Put the documents MTBL back into LMDB

We makes sure to write the documents into a file before
memory mapping it and putting it into LMDB, this way we avoid
moving it to RAM

public/script.js

@@ -63,8 +63,5 @@ $('#docs-count').text(function(index, text) {
 
 // Make the database a little bit easier to read
 $('#db-size').text(function(index, text) {
-  let arr = text.split("+");
+  return filesize(parseInt(text))
-  let database_size = filesize(parseInt(arr[0]));
-  let documents_size = filesize(parseInt(arr[1]));
-  return `${database_size} + ${documents_size}`
 });

src/bin/indexer.rs

@@ -1,5 +1,5 @@
 use std::convert::{TryFrom, TryInto};
-use std::fs::{File, OpenOptions};
+use std::fs::File;
 use std::io::{self, Read, Write};
 use std::iter::FromIterator;
 use std::path::PathBuf;
@@ -14,7 +14,7 @@ use flate2::read::GzDecoder;
 use fst::IntoStreamer;
 use heed::EnvOpenOptions;
 use heed::types::*;
-use log::debug;
+use log::{debug, info};
 use memmap::Mmap;
 use oxidized_mtbl::{Reader, Writer, Merger, Sorter, CompressionType};
 use rayon::prelude::*;
@@ -486,9 +486,9 @@ fn main() -> anyhow::Result<()> {
         .max_dbs(10)
         .open(&opt.database)?;
 
-    let mut index = Index::new(&env, &opt.database)?;
+    let before_indexing = Instant::now();
+    let index = Index::new(&env)?;
 
-    let documents_path = opt.database.join("documents.mtbl");
     let num_threads = rayon::current_num_threads();
     let arc_cache_size = opt.indexer.arc_cache_size;
     let max_nb_chunks = opt.indexer.max_nb_chunks;
@@ -566,17 +566,9 @@ fn main() -> anyhow::Result<()> {
         docs_stores.push(d);
     });
 
-    debug!("We are writing into LMDB and MTBL...");
+    debug!("We are writing the documents into MTBL on disk...");
-
-    // We run both merging steps in parallel.
-    let (lmdb, mtbl) = rayon::join(|| {
-        // We merge the postings lists into LMDB.
-        let mut wtxn = env.write_txn()?;
-        merge_into_lmdb(stores, |k, v| lmdb_writer(&mut wtxn, &index, k, v))?;
-        Ok(wtxn.commit()?) as anyhow::Result<_>
-    }, || {
     // We also merge the documents into its own MTBL store.
-        let file = OpenOptions::new().create(true).truncate(true).write(true).read(true).open(documents_path)?;
+    let file = tempfile::tempfile()?;
     let mut writer = Writer::builder()
         .compression_type(documents_compression_type)
         .compression_level(documents_compression_level)
@@ -584,14 +576,18 @@ fn main() -> anyhow::Result<()> {
     let mut builder = Merger::builder(docs_merge);
     builder.extend(docs_stores);
     builder.build().write_into(&mut writer)?;
-        Ok(writer.finish()?) as anyhow::Result<_>
+    let file = writer.into_inner()?;
-    });
+    let documents_mmap = unsafe { memmap::Mmap::map(&file)? };
 
-    lmdb.and(mtbl)?;
+    debug!("We are writing the postings lists and documents into LMDB on disk...");
-    index.refresh_documents()?;
+    // We merge the postings lists into LMDB.
-    let count = index.number_of_documents();
+    let mut wtxn = env.write_txn()?;
+    merge_into_lmdb(stores, |k, v| lmdb_writer(&mut wtxn, &index, k, v))?;
+    index.put_documents(&mut wtxn, &documents_mmap)?;
+    let count = index.number_of_documents(&wtxn)?;
+    wtxn.commit()?;
 
-    debug!("Wrote {} documents into LMDB", count);
+    info!("Wrote {} documents in {:.02?}", count, before_indexing.elapsed());
 
     Ok(())
 }

src/bin/infos.rs

@@ -96,7 +96,7 @@ fn main() -> anyhow::Result<()> {
         .open(&opt.database)?;
 
     // Open the LMDB database.
-    let index = Index::new(&env, opt.database)?;
+    let index = Index::new(&env)?;
     let rtxn = env.read_txn()?;
 
     match opt.command {
@@ -200,6 +200,11 @@ fn biggest_value_sizes(index: &Index, rtxn: &heed::RoTxn, limit: usize) -> anyho
             if heap.len() > limit { heap.pop(); }
         }
 
+        if let Some(documents) = index.main.get::<_, ByteSlice, ByteSlice>(rtxn, b"documents")? {
+            heap.push(Reverse((documents.len(), format!("documents"), main_name)));
+            if heap.len() > limit { heap.pop(); }
+        }
+
         for result in index.word_positions.as_polymorph().iter::<_, Str, ByteSlice>(rtxn)? {
             let (word, value) = result?;
             heap.push(Reverse((value.len(), word.to_string(), word_positions_name)));

src/bin/search.rs

@@ -49,7 +49,7 @@ fn main() -> anyhow::Result<()> {
         .open(&opt.database)?;
 
     // Open the LMDB database.
-    let index = Index::new(&env, opt.database)?;
+    let index = Index::new(&env)?;
     let rtxn = env.read_txn()?;
 
     let stdin = io::stdin();
@@ -68,7 +68,7 @@ fn main() -> anyhow::Result<()> {
             Some(headers) => headers,
             None => return Ok(()),
         };
-        let documents = index.documents(result.documents_ids.iter().cloned())?;
+        let documents = index.documents(&rtxn, result.documents_ids.iter().cloned())?;
 
         let mut stdout = io::stdout();
         stdout.write_all(&headers)?;

src/bin/serve.rs

@@ -62,7 +62,6 @@ fn highlight_string(string: &str, words: &HashSet<String>) -> String {
 struct IndexTemplate {
     db_name: String,
     db_size: usize,
-    docs_size: usize,
     docs_count: usize,
 }
 
@@ -83,28 +82,23 @@ async fn main() -> anyhow::Result<()> {
         .open(&opt.database)?;
 
     // Open the LMDB database.
-    let index = Index::new(&env, &opt.database)?;
+    let index = Index::new(&env)?;
 
     // Retrieve the database the file stem (w/o the extension),
     // the disk file size and the number of documents in the database.
     let db_name = opt.database.file_stem().and_then(|s| s.to_str()).unwrap_or("").to_string();
     let db_size = File::open(opt.database.join("data.mdb"))?.metadata()?.len() as usize;
-    let docs_size = File::open(opt.database.join("documents.mtbl"))?.metadata()?.len() as usize;
+
-    let docs_count = index.number_of_documents();
+    let rtxn = env.read_txn()?;
+    let docs_count = index.number_of_documents(&rtxn)? as usize;
+    drop(rtxn);
 
     // We run and wait on the HTTP server
 
     // Expose an HTML page to debug the search in a browser
     let dash_html_route = warp::filters::method::get()
         .and(warp::filters::path::end())
-        .map(move || {
+        .map(move || IndexTemplate { db_name: db_name.clone(), db_size, docs_count });
-            IndexTemplate {
-                db_name: db_name.clone(),
-                db_size,
-                docs_size,
-                docs_count: docs_count as usize,
-            }
-        });
 
     let dash_bulma_route = warp::filters::method::get()
         .and(warp::path!("bulma.min.css"))
@@ -192,7 +186,7 @@ async fn main() -> anyhow::Result<()> {
             if let Some(headers) = index.headers(&rtxn).unwrap() {
                 // We write the headers
                 body.extend_from_slice(headers);
-                let documents = index.documents(documents_ids).unwrap();
+                let documents = index.documents(&rtxn, documents_ids).unwrap();
 
                 for (_id, content) in documents {
                     let content = std::str::from_utf8(content.as_ref()).unwrap();

src/heed_codec/mod.rs

@@ -1,5 +1,7 @@
+mod mtbl_codec;
 mod roaring_bitmap_codec;
 mod str_beu32_codec;
 
+pub use self::mtbl_codec::MtblCodec;
 pub use self::roaring_bitmap_codec::RoaringBitmapCodec;
 pub use self::str_beu32_codec::StrBEU32Codec;

src/heed_codec/mtbl_codec.rs

@@ -0,0 +1,20 @@
+use std::borrow::Cow;
+use oxidized_mtbl::Reader;
+
+pub struct MtblCodec;
+
+impl<'a> heed::BytesDecode<'a> for MtblCodec {
+    type DItem = Reader<&'a [u8]>;
+
+    fn bytes_decode(bytes: &'a [u8]) -> Option<Self::DItem> {
+        Reader::new(bytes).ok()
+    }
+}
+
+impl heed::BytesEncode<'_> for MtblCodec {
+    type EItem = [u8];
+
+    fn bytes_encode(item: &Self::EItem) -> Option<Cow<[u8]>> {
+        Some(Cow::Borrowed(item))
+    }
+}

src/lib.rs

@@ -2,27 +2,20 @@ mod criterion;
 mod node;
 mod query_tokens;
 mod search;
-mod transitive_arc;
 pub mod heed_codec;
 pub mod lexer;
 
 use std::collections::HashMap;
-use std::fs::{File, OpenOptions};
 use std::hash::BuildHasherDefault;
-use std::path::{Path, PathBuf};
-use std::sync::Arc;
 
-use anyhow::Context;
+use anyhow::{bail, Context};
 use fxhash::{FxHasher32, FxHasher64};
 use heed::types::*;
 use heed::{PolyDatabase, Database};
-use memmap::Mmap;
-use oxidized_mtbl as omtbl;
 
 pub use self::search::{Search, SearchResult};
 pub use self::criterion::{Criterion, default_criteria};
-use self::heed_codec::{RoaringBitmapCodec, StrBEU32Codec};
+use self::heed_codec::{MtblCodec, RoaringBitmapCodec, StrBEU32Codec};
-use self::transitive_arc::TransitiveArc;
 
 pub type FastMap4<K, V> = HashMap<K, V, BuildHasherDefault<FxHasher32>>;
 pub type FastMap8<K, V> = HashMap<K, V, BuildHasherDefault<FxHasher64>>;
@@ -34,10 +27,12 @@ pub type DocumentId = u32;
 pub type Attribute = u32;
 pub type Position = u32;
 
+const WORDS_FST_KEY: &str = "words-fst";
+const HEADERS_KEY: &str = "headers";
+const DOCUMENTS_KEY: &str = "documents";
+
 #[derive(Clone)]
 pub struct Index {
-    // The database path, where the LMDB and MTBL files are.
-    path: PathBuf,
     /// Contains many different types (e.g. the documents CSV headers).
     pub main: PolyDatabase,
     /// A word and all the positions where it appears in the whole dataset.
@@ -46,44 +41,24 @@ pub struct Index {
     pub word_position_docids: Database<StrBEU32Codec, RoaringBitmapCodec>,
     /// Maps a word and an attribute (u32) to all the documents ids where the given word appears.
     pub word_attribute_docids: Database<StrBEU32Codec, RoaringBitmapCodec>,
-    /// The MTBL store that contains the documents content.
-    documents: omtbl::Reader<TransitiveArc<Mmap>>,
 }
 
 impl Index {
-    pub fn new<P: AsRef<Path>>(env: &heed::Env, path: P) -> anyhow::Result<Index> {
+    pub fn new(env: &heed::Env) -> anyhow::Result<Index> {
-        let documents_path = path.as_ref().join("documents.mtbl");
-        let mut documents = OpenOptions::new().create(true).write(true).read(true).open(documents_path)?;
-        // If the file is empty we must initialize it like an empty MTBL database.
-        if documents.metadata()?.len() == 0 {
-            omtbl::Writer::new(&mut documents).finish()?;
-        }
-        let documents = unsafe { memmap::Mmap::map(&documents)? };
-
         Ok(Index {
-            path: path.as_ref().to_path_buf(),
             main: env.create_poly_database(None)?,
             word_positions: env.create_database(Some("word-positions"))?,
             word_position_docids: env.create_database(Some("word-position-docids"))?,
             word_attribute_docids: env.create_database(Some("word-attribute-docids"))?,
-            documents: omtbl::Reader::new(TransitiveArc(Arc::new(documents)))?,
         })
     }
 
-    pub fn refresh_documents(&mut self) -> anyhow::Result<()> {
-        let documents_path = self.path.join("documents.mtbl");
-        let documents = File::open(&documents_path)?;
-        let documents = unsafe { memmap::Mmap::map(&documents)? };
-        self.documents = omtbl::Reader::new(TransitiveArc(Arc::new(documents)))?;
-        Ok(())
-    }
-
     pub fn put_headers(&self, wtxn: &mut heed::RwTxn, headers: &[u8]) -> anyhow::Result<()> {
-        Ok(self.main.put::<_, Str, ByteSlice>(wtxn, "headers", headers)?)
+        Ok(self.main.put::<_, Str, ByteSlice>(wtxn, HEADERS_KEY, headers)?)
     }
 
     pub fn headers<'t>(&self, rtxn: &'t heed::RoTxn) -> heed::Result<Option<&'t [u8]>> {
-        self.main.get::<_, Str, ByteSlice>(rtxn, "headers")
+        self.main.get::<_, Str, ByteSlice>(rtxn, HEADERS_KEY)
     }
 
     pub fn number_of_attributes<'t>(&self, rtxn: &'t heed::RoTxn) -> anyhow::Result<Option<usize>> {
@@ -98,29 +73,46 @@ impl Index {
     }
 
     pub fn put_fst<A: AsRef<[u8]>>(&self, wtxn: &mut heed::RwTxn, fst: &fst::Set<A>) -> anyhow::Result<()> {
-        Ok(self.main.put::<_, Str, ByteSlice>(wtxn, "words-fst", fst.as_fst().as_bytes())?)
+        Ok(self.main.put::<_, Str, ByteSlice>(wtxn, WORDS_FST_KEY, fst.as_fst().as_bytes())?)
     }
 
     pub fn fst<'t>(&self, rtxn: &'t heed::RoTxn) -> anyhow::Result<Option<fst::Set<&'t [u8]>>> {
-        match self.main.get::<_, Str, ByteSlice>(rtxn, "words-fst")? {
+        match self.main.get::<_, Str, ByteSlice>(rtxn, WORDS_FST_KEY)? {
             Some(bytes) => Ok(Some(fst::Set::new(bytes)?)),
             None => Ok(None),
         }
     }
 
     /// Returns a [`Vec`] of the requested documents. Returns an error if a document is missing.
-    pub fn documents<I: IntoIterator<Item=DocumentId>>(&self, iter: I) -> anyhow::Result<Vec<(DocumentId, Vec<u8>)>> {
+    pub fn documents<'t>(
+        &self,
+        rtxn: &'t heed::RoTxn,
+        iter: impl IntoIterator<Item=DocumentId>,
+    ) -> anyhow::Result<Vec<(DocumentId, Vec<u8>)>>
+    {
+        match self.main.get::<_, Str, MtblCodec>(rtxn, DOCUMENTS_KEY)? {
+            Some(documents) => {
                 iter.into_iter().map(|id| {
                     let key = id.to_be_bytes();
-            let content = self.documents.clone().get(&key)?.with_context(|| format!("Could not find document {}.", id))?;
+                    let content = documents.clone().get(&key)?
+                        .with_context(|| format!("Could not find document {}", id))?;
                     Ok((id, content.as_ref().to_vec()))
-        })
+                }).collect()
-        .collect()
+            },
+            None => bail!("No documents database found"),
+        }
+    }
+
+    pub fn put_documents(&self, wtxn: &mut heed::RwTxn, documents: &[u8]) -> anyhow::Result<()> {
+        Ok(self.main.put::<_, Str, MtblCodec>(wtxn, DOCUMENTS_KEY, documents)?)
     }
 
     /// Returns the number of documents indexed in the database.
-    pub fn number_of_documents(&self) -> usize {
+    pub fn number_of_documents<'t>(&self, rtxn: &'t heed::RoTxn) -> anyhow::Result<usize> {
-        self.documents.metadata().count_entries as usize
+        match self.main.get::<_, Str, MtblCodec>(rtxn, DOCUMENTS_KEY)? {
+            Some(documents) => Ok(documents.metadata().count_entries as usize),
+            None => return Ok(0),
+        }
     }
 
     pub fn search<'a>(&'a self, rtxn: &'a heed::RoTxn) -> Search<'a> {

src/transitive_arc.rs

@@ -1,16 +0,0 @@
-use std::sync::Arc;
-
-/// An `Arc<[u8]>` that is transitive over `AsRef<[u8]>`.
-pub struct TransitiveArc<T>(pub Arc<T>);
-
-impl<T: AsRef<[u8]>> AsRef<[u8]> for TransitiveArc<T> {
-    fn as_ref(&self) -> &[u8] {
-        self.0.as_ref().as_ref()
-    }
-}
-
-impl<T> Clone for TransitiveArc<T> {
-    fn clone(&self) -> TransitiveArc<T> {
-        TransitiveArc(self.0.clone())
-    }
-}

templates/index.html

@@ -34,7 +34,7 @@
           <div class="level-item has-text-centered">
             <div>
               <p class="heading">Database Size</p>
-              <p class="title" id="db-size">{{ db_size }} + {{ docs_size }}</p>
+              <p class="title" id="db-size">{{ db_size }}</p>
             </div>
           </div>
           <div class="level-item has-text-centered">