MVStore: store root pages first; better size estimation for serialized objects;…

MVStore: store root pages first; better size estimation for serialized objects; option to compress database content.

h2/src/docsrc/html/mvstore.html

@@ -266,6 +266,7 @@ Serialization is pluggable. The default serialization currently supports many co
 and uses Java serialization for other objects. The following classes are currently directly supported:
 <code>Boolean, Byte, Short, Character, Integer, Long, Float, Double, BigInteger, BigDecimal,
 String, UUID, Date</code> and arrays (both primitive arrays and object arrays).
+For serialized objects, the size estimate is adjusted using an exponential moving average.
 </p><p>
 Parameterized data types are supported
 (for example one could build a string data type that limits the length).
@@ -511,14 +512,14 @@ will result in the following two chunks (excluding metadata):
 </p>
 <p>
 <b>Chunk 1:</b><br />
-- Page 1: leaf with 140 entries (keys 0 - 139)<br />
-- Page 2: leaf with 260 entries (keys 140 - 399)<br />
-- Page 3: (root) node with 2 entries pointing to page 1 and 2<br />
+- Page 1: (root) node with 2 entries pointing to page 2 and 3<br />
+- Page 2: leaf with 140 entries (keys 0 - 139)<br />
+- Page 3: leaf with 260 entries (keys 140 - 399)<br />
 </p>
 <p>
 <b>Chunk 2:</b><br />
-- Page 4: leaf with 140 entries (keys 0 - 139)<br />
-- Page 5: (root) node with 2 entries pointing to page 4 and 2<br />
+- Page 4: (root) node with 2 entries pointing to page 3 and 5<br />
+- Page 5: leaf with 140 entries (keys 0 - 139)<br />
 </p>
 <p>
 That means each chunk contains the changes of one version:
@@ -650,7 +651,7 @@ and <a href="https://en.wikipedia.org/wiki/Variable-length_quantity">variable si
 </li><li>mapId (variable size int): The id of the map this page belongs to.
 </li><li>len (variable size int): The number of keys in the page.
 </li><li>type (byte): The page type (0 for leaf page, 1 for internal node;
-    plus 2 if the page data is compressed).
+    plus 2 if the keys and values are compressed).
 </li><li>children (array of long; internal nodes only): The position of the children.
 </li><li>childCounts (array of variable size long; internal nodes only):
     The total number of entries for the given child page.
@@ -658,8 +659,11 @@ and <a href="https://en.wikipedia.org/wiki/Variable-length_quantity">variable si
 </li><li>values (byte array; leaf pages only): All values, stored depending on the data type.
 </li></ul>
 <p>
-Even though this is not required by the file format, each B-tree is stored
-"upside down", that means the leaf pages first, then the internal nodes, and lastly the root page.
+Even though this is not required by the file format, pages are stored in the following order:
+For each map, the root page is stored first, then the internal nodes (if there are any), 
+and then the leaf pages.
+This should speed up reads for media where sequential reads are faster than random access reads.
+The metadata map is stored at the end of a chunk.
 </p>
 <p>
 Pointers to pages are stored as a long, using a special format:
@@ -680,7 +684,7 @@ and when a page is marked as removed, the live maximum length is adjusted.
 This allows to estimate the amount of free space within a block, in addition to the number of free pages.
 </p>
 <p>
-The total number of entries in a child nodes is kept to allow efficient range counting,
+The total number of entries in child nodes are kept to allow efficient range counting,
 lookup by index, and skip operations.
 The pages form a <a href="http://www.chiark.greenend.org.uk/~sgtatham/algorithms/cbtree.html">counted B-tree</a>.
 </p>

h2/src/main/org/h2/constant/DbSettings.java

@@ -327,6 +327,13 @@ public class DbSettings extends SettingsBase {
      * Use the MVStore storage engine.
      */
     public final boolean mvStore = get("MV_STORE", false);
+    
+    /**
+     * Database setting <code>COMPRESS</code>
+     * (default: false).<br />
+     * Compress data when storing.
+     */
+    public final boolean compressData = get("COMPRESS", false);
 
     private DbSettings(HashMap<String, String> s) {
         super(s);

h2/src/main/org/h2/mvstore/MVStore.java

@@ -51,12 +51,7 @@ MVStore:
 
 - maybe change the length code to have lower gaps
 
-- improve memory calculation for transient and cache
-    specially for large pages (when using the StreamStore)
-
 - automated 'kill process' and 'power failure' test
-- update checkstyle
-- feature to auto-compact from time to time and on close
 - test and possibly improve compact operation (for large dbs)
 - possibly split chunk metadata into immutable and mutable
 - compact: avoid processing pages using a counting bloom filter
@@ -75,7 +70,6 @@ MVStore:
 - serialization for lists, sets, sets, sorted sets, maps, sorted maps
 - maybe rename 'rollback' to 'revert' to distinguish from transactions
 - support other compression algorithms (deflate, LZ4,...)
-- support opening (existing) maps by id
 - remove features that are not really needed; simplify the code
     possibly using a separate layer or tools
     (retainVersion?)
@@ -110,6 +104,8 @@ MVStore:
     or use a small page size for metadata
 - data type "string": maybe use prefix compression for keys
 - test chunk id rollover
+- feature to auto-compact from time to time and on close
+- compact very small chunks
 
 */
 
@@ -790,7 +786,7 @@ public class MVStore {
      * @param pos the position
      * @return the chunk
      */
-    Chunk getChunk(long pos) {
+    private Chunk getChunk(long pos) {
         int chunkId = DataUtils.getPageChunkId(pos);
         Chunk c = chunks.get(chunkId);
         if (c == null) {

h2/src/main/org/h2/mvstore/MVStoreTool.java

@@ -113,10 +113,6 @@ public class MVStoreTool {
                             pageSize);
                     p += pageSize;
                     remaining--;
-                    if (compressed) {
-                        continue;
-                    }
-                    String[] keys = new String[entries];
                     long[] children = null;
                     long[] counts = null;
                     if (node) {
@@ -130,10 +126,13 @@ public class MVStoreTool {
                             counts[i] = s;
                         }
                     }
+                    String[] keys = new String[entries];
                     if (mapId == 0) {
-                        for (int i = 0; i < entries; i++) {
-                            String k = StringDataType.INSTANCE.read(chunk);
-                            keys[i] = k;
+                        if (!compressed) {
+                            for (int i = 0; i < entries; i++) {
+                                String k = StringDataType.INSTANCE.read(chunk);
+                                keys[i] = k;
+                            }
                         }
                         if (node) {
                             // meta map node
@@ -151,7 +150,7 @@ public class MVStoreTool {
                                     keys[entries],
                                     DataUtils.getPageChunkId(cp),
                                     DataUtils.getPageOffset(cp));
-                        } else {
+                        } else if (!compressed) {
                             // meta map leaf
                             String[] values = new String[entries];
                             for (int i = 0; i < entries; i++) {

h2/src/main/org/h2/mvstore/Page.java

@@ -113,7 +113,7 @@ public class Page {
      * @param version the version
      * @return the new page
      */
-    public static Page createEmpty(MVMap<?, ?> map, long version) {
+    static Page createEmpty(MVMap<?, ?> map, long version) {
         return create(map, version,
                 0, EMPTY_OBJECT_ARRAY, EMPTY_OBJECT_ARRAY,
                 0, null, null, null,
@@ -355,7 +355,7 @@ public class Page {
      * @param at the split index
      * @return the page with the entries after the split index
      */
-    public Page split(int at) {
+    Page split(int at) {
         return isLeaf() ? splitLeaf(at) : splitNode(at);
     }
 
@@ -500,7 +500,7 @@ public class Page {
      * @param index the index
      * @param total the new value
      */
-    public void setCounts(int index, long total) {
+    private void setCounts(int index, long total) {
         if (total != counts[index]) {
             if ((sharedFlags & SHARED_COUNTS) != 0) {
                 counts = Arrays.copyOf(counts, counts.length);
@@ -748,17 +748,6 @@ public class Page {
         keyCount = len;
         int type = buff.get();
         boolean node = (type & 1) == DataUtils.PAGE_TYPE_NODE;
-        boolean compressed = (type & DataUtils.PAGE_COMPRESSED) != 0;
-        if (compressed) {
-            Compressor compressor = map.getStore().getCompressor();
-            int lenAdd = DataUtils.readVarInt(buff);
-            int compLen = pageLength + start - buff.position();
-            byte[] comp = DataUtils.newBytes(compLen);
-            buff.get(comp);
-            int l = compLen + lenAdd;
-            buff = ByteBuffer.allocate(l);
-            compressor.expand(comp, 0, compLen, buff.array(), buff.arrayOffset(), l);
-        }
         if (node) {
             childCount = len + 1;
             children = new long[len + 1];
@@ -775,6 +764,17 @@ public class Page {
             }
             totalCount = total;
         }
+        boolean compressed = (type & DataUtils.PAGE_COMPRESSED) != 0;
+        if (compressed) {
+            Compressor compressor = map.getStore().getCompressor();
+            int lenAdd = DataUtils.readVarInt(buff);
+            int compLen = pageLength + start - buff.position();
+            byte[] comp = DataUtils.newBytes(compLen);
+            buff.get(comp);
+            int l = compLen + lenAdd;
+            buff = ByteBuffer.allocate(l);
+            compressor.expand(comp, 0, compLen, buff.array(), buff.arrayOffset(), l);
+        }
         map.getKeyType().read(buff, keys, len, true);
         if (!node) {
             values = new Object[len];
@@ -789,8 +789,9 @@ public class Page {
      *
      * @param chunk the chunk
      * @param buff the target buffer
+     * @return the position of the buffer just after the type
      */
-    private void write(Chunk chunk, WriteBuffer buff) {
+    private int write(Chunk chunk, WriteBuffer buff) {
         int start = buff.position();
         int len = keyCount;
         int type = children != null ? DataUtils.PAGE_TYPE_NODE
@@ -798,17 +799,16 @@ public class Page {
         buff.putInt(0).
             putShort((byte) 0).
             putVarInt(map.getId()).
-            putVarInt(len).
-            put((byte) type);
-        int compressStart = buff.position();
+            putVarInt(len);
+        int typePos = buff.position();
+        buff.put((byte) type);
         if (type == DataUtils.PAGE_TYPE_NODE) {
-            for (int i = 0; i <= len; i++) {
-                buff.putLong(children[i]);
-            }
+            writeChildren(buff);
             for (int i = 0; i <= len; i++) {
                 buff.putVarLong(counts[i]);
             }
         }
+        int compressStart = buff.position();
         map.getKeyType().write(buff, keys, len, true);
         if (type == DataUtils.PAGE_TYPE_LEAF) {
             map.getValueType().write(buff, values, len, false);
@@ -818,13 +818,13 @@ public class Page {
             Compressor compressor = map.getStore().getCompressor();
             int expLen = buff.position() - compressStart;
             byte[] exp = new byte[expLen];
-            buff.position(compressStart).
-                get(exp);
+            buff.position(compressStart).get(exp);
             byte[] comp = new byte[exp.length * 2];
             int compLen = compressor.compress(exp, exp.length, comp, 0);
             if (compLen + DataUtils.getVarIntLen(compLen - expLen) < expLen) {
-                buff.position(compressStart - 1).
-                    put((byte) (type + DataUtils.PAGE_COMPRESSED)).
+                buff.position(typePos).
+                    put((byte) (type + DataUtils.PAGE_COMPRESSED));
+                buff.position(compressStart).
                     putVarInt(expLen - compLen).
                     put(comp, 0, compLen);
             }
@@ -847,6 +847,14 @@ public class Page {
         chunk.maxLenLive += max;
         chunk.pageCount++;
         chunk.pageCountLive++;
+        return typePos + 1;
+    }
+    
+    private void writeChildren(WriteBuffer buff) {
+        int len = keyCount;
+        for (int i = 0; i <= len; i++) {
+            buff.putLong(children[i]);
+        }
     }
 
     /**
@@ -861,6 +869,7 @@ public class Page {
             // already stored before
             return;
         }
+        int patch = write(chunk, buff);
         if (!isLeaf()) {
             int len = childCount;
             for (int i = 0; i < len; i++) {
@@ -870,8 +879,11 @@ public class Page {
                     children[i] = p.getPos();
                 }
             }
+            int old = buff.position();
+            buff.position(patch);
+            writeChildren(buff);
+            buff.position(old);
         }
-        write(chunk, buff);
     }
 
     /**

h2/src/main/org/h2/mvstore/db/MVTableEngine.java

@@ -77,6 +77,11 @@ public class MVTableEngine implements TableEngine {
                 }
                 builder.encryptionKey(password);
             }
+            if (db.getSettings().compressData) {
+                builder.compressData();
+                // use a larger page split size to improve the compression ratio
+                builder.pageSplitSize(64 * 1024);
+            }
             builder.backgroundExceptionHandler(new UncaughtExceptionHandler() {
 
                 @Override

h2/src/main/org/h2/mvstore/type/ObjectDataType.java

@@ -1471,6 +1471,8 @@ public class ObjectDataType implements DataType {
      * The type for serialized objects.
      */
     class SerializedObjectType extends AutoDetectDataType {
+        
+        int averageSize = 10000;
 
         SerializedObjectType(ObjectDataType base) {
             super(base, TYPE_SERIALIZED_OBJECT);
@@ -1508,7 +1510,7 @@ public class ObjectDataType implements DataType {
         public int getMemory(Object obj) {
             DataType t = getType(obj);
             if (t == this) {
-                return 1000;
+                return averageSize;
             }
             return t.getMemory(obj);
         }
@@ -1521,6 +1523,10 @@ public class ObjectDataType implements DataType {
                 return;
             }
             byte[] data = serialize(obj);
+            int size = data.length;
+            // adjust the average size
+            // using an exponential moving average
+            averageSize = (size + 15 * averageSize) / 16;
             buff.put((byte) TYPE_SERIALIZED_OBJECT).putVarInt(data.length)
                     .put(data);
         }

h2/src/test/org/h2/test/store/TestBenchmark.java

@@ -10,6 +10,7 @@ import java.sql.PreparedStatement;
 import java.sql.Statement;
 import java.util.Random;
 
+import org.h2.store.FileLister;
 import org.h2.store.fs.FileUtils;
 import org.h2.test.TestBase;
 
@@ -42,6 +43,8 @@ public class TestBenchmark extends TestBase {
     }
 
     private void test(boolean mvStore) throws Exception {
+        // testInsertSelect(mvStore);
+        // testBinary(mvStore);
         testCreateIndex(mvStore);
     }
 
@@ -51,7 +54,7 @@ public class TestBenchmark extends TestBase {
         Statement stat;
         String url = "mvstore";
         if (mvStore) {
-            url += ";MV_STORE=TRUE;MV_STORE=TRUE";
+            url += ";MV_STORE=TRUE"; // ;COMPRESS=TRUE";
         }
 
         url = getURL(url, true);
@@ -84,7 +87,11 @@ public class TestBenchmark extends TestBase {
 
         System.out.println((System.currentTimeMillis() - start) + " "
                 + (mvStore ? "mvstore" : "default"));
+        conn.createStatement().execute("shutdown compact");
         conn.close();
+        for (String f : FileLister.getDatabaseFiles(getBaseDir(), "mvstore", true)) {
+            System.out.println("   " + f + " " + FileUtils.size(f));
+        }
     }
 
     private void testBinary(boolean mvStore) throws Exception {
@@ -93,7 +100,7 @@ public class TestBenchmark extends TestBase {
         Statement stat;
         String url = "mvstore";
         if (mvStore) {
-            url += ";MV_STORE=TRUE;MV_STORE=TRUE";
+            url += ";MV_STORE=TRUE";
         }
 
         url = getURL(url, true);
@@ -143,7 +150,7 @@ public class TestBenchmark extends TestBase {
         Statement stat;
         String url = "mvstore";
         if (mvStore) {
-            url += ";MV_STORE=TRUE;LOG=0";
+            url += ";MV_STORE=TRUE;LOG=0;COMPRESS=TRUE";
         }
 
         url = getURL(url, true);
@@ -176,7 +183,11 @@ public class TestBenchmark extends TestBase {
 
         System.out.println((System.currentTimeMillis() - start) + " "
                 + (mvStore ? "mvstore" : "default"));
+        conn.createStatement().execute("shutdown compact");
         conn.close();
+        for (String f : FileLister.getDatabaseFiles(getBaseDir(), "mvstore", true)) {
+            System.out.println("   " + f + " " + FileUtils.size(f));
+        }
 
     }
 

h2/src/test/org/h2/test/store/TestMVStore.java

@@ -49,6 +49,7 @@ public class TestMVStore extends TestBase {
     public void test() throws Exception {
         FileUtils.deleteRecursive(getBaseDir(), true);
         FileUtils.createDirectories(getBaseDir());
+        testCompressed();
         testFileFormatExample();
         testMaxChunkLength();
         testCacheInfo();
@@ -102,6 +103,23 @@ public class TestMVStore extends TestBase {
         // longer running tests
         testLargerThan2G();
     }
+    
+    private void testCompressed() {
+        String fileName = getBaseDir() + "/testCompressed.h3";
+        MVStore s = new MVStore.Builder().fileName(fileName).compressData().open();
+        MVMap<String, String> map = s.openMap("data");
+        String data = "xxxxxxxxxx";
+        for (int i = 0; i < 400; i++) {
+            map.put(data + i, data);
+        }
+        s.close();
+        s = new MVStore.Builder().fileName(fileName).open();
+        map = s.openMap("data");
+        for (int i = 0; i < 400; i++) {
+            assertEquals(data, map.get(data + i));
+        }
+        s.close();
+    }
 
     private void testFileFormatExample() {
         String fileName = getBaseDir() + "/testFileFormatExample.h3";
@@ -116,7 +134,7 @@ public class TestMVStore extends TestBase {
         }
         s.commit();
         s.close();
-        // MVStoreTool.dump(fileName);
+        // ;MVStoreTool.dump(fileName);
     }
 
     private void testMaxChunkLength() {