Fix GC issue (sirixdb#607)

* Fix GC issue * Disable tests and delete everything during setup * Fix bug regarding concurrent/parallel access. * Update build.gradle --------- Co-authored-by: Johannes Lichtenberger <[email protected]>
sband · Apr 24, 2023 · 5d49a46 · 5d49a46
1 parent 0049706
commit 5d49a46
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Showing 13 changed files with 64 additions and 45 deletions.
diff --git a/bundles/sirix-core/src/main/java/org/sirix/access/LocalDatabase.java b/bundles/sirix-core/src/main/java/org/sirix/access/LocalDatabase.java
@@ -119,9 +119,9 @@ public LocalDatabase(final TransactionManager transactionManager, final Database
 
   private void addResourceToBufferManagerMapping(Path resourceFile, ResourceConfiguration resourceConfig) {
     if (resourceConfig.getStorageType() == StorageType.MEMORY_MAPPED) {
-      bufferManagers.put(resourceFile, new BufferManagerImpl(100, 10_000_000, 100_000, 50_000_000, 1_000, 20));
+      bufferManagers.put(resourceFile, new BufferManagerImpl(100, 1_000, 5_000, 50_000, 500, 20));
     } else {
-      bufferManagers.put(resourceFile, new BufferManagerImpl(50_000, 10_000_000, 100_000, 50_000_000, 1_000, 20));
+      bufferManagers.put(resourceFile, new BufferManagerImpl(500, 1_000, 5_000, 50_000, 500, 20));
     }
   }
 

diff --git a/bundles/sirix-core/src/main/java/org/sirix/access/trx/page/NodePageReadOnlyTrx.java b/bundles/sirix-core/src/main/java/org/sirix/access/trx/page/NodePageReadOnlyTrx.java
@@ -245,7 +245,6 @@ void assertNotClosed() {
     }
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   public <V extends DataRecord> V getRecord(final long recordKey, @NonNull final IndexType indexType,
       @NonNegative final int index) {
@@ -571,7 +570,6 @@ PageReference getLeafPageReference(final PageReference pageReferenceToSubtree, f
    * @return dereferenced pages
    * @throws SirixIOException if an I/O-error occurs within the creation process
    */
-  @SuppressWarnings("unchecked")
   List<KeyValuePage<DataRecord>> getPageFragments(final PageReference pageReference) {
     assert pageReference != null;
     final ResourceConfiguration config = resourceSession.getResourceConfig();
@@ -618,7 +616,6 @@ private List<KeyValuePage<DataRecord>> getPreviousPageFragments(final List<PageF
                           .collect(Collectors.toList());
   }
 
-  @SuppressWarnings("unchecked")
   private CompletableFuture<KeyValuePage<DataRecord>> readPage(final PageFragmentKey pageFragmentKey) {
     final var pageReference = new PageReference().setKey(pageFragmentKey.key());
     if (trxIntentLog == null) {
@@ -629,7 +626,6 @@ private CompletableFuture<KeyValuePage<DataRecord>> readPage(final PageFragmentK
       }
     }
     final var pageReadOnlyTrx = resourceSession.beginPageReadOnlyTrx(pageFragmentKey.revision());
-    //noinspection unchecked
     return (CompletableFuture<KeyValuePage<DataRecord>>) pageReadOnlyTrx.getReader()
                                                                         .readAsync(pageReference, pageReadOnlyTrx)
                                                                         .whenComplete((page, exception) -> {

diff --git a/bundles/sirix-core/src/main/java/org/sirix/access/trx/page/NodePageTrx.java b/bundles/sirix-core/src/main/java/org/sirix/access/trx/page/NodePageTrx.java
@@ -313,7 +313,6 @@ public <V extends DataRecord> V getRecord(final long recordKey, @NonNull final I
       if (node == null) {
         node = pageRtx.getValue(((KeyValueLeafPage) pageCont.getComplete()), recordKey);
       }
-      //noinspection unchecked
       return (V) pageRtx.checkItemIfDeleted(node);
     }
   }

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/Cache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/Cache.java
@@ -21,6 +21,7 @@
 
 package org.sirix.cache;
 
+import com.github.benmanes.caffeine.cache.Scheduler;
 import org.checkerframework.checker.nullness.qual.NonNull;
 
 import java.util.Map;
@@ -37,6 +38,8 @@
  * @param <V> the value
  */
 public interface Cache<K, V> {
+  Scheduler scheduler = Scheduler.systemScheduler();
+
   /**
    * Clearing the cache. That is removing all elements.
    */

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/IndexLogKey.java b/bundles/sirix-core/src/main/java/org/sirix/cache/IndexLogKey.java
@@ -9,10 +9,10 @@
  * @author Johannes Lichtenberger
  */
 public final class IndexLogKey {
-  private final IndexType indexType;
-  private final long recordPageKey;
-  private final @NonNegative int indexNumber;
-  private final @NonNegative int revisionNumber;
+  private IndexType indexType;
+  private long recordPageKey;
+  private @NonNegative int indexNumber;
+  private @NonNegative int revisionNumber;
 
   public IndexLogKey(IndexType indexType, long recordPageKey, @NonNegative int indexNumber,
       @NonNegative int revisionNumber) {
@@ -22,6 +22,26 @@ public IndexLogKey(IndexType indexType, long recordPageKey, @NonNegative int ind
     this.revisionNumber = revisionNumber;
   }
 
+  public IndexLogKey setIndexType(IndexType indexType) {
+    this.indexType = indexType;
+    return this;
+  }
+
+  public IndexLogKey setRecordPageKey(long recordPageKey) {
+    this.recordPageKey = recordPageKey;
+    return this;
+  }
+
+  public IndexLogKey setIndexNumber(int indexNumber) {
+    this.indexNumber = indexNumber;
+    return this;
+  }
+
+  public IndexLogKey setRevisionNumber(int revisionNumber) {
+    this.revisionNumber = revisionNumber;
+    return this;
+  }
+
   private int hash;
 
   @Override
@@ -48,22 +68,6 @@ public int getRevisionNumber() {
     return revisionNumber;
   }
 
-  public IndexType indexType() {
-    return indexType;
-  }
-
-  public long recordPageKey() {
-    return recordPageKey;
-  }
-
-  public @NonNegative int indexNumber() {
-    return indexNumber;
-  }
-
-  public @NonNegative int revisionNumber() {
-    return revisionNumber;
-  }
-
   @Override
   public boolean equals(Object obj) {
     if (obj == this)

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/NamesCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/NamesCache.java
@@ -6,13 +6,15 @@
 import java.util.Map;
 import java.util.concurrent.TimeUnit;
 
-public class NamesCache implements Cache<NamesCacheKey, Names> {
+public final class NamesCache implements Cache<NamesCacheKey, Names> {
 
   private final com.github.benmanes.caffeine.cache.Cache<NamesCacheKey, Names> cache;
 
   public NamesCache(final int maxSize) {
     cache = Caffeine.newBuilder()
                     .maximumSize(maxSize)
+                    .expireAfterAccess(5, TimeUnit.MINUTES)
+                    .scheduler(scheduler)
                     .build();
   }
 

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/PageCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/PageCache.java
@@ -7,17 +7,24 @@
 import org.sirix.page.interfaces.Page;
 
 import java.util.Map;
+import java.util.concurrent.TimeUnit;
 
 public final class PageCache implements Cache<PageReference, Page> {
 
   private final com.github.benmanes.caffeine.cache.Cache<PageReference, Page> pageCache;
 
   public PageCache(final int maxSize) {
-    RemovalListener<PageReference, Page> removalListener =
-        (PageReference key, Page value, RemovalCause cause) -> key.setPage(null);
+    RemovalListener<PageReference, Page> removalListener = (PageReference key, Page value, RemovalCause cause) -> {
+      key.setPage(null);
+      //      if (value instanceof KeyValueLeafPage keyValueLeafPage) {
+      //        keyValueLeafPage.clearPage();
+      //      }
+    };
 
     pageCache = Caffeine.newBuilder()
                         .maximumSize(maxSize)
+                        .expireAfterAccess(5, TimeUnit.MINUTES)
+                        .scheduler(scheduler)
                         .removalListener(removalListener)
                         .build();
   }
@@ -58,5 +65,6 @@ public void remove(PageReference key) {
   }
 
   @Override
-  public void close() {}
+  public void close() {
+  }
 }
diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/PathSummaryCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/PathSummaryCache.java
@@ -3,6 +3,7 @@
 import com.github.benmanes.caffeine.cache.Caffeine;
 
 import java.util.Map;
+import java.util.concurrent.TimeUnit;
 
 public class PathSummaryCache implements Cache<Integer, PathSummaryData> {
 
@@ -11,6 +12,7 @@ public class PathSummaryCache implements Cache<Integer, PathSummaryData> {
   public PathSummaryCache(final int maxSize) {
     cache = Caffeine.newBuilder()
                     .maximumSize(maxSize)
+                    .expireAfterAccess(5, TimeUnit.MINUTES)
                     .build();
   }
 

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/RecordPageCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/RecordPageCache.java
@@ -15,15 +15,18 @@ public final class RecordPageCache implements Cache<PageReference, Page> {
   private final com.github.benmanes.caffeine.cache.Cache<PageReference, Page> pageCache;
 
   public RecordPageCache(final int maxSize) {
-    final RemovalListener<PageReference, Page> removalListener = (PageReference key, Page value, RemovalCause cause) -> {
-      assert key != null;
-      key.setPage(null);
-    };
+    final RemovalListener<PageReference, Page> removalListener =
+        (PageReference key, Page value, RemovalCause cause) -> {
+          key.setPage(null);
+          //      if (value instanceof KeyValueLeafPage keyValueLeafPage) {
+          //        keyValueLeafPage.clearPage();
+          //      }
+        };
 
     pageCache = Caffeine.newBuilder()
                         .maximumSize(maxSize)
-                        .expireAfterWrite(15, TimeUnit.SECONDS)
-                        .expireAfterAccess(15, TimeUnit.SECONDS)
+                        .expireAfterAccess(5, TimeUnit.MINUTES)
+                        .scheduler(scheduler)
                         .removalListener(removalListener)
                         .build();
   }

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/RedBlackTreeNodeCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/RedBlackTreeNodeCache.java
@@ -28,7 +28,7 @@ public RedBlackTreeNodeCache(final int maxSize) {
           }
         };
 
-    cache = Caffeine.newBuilder().maximumSize(maxSize).removalListener(removalListener).build();
+    cache = Caffeine.newBuilder().maximumSize(maxSize).removalListener(removalListener).scheduler(scheduler).build();
   }
 
   @Override

diff --git a/bundles/sirix-core/src/main/java/org/sirix/cache/RevisionRootPageCache.java b/bundles/sirix-core/src/main/java/org/sirix/cache/RevisionRootPageCache.java
@@ -27,10 +27,11 @@
  */
 package org.sirix.cache;
 
+import com.github.benmanes.caffeine.cache.Caffeine;
+import org.sirix.page.RevisionRootPage;
+
 import java.util.Map;
 import java.util.concurrent.TimeUnit;
-import org.sirix.page.RevisionRootPage;
-import com.github.benmanes.caffeine.cache.Caffeine;
 
 /**
  * @author Johannes Lichtenberger <a href="mailto:[email protected]">mail</a>
@@ -42,8 +43,8 @@ public final class RevisionRootPageCache implements Cache<Integer, RevisionRootP
   public RevisionRootPageCache(final int maxSize) {
     pageCache = Caffeine.newBuilder()
                         .maximumSize(maxSize)
-                        .expireAfterWrite(30, TimeUnit.SECONDS)
-                        .expireAfterAccess(30, TimeUnit.SECONDS)
+                        .expireAfterAccess(5, TimeUnit.MINUTES)
+                        .scheduler(scheduler)
                         .build();
   }
 
@@ -83,5 +84,6 @@ public void remove(Integer key) {
   }
 
   @Override
-  public void close() {}
+  public void close() {
+  }
 }
diff --git a/bundles/sirix-core/src/main/java/org/sirix/page/PageReference.java b/bundles/sirix-core/src/main/java/org/sirix/page/PageReference.java
@@ -41,7 +41,7 @@
 public final class PageReference {
 
   /** In-memory deserialized page instance. */
-  private Page page;
+  private volatile Page page;
 
   /** Key in persistent storage. */
   private long key = Constants.NULL_ID_LONG;

diff --git a/libraries.gradle b/libraries.gradle
@@ -18,7 +18,7 @@ implLibraries = [
         guavaTestlib                : 'com.google.guava:guava-testlib:31.0.1-jre',
         checkerFramework            : 'org.checkerframework:checker:3.21.2',
         brackit                     : 'io.sirix:brackit:0.3-SNAPSHOT',
-        caffeine                    : 'com.github.ben-manes.caffeine:caffeine:2.8.1',
+        caffeine                    : 'com.github.ben-manes.caffeine:caffeine:3.1.6',
         snappyJava                  : 'org.xerial.snappy:snappy-java:1.1.8.4',
         lz4                         : 'org.lz4:lz4-java:1.8.0',
         browniesCollections         : 'org.magicwerk:brownies-collections:0.9.14',
-Original file line number
+Diff line change
@@ Expand Up / @@ -28,7 +28,7 @@ public RedBlackTreeNodeCache(final int maxSize) { @@
               }
             };
-        cache = Caffeine.newBuilder().maximumSize(maxSize).removalListener(removalListener).build();
+        cache = Caffeine.newBuilder().maximumSize(maxSize).removalListener(removalListener).scheduler(scheduler).build();
       }
       @Override
@@ Expand Down @@