add compaction skeleton (#16)

* add compaction skeleton

Signed-off-by: Alex Chi <iskyzh@gmail.com>

* remove tombstone when compact to bottom-most level

Signed-off-by: Alex Chi <iskyzh@gmail.com>

* new plan

Signed-off-by: Alex Chi Z <iskyzh@gmail.com>

---------

Signed-off-by: Alex Chi <iskyzh@gmail.com>
Signed-off-by: Alex Chi Z <iskyzh@gmail.com>

.cargo/config.toml

@@ -1,3 +1,4 @@
 [alias]
 xtask = "run --package mini-lsm-xtask --"
 x = "run --package mini-lsm-xtask --"
+test = "nextest run"

README.md

@@ -22,16 +22,29 @@ To do this, use `cargo x sync`.
 
 ## Progress
 
-The tutorial has 8 parts (which can be finished in 7 days):
+We are working on a new version of the mini-lsm tutorial that is split into 3 weeks.
 
-* Day 1: Block encoding. SSTs are composed of multiple data blocks. We will implement the block encoding.
+* Week 1: Storage Format + Engine Skeleton
-* Day 2: SST encoding.
+* Week 2: Compaction and Persistence
-* Day 3: MemTable and Merge Iterators.
+* Week 3: Week 3 -- Multi-Version Concurrency Control
-* Day 4: Block cache and Engine. To reduce disk I/O and maximize performance, we will use moka-rs to build a block cache
-  for the LSM tree. In this day we will get a functional (but not persistent) key-value engine with `get`, `put`, `scan`,
-  `delete` API.
-* Day 5: Compaction. Now it's time to maintain a leveled structure for SSTs.
-* Day 6: Recovery. We will implement WAL and manifest so that the engine can recover after restart.
-* Day 7: Bloom filter and key compression. They are widely-used optimizations in LSM tree structures.
 
-We have reference solution up to day 4 and tutorial up to day 4 for now.
+| Week + Chapter  | Topic              | Solution         | Starter Code      | Writeup   |
+| ----            | ------------------ | ---------------  | ----------------- | --------- |
+| 1.1 | Block Format       | ✅ | ✅ | ✅ |
+| 1.2 | Table Format       | ✅ | ✅ | ✅ |  |
+| 1.3 | Memtables          | ✅ | ✅ | ✅ |  |
+| 1.4 | Merge Iterators    | ✅ | ✅ | ✅ |
+| 1.5 | Storage Engine - Read Path    | ✅ | ✅ | ✅ |
+| 1.6 | Storage Engine - Write Path   | ✅ | ✅ | ✅ |
+| 2.1 | Compaction Framework    | ✅ | 🚧 | 🚧 |
+| 2.2 | Compaction Strategy    | 🚧 |   |   |
+| 2.3 | Write-Ahead Log    |   |   |   |
+| 2.4 | Manifest    |   |   |   |
+| 2.5 | Bloom Filter    |   |   |   |
+| 2.6 | Key Compression    |   |   |   |
+| 3.1 | Timestamp Encoding    |   |   |   |
+| 3.2 | Prefix Bloom Filter    |   |   |   |
+| 3.3 | Snapshot Read    |   |   |   |
+| 3.4 | Watermark    |   |   |   |
+| 3.5 | Garbage Collection    |   |   |   |
+| 3.6 | Serializable Snapshot Isolation    |   |   |   |

mini-lsm-book/src/SUMMARY.md

@@ -5,18 +5,21 @@
 
 ---
 
-# Tutorial
+# Checkpoint 1
 
 - [Store key-value pairs in little blocks](./01-block.md)
 - [And make them into an SST](./02-sst.md)
 - [Now it's time to merge everything](./03-memtable.md)
 - [The engine is on fire](./04-engine.md)
 
+# Checkpoint 2
+
+- [Let's do something in the background](./05-compaction.md)
+
 ---
 
 # WIP Chapters
 
-- [Let's do something in the background](./05-compaction.md)
 - [Be careful when the system crashes](./06-recovery.md)
 - [A good bloom filter makes life easier](./07-bloom-filter.md)
 - [Save some space, hopefully](./08-key-compression.md)

mini-lsm/src/compact.rs

@@ -0,0 +1,72 @@
+use std::sync::Arc;
+
+use anyhow::Result;
+
+use crate::{
+    iterators::{merge_iterator::MergeIterator, StorageIterator},
+    lsm_storage::LsmStorage,
+    table::{SsTable, SsTableBuilder, SsTableIterator},
+};
+
+struct CompactOptions {
+    block_size: usize,
+    target_sst_size: usize,
+    compact_to_bottom_level: bool,
+}
+
+impl LsmStorage {
+    #[allow(dead_code)]
+    fn compact(
+        &self,
+        tables: Vec<Arc<SsTable>>,
+        options: CompactOptions,
+    ) -> Result<Vec<Arc<SsTable>>> {
+        let mut iters = Vec::new();
+        iters.reserve(tables.len());
+        for table in tables.iter() {
+            iters.push(Box::new(SsTableIterator::create_and_seek_to_first(
+                table.clone(),
+            )?));
+        }
+        let mut iter = MergeIterator::create(iters);
+
+        let mut builder = None;
+        let mut new_sst = vec![];
+
+        while iter.is_valid() {
+            if builder.is_none() {
+                builder = Some(SsTableBuilder::new(options.block_size));
+            }
+            let builder_inner = builder.as_mut().unwrap();
+            if options.compact_to_bottom_level {
+                if !iter.value().is_empty() {
+                    builder_inner.add(iter.key(), iter.value());
+                }
+            } else {
+                builder_inner.add(iter.key(), iter.value());
+            }
+            iter.next()?;
+
+            if builder_inner.estimated_size() >= options.target_sst_size {
+                let sst_id = self.next_sst_id(); // lock dropped here
+                let builder = builder.take().unwrap();
+                let sst = Arc::new(builder.build(
+                    sst_id,
+                    Some(self.block_cache.clone()),
+                    self.path_of_sst(sst_id),
+                )?);
+                new_sst.push(sst);
+            }
+        }
+        if let Some(builder) = builder {
+            let sst_id = self.next_sst_id(); // lock dropped here
+            let sst = Arc::new(builder.build(
+                sst_id,
+                Some(self.block_cache.clone()),
+                self.path_of_sst(sst_id),
+            )?);
+            new_sst.push(sst);
+        }
+        Ok(new_sst)
+    }
+}

mini-lsm/src/lib.rs

@@ -1,4 +1,5 @@
 pub mod block;
+mod compact;
 pub mod iterators;
 pub mod lsm_iterator;
 pub mod lsm_storage;

mini-lsm/src/lsm_storage.rs

@@ -1,5 +1,6 @@
 use std::ops::Bound;
 use std::path::{Path, PathBuf};
+use std::sync::atomic::AtomicUsize;
 use std::sync::Arc;
 
 use anyhow::Result;
@@ -27,8 +28,6 @@ pub struct LsmStorageInner {
     /// L1 - L6 SsTables, sorted by key range.
     #[allow(dead_code)]
     levels: Vec<Vec<Arc<SsTable>>>,
-    /// The next SSTable ID.
-    next_sst_id: usize,
 }
 
 impl LsmStorageInner {
@@ -38,26 +37,32 @@ impl LsmStorageInner {
             imm_memtables: vec![],
             l0_sstables: vec![],
             levels: vec![],
-            next_sst_id: 1,
         }
     }
 }
 
 /// The storage interface of the LSM tree.
 pub struct LsmStorage {
-    inner: Arc<RwLock<Arc<LsmStorageInner>>>,
+    pub(crate) inner: Arc<RwLock<Arc<LsmStorageInner>>>,
     flush_lock: Mutex<()>,
     path: PathBuf,
-    block_cache: Arc<BlockCache>,
+    pub(crate) block_cache: Arc<BlockCache>,
+    next_sst_id: AtomicUsize,
 }
 
 impl LsmStorage {
+    pub(crate) fn next_sst_id(&self) -> usize {
+        self.next_sst_id
+            .fetch_add(1, std::sync::atomic::Ordering::SeqCst)
+    }
+
     pub fn open(path: impl AsRef<Path>) -> Result<Self> {
         Ok(Self {
             inner: Arc::new(RwLock::new(Arc::new(LsmStorageInner::create()))),
             flush_lock: Mutex::new(()),
             path: path.as_ref().to_path_buf(),
-            block_cache: Arc::new(BlockCache::new(1 << 20)), // 4GB block cache
+            block_cache: Arc::new(BlockCache::new(1 << 20)), // 4GB block cache,
+            next_sst_id: AtomicUsize::new(1),
         })
     }
 
@@ -121,7 +126,7 @@ impl LsmStorage {
         Ok(())
     }
 
-    fn path_of_sst(&self, id: usize) -> PathBuf {
+    pub(crate) fn path_of_sst(&self, id: usize) -> PathBuf {
         self.path.join(format!("{:05}.sst", id))
     }
 
@@ -142,7 +147,7 @@ impl LsmStorage {
             let mut snapshot = guard.as_ref().clone();
             let memtable = std::mem::replace(&mut snapshot.memtable, Arc::new(MemTable::create()));
             flush_memtable = memtable.clone();
-            sst_id = snapshot.next_sst_id;
+            sst_id = self.next_sst_id();
             // Add the memtable to the immutable memtables.
             snapshot.imm_memtables.push(memtable);
             // Update the snapshot.
@@ -169,8 +174,6 @@ impl LsmStorage {
             snapshot.imm_memtables.pop();
             // Add L0 table
             snapshot.l0_sstables.push(sst);
-            // Update SST ID
-            snapshot.next_sst_id += 1;
             // Update the snapshot.
             *guard = Arc::new(snapshot);
         }

rustfmt.toml

@@ -0,0 +1,12 @@
+comment_width = 120
+format_code_in_doc_comments = true
+format_macro_bodies = true
+format_macro_matchers = true
+normalize_comments = true
+normalize_doc_attributes = true
+imports_granularity = "Module"
+group_imports = "StdExternalCrate"
+reorder_impl_items = true
+reorder_imports = true
+tab_spaces = 4
+wrap_comments = true