+				"Item not deleted from Merkle todo because it changed: {:?}",
+				k
+			);
+		}
+		Ok(())
+	}
+
+	fn update_item_rec(
+		&self,
+		tx: &TransactionalTree,
+		k: &[u8],
+		khash: Hash,
+		key: &MerkleNodeKey,
+		new_vhash: Option<Hash>,
+	) -> ConflictableTransactionResult<Option<Hash>, Error> {
+		let i = key.prefix.len();
+		let mutate = match self.read_node_txn(tx, &key)? {
+			MerkleNode::Empty => {
+				if let Some(vhv) = new_vhash {
+					Some(MerkleNode::Leaf(k.to_vec(), vhv))
+				} else {
+					None
+				}
+			}
+			MerkleNode::Intermediate(mut children) => {
+				let key2 = key.next_key(khash);
+				if let Some(subhash) = self.update_item_rec(tx, k, khash, &key2, new_vhash)? {
+					if subhash == self.empty_node_hash {
+						intermediate_rm_child(&mut children, key2.prefix[i]);
+					} else {
+						intermediate_set_child(&mut children, key2.prefix[i], subhash);
+					}
+					if children.len() == 0 {
+						// should not happen
+						warn!("Replacing intermediate node with empty node, should not happen.");
+						Some(MerkleNode::Empty)
+					} else if children.len() == 1 {
+						// move node down to this level
+						let key_sub = key.add_byte(children[0].0);
+						let subnode = self.read_node_txn(tx, &key_sub)?;
+						tx.remove(key_sub.encode())?;
+						Some(subnode)
+					} else {
+						Some(MerkleNode::Intermediate(children))
+					}
+				} else {
+					None
+				}
+			}
+			MerkleNode::Leaf(exlf_key, exlf_hash) => {
+				if exlf_key == k {
+					match new_vhash {
+						Some(vhv) if vhv == exlf_hash => None,
+						Some(vhv) => Some(MerkleNode::Leaf(k.to_vec(), vhv)),
+						None => Some(MerkleNode::Empty),
+					}
+				} else {
+					if let Some(vhv) = new_vhash {
+						// Create two sub-nodes and replace by intermediary node
+						let (pos1, h1) = {
+							let key2 = key.next_key(blake2sum(&exlf_key[..]));
+							let subhash =
+								self.put_node_txn(tx, &key2, &MerkleNode::Leaf(exlf_key, exlf_hash))?;
+							(key2.prefix[i], subhash)
+						};
+						let (pos2, h2) = {
+							let key2 = key.next_key(khash);
+							let subhash =
+								self.put_node_txn(tx, &key2, &MerkleNode::Leaf(k.to_vec(), vhv))?;
+							(key2.prefix[i], subhash)
+						};
+						let mut int = vec![];
+						intermediate_set_child(&mut int, pos1, h1);
+						intermediate_set_child(&mut int, pos2, h2);
+						Some(MerkleNode::Intermediate(int))
+					} else {
+						None
+					}
+				}
+			}
+		};
+
+		if let Some(new_node) = mutate {
+			let hash = self.put_node_txn(tx, &key, &new_node)?;
+			Ok(Some(hash))
+		} else {
+			Ok(None)
+		}
+	}
+
+	// Merkle tree node manipulation
+
+	fn read_node_txn(
+		&self,
+		tx: &TransactionalTree,
+		k: &MerkleNodeKey,
+	) -> ConflictableTransactionResult<MerkleNode, Error> {
+		let ent = tx.get(k.encode())?;
+		match ent {
+			None => Ok(MerkleNode::Empty),
+			Some(v) => Ok(rmp_serde::decode::from_read_ref::<_, MerkleNode>(&v[..])
+				.map_err(|e| ConflictableTransactionError::Abort(e.into()))?),
+		}
+	}
+
+	fn put_node_txn(
+		&self,
+		tx: &TransactionalTree,
+		k: &MerkleNodeKey,
+		v: &MerkleNode,
+	) -> ConflictableTransactionResult<Hash, Error> {
+		if *v == MerkleNode::Empty {
+			tx.remove(k.encode())?;
+			Ok(self.empty_node_hash)
+		} else {
+			let vby = rmp_to_vec_all_named(v)
+				.map_err(|e| ConflictableTransactionError::Abort(e.into()))?;
+			let rethash = blake2sum(&vby[..]);
+			tx.insert(k.encode(), vby)?;
+			Ok(rethash)
+		}
+	}
+
+	pub(crate) fn read_node(
+		&self,
+		k: &MerkleNodeKey,
+	) -> Result<MerkleNode, Error> {
+		let ent = self.merkle_tree.get(k.encode())?;
+		match ent {
+			None => Ok(MerkleNode::Empty),
+			Some(v) => Ok(rmp_serde::decode::from_read_ref::<_, MerkleNode>(&v[..])?)
+		}
+	}
+}
+
+impl MerkleNodeKey {
+	fn encode(&self) -> Vec<u8> {
+		let mut ret = Vec::with_capacity(2 + self.prefix.len());
+		ret.extend(&self.partition[..]);
+		ret.extend(&self.prefix[..]);
+		ret
+	}
+
+	pub fn next_key(&self, h: Hash) -> Self {
+		assert!(&h.as_slice()[0..self.prefix.len()] == &self.prefix[..]);
+		let mut s2 = self.clone();
+		s2.prefix.push(h.as_slice()[self.prefix.len()]);
+		s2
+	}
+
+	pub fn add_byte(&self, b: u8) -> Self {
+		let mut s2 = self.clone();
+		s2.prefix.push(b);
+		s2
+	}
+}
+
+fn intermediate_set_child(ch: &mut Vec<(u8, Hash)>, pos: u8, v: Hash) {
+	for i in 0..ch.len() {
+		if ch[i].0 == pos {
+			ch[i].1 = v;
+			return;
+		} else if ch[i].0 > pos {
+			ch.insert(i, (pos, v));
+			return;
+		}
+	}
+	ch.insert(ch.len(), (pos, v));
+}
+
+fn intermediate_rm_child(ch: &mut Vec<(u8, Hash)>, pos: u8) {
+	for i in 0..ch.len() {
+		if ch[i].0 == pos {
+			ch.remove(i);
+			return;
+		}
+	}
+}
+
+#[test]
+fn test_intermediate_aux() {
+	let mut v = vec![];
+	
+	intermediate_set_child(&mut v, 12u8, [12u8; 32].into());
+	assert!(v == vec![(12u8, [12u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 42u8, [42u8; 32].into());
+	assert!(v == vec![(12u8, [12u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 4u8, [4u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [12u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 12u8, [8u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [8u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 6u8, [6u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into()), (42u8, [42u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 42u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 11u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 6u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [8u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 6u8, [7u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [7u8; 32].into()), (12u8, [8u8; 32].into())]);
+}

src/table/table.rs

@@ -8,6 +8,7 @@ use arc_swap::ArcSwapOption;
 use futures::stream::*;
 use serde::{Deserialize, Serialize};
 use serde_bytes::ByteBuf;
+use sled::Transactional;
 
 use garage_util::data::*;
 use garage_util::error::Error;
@@ -18,6 +19,7 @@ use garage_rpc::rpc_client::*;
 use garage_rpc::rpc_server::*;
 
 use crate::crdt::CRDT;
+use crate::merkle::*;
 use crate::schema::*;
 use crate::table_sync::*;
 
@@ -33,6 +35,7 @@ pub struct Table<F: TableSchema, R: TableReplication> {
 	pub system: Arc<System>,
 	pub store: sled::Tree,
 	pub syncer: ArcSwapOption<TableSyncer<F, R>>,
+	merkle_updater: Arc<MerkleUpdater>,
 }
 
 #[derive(Serialize, Deserialize)]
@@ -77,7 +80,7 @@ where
 {
 	// =============== PUBLIC INTERFACE FUNCTIONS (new, insert, get, etc) ===============
 
-	pub async fn new(
+	pub fn new(
 		instance: F,
 		replication: R,
 		system: Arc<System>,
@@ -85,11 +88,27 @@ where
 		name: String,
 		rpc_server: &mut RpcServer,
 	) -> Arc<Self> {
-		let store = db.open_tree(&name).expect("Unable to open DB tree");
+		let store = db
+			.open_tree(&format!("{}:table", name))
+			.expect("Unable to open DB tree");
+
+		let merkle_todo_store = db
+			.open_tree(&format!("{}:merkle_todo", name))
+			.expect("Unable to open DB Merkle TODO tree");
+		let merkle_tree_store = db
+			.open_tree(&format!("{}:merkle_tree", name))
+			.expect("Unable to open DB Merkle tree tree");
 
 		let rpc_path = format!("table_{}", name);
 		let rpc_client = system.rpc_client::<TableRPC<F>>(&rpc_path);
 
+		let merkle_updater = MerkleUpdater::new(
+			name.clone(),
+			system.background.clone(),
+			merkle_todo_store,
+			merkle_tree_store,
+		);
+
 		let table = Arc::new(Self {
 			instance,
 			replication,
@@ -98,12 +117,15 @@ where
 			system,
 			store,
 			syncer: ArcSwapOption::from(None),
+			merkle_updater,
 		});
 		table.clone().register_handler(rpc_server, rpc_path);
 
-		let syncer = TableSyncer::launch(table.clone()).await;
+		let syncer = TableSyncer::launch(table.clone());
 		table.syncer.swap(Some(syncer));
 
+		table.merkle_updater.launch();
+
 		table
 	}
 
@@ -322,7 +344,7 @@ where
 				Ok(TableRPC::Update(values))
 			}
 			TableRPC::Update(pairs) => {
-				self.handle_update(pairs).await?;
+				self.handle_update(pairs)?;
 				Ok(TableRPC::Ok)
 			}
 			TableRPC::SyncRPC(rpc) => {
@@ -380,53 +402,64 @@ where
 		Ok(ret)
 	}
 
-	pub async fn handle_update(self: &Arc<Self>, entries: &[Arc<ByteBuf>]) -> Result<(), Error> {
-		let syncer = self.syncer.load_full().unwrap();
+	// ========== CODE THAT ACTUALLY MODIFIES THE TREE ================
 
+	pub fn handle_update(self: &Arc<Self>, entries: &[Arc<ByteBuf>]) -> Result<(), Error> {
 		for update_bytes in entries.iter() {
-			let update = self.decode_entry(update_bytes.as_slice())?;
+			self.update_entry(update_bytes.as_slice())?;
+		}
+		Ok(())
+	}
 
-			let tree_key = self.tree_key(update.partition_key(), update.sort_key());
+	pub(crate) fn update_entry(self: &Arc<Self>, update_bytes: &[u8]) -> Result<(), Error> {
+		let update = self.decode_entry(update_bytes)?;
+		let tree_key = self.tree_key(update.partition_key(), update.sort_key());
 
-			let (old_entry, new_entry) = self.store.transaction(|db| {
-				let (old_entry, new_entry) = match db.get(&tree_key)? {
-					Some(prev_bytes) => {
-						let old_entry = self
-							.decode_entry(&prev_bytes)
-							.map_err(sled::transaction::ConflictableTransactionError::Abort)?;
-						let mut new_entry = old_entry.clone();
-						new_entry.merge(&update);
-						(Some(old_entry), new_entry)
-					}
-					None => (None, update.clone()),
-				};
+		let changed = (&self.store, &self.merkle_updater.todo).transaction(|(db, mkl_todo)| {
+			let (old_entry, new_entry) = match db.get(&tree_key)? {
+				Some(prev_bytes) => {
+					let old_entry = self
+						.decode_entry(&prev_bytes)
+						.map_err(sled::transaction::ConflictableTransactionError::Abort)?;
+					let mut new_entry = old_entry.clone();
+					new_entry.merge(&update);
+					(Some(old_entry), new_entry)
+				}
+				None => (None, update.clone()),
+			};
 
+			if Some(&new_entry) != old_entry.as_ref() {
 				let new_bytes = rmp_to_vec_all_named(&new_entry)
 					.map_err(Error::RMPEncode)
 					.map_err(sled::transaction::ConflictableTransactionError::Abort)?;
+				mkl_todo.insert(tree_key.clone(), blake2sum(&new_bytes[..]).to_vec())?;
 				db.insert(tree_key.clone(), new_bytes)?;
-				Ok((old_entry, new_entry))
-			})?;
-
-			if old_entry.as_ref() != Some(&new_entry) {
-				self.instance.updated(old_entry, Some(new_entry));
-				syncer.invalidate(&tree_key[..]);
+				Ok(Some((old_entry, new_entry)))
+			} else {
+				Ok(None)
 			}
+		})?;
+
+		if let Some((old_entry, new_entry)) = changed {
+			self.instance.updated(old_entry, Some(new_entry));
+			self.syncer.load_full().unwrap().invalidate(&tree_key[..]);
 		}
 
 		Ok(())
 	}
 
 	pub(crate) fn delete_if_equal(self: &Arc<Self>, k: &[u8], v: &[u8]) -> Result<bool, Error> {
-		let removed = self.store.transaction(|txn| {
+		let removed = (&self.store, &self.merkle_updater.todo).transaction(|(txn, mkl_todo)| {
 			if let Some(cur_v) = txn.get(k)? {
 				if cur_v == v {
 					txn.remove(k)?;
+					mkl_todo.insert(k, vec![])?;
 					return Ok(true);
 				}
 			}
 			Ok(false)
 		})?;
+
 		if removed {
 			let old_entry = self.decode_entry(v)?;
 			self.instance.updated(Some(old_entry), None);

src/table/table_sync.rs

@@ -106,7 +106,7 @@ where
 	F: TableSchema + 'static,
 	R: TableReplication + 'static,
 {
-	pub(crate) async fn launch(table: Arc<Table<F, R>>) -> Arc<Self> {
+	pub(crate) fn launch(table: Arc<Table<F, R>>) -> Arc<Self> {
 		let todo = SyncTodo { todo: Vec::new() };
 		let syncer = Arc::new(TableSyncer {
 			table: table.clone(),
@@ -119,24 +119,16 @@ where
 		let (busy_tx, busy_rx) = mpsc::unbounded_channel();
 
 		let s1 = syncer.clone();
-		table
-			.system
-			.background
-			.spawn_worker(
-				format!("table sync watcher for {}", table.name),
-				move |must_exit: watch::Receiver<bool>| s1.watcher_task(must_exit, busy_rx),
-			)
-			.await;
+		table.system.background.spawn_worker(
+			format!("table sync watcher for {}", table.name),
+			move |must_exit: watch::Receiver<bool>| s1.watcher_task(must_exit, busy_rx),
+		);
 
 		let s2 = syncer.clone();
-		table
-			.system
-			.background
-			.spawn_worker(
-				format!("table syncer for {}", table.name),
-				move |must_exit: watch::Receiver<bool>| s2.syncer_task(must_exit, busy_tx),
-			)
-			.await;
+		table.system.background.spawn_worker(
+			format!("table syncer for {}", table.name),
+			move |must_exit: watch::Receiver<bool>| s2.syncer_task(must_exit, busy_tx),
+		);
 
 		let s3 = syncer.clone();
 		tokio::spawn(async move {
@@ -630,7 +622,7 @@ where
 					}
 				}
 				if diff_items.len() > 0 {
-					self.table.handle_update(&diff_items[..]).await?;
+					self.table.handle_update(&diff_items[..])?;
 				}
 				if items_to_send.len() > 0 {
 					self.send_items(who, items_to_send).await?;