Disable gc for LMDB store and use correct uptime of JVM.

Author: kenwenzel

core/sail/lmdb/src/main/java/org/eclipse/rdf4j/sail/lmdb/LmdbSailStore.java

@@ -73,6 +73,7 @@ class LmdbSailStore implements SailStore {
 	private volatile boolean nextTransactionAsync;
 
 	boolean enableMultiThreading = true;
+	boolean enableGc = true;
 
 	private PersistentSetFactory<Long> setFactory;
 	private PersistentSet<Long> unusedIds, nextUnusedIds;
@@ -760,9 +761,11 @@ private long removeStatements(long subj, long pred, long obj, boolean explicit,
 			for (long contextId : contexts) {
 				tripleStore.removeTriplesByContext(subj, pred, obj, contextId, explicit, quad -> {
 					removeCount[0]++;
-					for (long id : quad) {
-						if (id != 0L) {
-							unusedIds.add(id);
+					if (enableGc) {
+						for (long id : quad) {
+							if (id != 0L) {
+								unusedIds.add(id);
+							}
 						}
 					}
 				});

core/sail/lmdb/src/main/java/org/eclipse/rdf4j/sail/lmdb/LmdbStore.java

@@ -258,6 +258,7 @@ protected LmdbSailStore createSailStore(File dataDir) throws IOException, SailEx
 					LmdbStoreConfig overflowConfig = new LmdbStoreConfig();
 					LmdbSailStore store = new LmdbSailStore(dataDir, overflowConfig);
 					store.enableMultiThreading = false;
+					store.enableGc = false;
 					// does not need to isolate transactions and therefore can optimize autogrow and others
 					store.setTransactionIsolation(false);
 					return store;

core/sail/lmdb/src/main/java/org/eclipse/rdf4j/sail/lmdb/MemoryOverflowModel.java

@@ -17,6 +17,7 @@
 import java.io.ObjectOutputStream;
 import java.lang.management.GarbageCollectorMXBean;
 import java.lang.management.ManagementFactory;
+import java.lang.management.RuntimeMXBean;
 import java.nio.file.Files;
 import java.util.Collection;
 import java.util.HashSet;
@@ -88,11 +89,13 @@ abstract class MemoryOverflowModel extends AbstractModel implements AutoCloseabl
 	private static volatile List<GcInfo> gcInfos = new CopyOnWriteArrayList<>();
 	static {
 		List<GarbageCollectorMXBean> gcBeans = ManagementFactory.getGarbageCollectorMXBeans();
+		RuntimeMXBean runtimeMXBean = ManagementFactory.getRuntimeMXBean();
 		for (GarbageCollectorMXBean gcBean : gcBeans) {
 			NotificationEmitter emitter = (NotificationEmitter) gcBean;
 			emitter.addNotificationListener((notification, o) -> {
+				long uptimeInMillis = runtimeMXBean.getUptime();
 				while (! gcInfos.isEmpty()) {
-					if (System.currentTimeMillis() - gcInfos.get(0).getEndTime() > 5000) {
+					if (uptimeInMillis - gcInfos.get(0).getEndTime() > 5000) {
 						gcSum -= gcInfos.remove(0).getDuration();
 					} else {
 						break;
@@ -104,8 +107,8 @@ abstract class MemoryOverflowModel extends AbstractModel implements AutoCloseabl
 				GcInfo gcInfo = gcNotificationInfo.getGcInfo();
 				gcInfos.add(gcInfo);
 				gcSum += gcInfo.getDuration();
-				System.out.println("gcSum: " + gcSum);
 				if (gcSum > 1000 || gcInfos.size() > 4) {
+					System.out.println("high gc load: sum=" + gcSum + " count=" + gcInfos.size());
 					highGcLoad = true;
 					lastGcUpdate = System.currentTimeMillis();
 				} else if (System.currentTimeMillis() - lastGcUpdate > 10000) {