Propagate max_auto_id_timestamp in peer recovery (elastic#33693)

Today we don't store the auto-generated timestamp of append-only
operations in Lucene; and assign -1 to every index operations
constructed from LuceneChangesSnapshot. This looks innocent but it
generates duplicate documents on a replica if a retry append-only
arrives first via peer-recovery; then an original append-only arrives
via replication. Since the retry append-only (delivered via recovery)
does not have timestamp, the replica will happily optimizes the original
request while it should not.

This change transmits the max auto-generated timestamp from the primary
to replicas before translog phase in peer recovery. This timestamp will
prevent replicas from optimizing append-only requests if retry
counterparts have been processed.

Relates elastic#33656
Relates elastic#33222

Author: dnhatn

server/src/main/java/org/elasticsearch/index/engine/Engine.java

@@ -45,6 +45,7 @@
 import org.apache.lucene.util.Accountables;
 import org.apache.lucene.util.SetOnce;
 import org.elasticsearch.ExceptionsHelper;
+import org.elasticsearch.action.index.IndexRequest;
 import org.elasticsearch.common.CheckedRunnable;
 import org.elasticsearch.common.FieldMemoryStats;
 import org.elasticsearch.common.Nullable;
@@ -1767,6 +1768,21 @@ public boolean isRecovering() {
      */
     public abstract void maybePruneDeletes();
 
+    /**
+     * Returns the maximum auto_id_timestamp of all append-only index requests have been processed by this engine
+     * or the auto_id_timestamp received from its primary shard via {@link #updateMaxUnsafeAutoIdTimestamp(long)}.
+     * Notes this method returns the auto_id_timestamp of all append-only requests, not max_unsafe_auto_id_timestamp.
+     */
+    public long getMaxSeenAutoIdTimestamp() {
+        return IndexRequest.UNSET_AUTO_GENERATED_TIMESTAMP;
+    }
+
+    /**
+     * Forces this engine to advance its max_unsafe_auto_id_timestamp marker to at least the given timestamp.
+     * The engine will disable optimization for all append-only whose timestamp at most {@code newTimestamp}.
+     */
+    public abstract void updateMaxUnsafeAutoIdTimestamp(long newTimestamp);
+
     @FunctionalInterface
     public interface TranslogRecoveryRunner {
         int run(Engine engine, Translog.Snapshot snapshot) throws IOException;

server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java

@@ -144,6 +144,7 @@ public class InternalEngine extends Engine {
     private final AtomicBoolean pendingTranslogRecovery = new AtomicBoolean(false);
     public static final String MAX_UNSAFE_AUTO_ID_TIMESTAMP_COMMIT_ID = "max_unsafe_auto_id_timestamp";
     private final AtomicLong maxUnsafeAutoIdTimestamp = new AtomicLong(-1);
+    private final AtomicLong maxSeenAutoIdTimestamp = new AtomicLong(-1);
     private final AtomicLong maxSeqNoOfNonAppendOnlyOperations = new AtomicLong(SequenceNumbers.NO_OPS_PERFORMED);
     private final CounterMetric numVersionLookups = new CounterMetric();
     private final CounterMetric numIndexVersionsLookups = new CounterMetric();
@@ -170,7 +171,7 @@ public InternalEngine(EngineConfig engineConfig) {
             final BiFunction<Long, Long, LocalCheckpointTracker> localCheckpointTrackerSupplier) {
         super(engineConfig);
         if (engineConfig.isAutoGeneratedIDsOptimizationEnabled() == false) {
-            maxUnsafeAutoIdTimestamp.set(Long.MAX_VALUE);
+            updateAutoIdTimestamp(Long.MAX_VALUE, true);
         }
         this.uidField = engineConfig.getIndexSettings().isSingleType() ? IdFieldMapper.NAME : UidFieldMapper.NAME;
         final TranslogDeletionPolicy translogDeletionPolicy = new TranslogDeletionPolicy(
@@ -374,7 +375,7 @@ private void bootstrapAppendOnlyInfoFromWriter(IndexWriter writer) {
             if (key.equals(MAX_UNSAFE_AUTO_ID_TIMESTAMP_COMMIT_ID)) {
                 assert maxUnsafeAutoIdTimestamp.get() == -1 :
                     "max unsafe timestamp was assigned already [" + maxUnsafeAutoIdTimestamp.get() + "]";
-                maxUnsafeAutoIdTimestamp.set(Long.parseLong(entry.getValue()));
+                updateAutoIdTimestamp(Long.parseLong(entry.getValue()), true);
             }
             if (key.equals(SequenceNumbers.MAX_SEQ_NO)) {
                 assert maxSeqNoOfNonAppendOnlyOperations.get() == -1 :
@@ -1075,11 +1076,12 @@ private boolean mayHaveBeenIndexedBefore(Index index) {
         final boolean mayHaveBeenIndexBefore;
         if (index.isRetry()) {
             mayHaveBeenIndexBefore = true;
-            maxUnsafeAutoIdTimestamp.updateAndGet(curr -> Math.max(index.getAutoGeneratedIdTimestamp(), curr));
+            updateAutoIdTimestamp(index.getAutoGeneratedIdTimestamp(), true);
             assert maxUnsafeAutoIdTimestamp.get() >= index.getAutoGeneratedIdTimestamp();
         } else {
             // in this case we force
             mayHaveBeenIndexBefore = maxUnsafeAutoIdTimestamp.get() >= index.getAutoGeneratedIdTimestamp();
+            updateAutoIdTimestamp(index.getAutoGeneratedIdTimestamp(), false);
         }
         return mayHaveBeenIndexBefore;
     }
@@ -2367,7 +2369,7 @@ public void onSettingsChanged() {
             // this is an anti-viral settings you can only opt out for the entire index
             // only if a shard starts up again due to relocation or if the index is closed
             // the setting will be re-interpreted if it's set to true
-            this.maxUnsafeAutoIdTimestamp.set(Long.MAX_VALUE);
+            updateAutoIdTimestamp(Long.MAX_VALUE, true);
         }
         final TranslogDeletionPolicy translogDeletionPolicy = translog.getDeletionPolicy();
         final IndexSettings indexSettings = engineConfig.getIndexSettings();
@@ -2606,4 +2608,24 @@ void updateRefreshedCheckpoint(long checkpoint) {
             assert refreshedCheckpoint.get() >= checkpoint : refreshedCheckpoint.get() + " < " + checkpoint;
         }
     }
+
+    @Override
+    public final long getMaxSeenAutoIdTimestamp() {
+        return maxSeenAutoIdTimestamp.get();
+    }
+
+    @Override
+    public final void updateMaxUnsafeAutoIdTimestamp(long newTimestamp) {
+        updateAutoIdTimestamp(newTimestamp, true);
+    }
+
+    private void updateAutoIdTimestamp(long newTimestamp, boolean unsafe) {
+        assert newTimestamp >= -1 : "invalid timestamp [" + newTimestamp + "]";
+        maxSeenAutoIdTimestamp.updateAndGet(curr -> Math.max(curr, newTimestamp));
+        if (unsafe) {
+            maxUnsafeAutoIdTimestamp.updateAndGet(curr -> Math.max(curr, newTimestamp));
+        }
+        assert maxUnsafeAutoIdTimestamp.get() <= maxSeenAutoIdTimestamp.get();
+    }
+
 }

server/src/main/java/org/elasticsearch/index/engine/ReadOnlyEngine.java

@@ -374,4 +374,9 @@ public void maybePruneDeletes() {
     public DocsStats docStats() {
         return docsStats;
     }
+
+    @Override
+    public void updateMaxUnsafeAutoIdTimestamp(long newTimestamp) {
+
+    }
 }

server/src/main/java/org/elasticsearch/index/shard/IndexShard.java

@@ -1257,6 +1257,29 @@ public void trimOperationOfPreviousPrimaryTerms(long aboveSeqNo) {
         getEngine().trimOperationsFromTranslog(operationPrimaryTerm, aboveSeqNo);
     }
 
+    /**
+     * Returns the maximum auto_id_timestamp of all append-only requests have been processed by this shard or the auto_id_timestamp received
+     * from the primary via {@link #updateMaxUnsafeAutoIdTimestamp(long)} at the beginning of a peer-recovery or a primary-replica resync.
+     *
+     * @see #updateMaxUnsafeAutoIdTimestamp(long)
+     */
+    public long getMaxSeenAutoIdTimestamp() {
+        return getEngine().getMaxSeenAutoIdTimestamp();
+    }
+
+    /**
+     * Since operations stored in soft-deletes do not have max_auto_id_timestamp, the primary has to propagate its max_auto_id_timestamp
+     * (via {@link #getMaxSeenAutoIdTimestamp()} of all processed append-only requests to replicas at the beginning of a peer-recovery
+     * or a primary-replica resync to force a replica to disable optimization for all append-only requests which are replicated via
+     * replication while its retry variants are replicated via recovery without auto_id_timestamp.
+     * <p>
+     * Without this force-update, a replica can generate duplicate documents (for the same id) if it first receives
+     * a retry append-only (without timestamp) via recovery, then an original append-only (with timestamp) via replication.
+     */
+    public void updateMaxUnsafeAutoIdTimestamp(long maxSeenAutoIdTimestampFromPrimary) {
+        getEngine().updateMaxUnsafeAutoIdTimestamp(maxSeenAutoIdTimestampFromPrimary);
+    }
+
     public Engine.Result applyTranslogOperation(Translog.Operation operation, Engine.Operation.Origin origin) throws IOException {
         final Engine.Result result;
         switch (operation.opType()) {

server/src/main/java/org/elasticsearch/indices/recovery/PeerRecoveryTargetService.java

@@ -451,7 +451,8 @@ public void messageReceived(final RecoveryTranslogOperationsRequest request, fin
                 final ClusterStateObserver observer = new ClusterStateObserver(clusterService, null, logger, threadPool.getThreadContext());
                 final RecoveryTarget recoveryTarget = recoveryRef.target();
                 try {
-                    recoveryTarget.indexTranslogOperations(request.operations(), request.totalTranslogOps());
+                    recoveryTarget.indexTranslogOperations(request.operations(), request.totalTranslogOps(),
+                        request.maxSeenAutoIdTimestampOnPrimary());
                     channel.sendResponse(new RecoveryTranslogOperationsResponse(recoveryTarget.indexShard().getLocalCheckpoint()));
                 } catch (MapperException exception) {
                     // in very rare cases a translog replay from primary is processed before a mapping update on this node

server/src/main/java/org/elasticsearch/indices/recovery/RecoverySourceHandler.java

@@ -215,7 +215,10 @@ public RecoveryResponse recoverToTarget() throws IOException {
             }
             final long targetLocalCheckpoint;
             try (Translog.Snapshot snapshot = shard.getHistoryOperations("peer-recovery", startingSeqNo)) {
-                targetLocalCheckpoint = phase2(startingSeqNo, requiredSeqNoRangeStart, endingSeqNo, snapshot);
+                // We have to capture the max auto_id_timestamp after taking a snapshot of operations to guarantee
+                // that the auto_id_timestamp of every operation in the snapshot is at most this timestamp value.
+                final long maxSeenAutoIdTimestamp = shard.getMaxSeenAutoIdTimestamp();
+                targetLocalCheckpoint = phase2(startingSeqNo, requiredSeqNoRangeStart, endingSeqNo, snapshot, maxSeenAutoIdTimestamp);
             } catch (Exception e) {
                 throw new RecoveryEngineException(shard.shardId(), 2, "phase2 failed", e);
             }
@@ -447,9 +450,11 @@ void prepareTargetForTranslog(final boolean fileBasedRecovery, final int totalTr
      * @param requiredSeqNoRangeStart the lower sequence number of the required range (ending with endingSeqNo)
      * @param endingSeqNo             the highest sequence number that should be sent
      * @param snapshot                a snapshot of the translog
+     * @param maxSeenAutoIdTimestamp  the max auto_id_timestamp of append-only requests on the primary
      * @return the local checkpoint on the target
      */
-    long phase2(final long startingSeqNo, long requiredSeqNoRangeStart, long endingSeqNo, final Translog.Snapshot snapshot)
+    long phase2(final long startingSeqNo, long requiredSeqNoRangeStart, long endingSeqNo, final Translog.Snapshot snapshot,
+                final long maxSeenAutoIdTimestamp)
         throws IOException {
         if (shard.state() == IndexShardState.CLOSED) {
             throw new IndexShardClosedException(request.shardId());
@@ -462,7 +467,8 @@ long phase2(final long startingSeqNo, long requiredSeqNoRangeStart, long endingS
             "required [" + requiredSeqNoRangeStart + ":" + endingSeqNo + "]");
 
         // send all the snapshot's translog operations to the target
-        final SendSnapshotResult result = sendSnapshot(startingSeqNo, requiredSeqNoRangeStart, endingSeqNo, snapshot);
+        final SendSnapshotResult result = sendSnapshot(
+            startingSeqNo, requiredSeqNoRangeStart, endingSeqNo, snapshot, maxSeenAutoIdTimestamp);
 
         stopWatch.stop();
         logger.trace("recovery [phase2]: took [{}]", stopWatch.totalTime());
@@ -530,10 +536,11 @@ static class SendSnapshotResult {
      * @param endingSeqNo             the upper bound of the sequence number range to be sent (inclusive)
      * @param snapshot                the translog snapshot to replay operations from  @return the local checkpoint on the target and the
      *                                total number of operations sent
+     * @param maxSeenAutoIdTimestamp  the max auto_id_timestamp of append-only requests on the primary
      * @throws IOException if an I/O exception occurred reading the translog snapshot
      */
     protected SendSnapshotResult sendSnapshot(final long startingSeqNo, long requiredSeqNoRangeStart, long endingSeqNo,
-                                              final Translog.Snapshot snapshot) throws IOException {
+                                              final Translog.Snapshot snapshot, final long maxSeenAutoIdTimestamp) throws IOException {
         assert requiredSeqNoRangeStart <= endingSeqNo + 1:
             "requiredSeqNoRangeStart " + requiredSeqNoRangeStart + " is larger than endingSeqNo " + endingSeqNo;
         assert startingSeqNo <= requiredSeqNoRangeStart :
@@ -551,8 +558,8 @@ protected SendSnapshotResult sendSnapshot(final long startingSeqNo, long require
             logger.trace("no translog operations to send");
         }
 
-        final CancellableThreads.IOInterruptable sendBatch =
-                () -> targetLocalCheckpoint.set(recoveryTarget.indexTranslogOperations(operations, expectedTotalOps));
+        final CancellableThreads.IOInterruptable sendBatch = () ->
+            targetLocalCheckpoint.set(recoveryTarget.indexTranslogOperations(operations, expectedTotalOps, maxSeenAutoIdTimestamp));
 
         // send operations in batches
         Translog.Operation operation;

server/src/main/java/org/elasticsearch/indices/recovery/RecoveryTarget.java

@@ -389,13 +389,21 @@ public void handoffPrimaryContext(final ReplicationTracker.PrimaryContext primar
     }
 
     @Override
-    public long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps) throws IOException {
+    public long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps,
+                                        long maxSeenAutoIdTimestampOnPrimary) throws IOException {
         final RecoveryState.Translog translog = state().getTranslog();
         translog.totalOperations(totalTranslogOps);
         assert indexShard().recoveryState() == state();
         if (indexShard().state() != IndexShardState.RECOVERING) {
             throw new IndexShardNotRecoveringException(shardId, indexShard().state());
         }
+        /*
+         * The maxSeenAutoIdTimestampOnPrimary received from the primary is at least the highest auto_id_timestamp from any operation
+         * will be replayed. Bootstrapping this timestamp here will disable the optimization for original append-only requests
+         * (source of these operations) replicated via replication. Without this step, we may have duplicate documents if we
+         * replay these operations first (without timestamp), then optimize append-only requests (with timestamp).
+         */
+        indexShard().updateMaxUnsafeAutoIdTimestamp(maxSeenAutoIdTimestampOnPrimary);
         for (Translog.Operation operation : operations) {
             Engine.Result result = indexShard().applyTranslogOperation(operation, Engine.Operation.Origin.PEER_RECOVERY);
             if (result.getResultType() == Engine.Result.Type.MAPPING_UPDATE_REQUIRED) {

server/src/main/java/org/elasticsearch/indices/recovery/RecoveryTargetHandler.java

@@ -60,12 +60,13 @@ public interface RecoveryTargetHandler {
 
     /**
      * Index a set of translog operations on the target
-     * @param operations operations to index
-     * @param totalTranslogOps current number of total operations expected to be indexed
-     *
+     * @param operations                      operations to index
+     * @param totalTranslogOps                current number of total operations expected to be indexed
+     * @param maxSeenAutoIdTimestampOnPrimary the maximum auto_id_timestamp of all append-only requests processed by the primary shard
      * @return the local checkpoint on the target shard
      */
-    long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps) throws IOException;
+    long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps,
+                                 long maxSeenAutoIdTimestampOnPrimary) throws IOException;
 
     /**
      * Notifies the target of the files it is going to receive

server/src/main/java/org/elasticsearch/indices/recovery/RecoveryTranslogOperationsRequest.java

@@ -19,6 +19,8 @@
 
 package org.elasticsearch.indices.recovery;
 
+import org.elasticsearch.Version;
+import org.elasticsearch.action.index.IndexRequest;
 import org.elasticsearch.common.io.stream.StreamInput;
 import org.elasticsearch.common.io.stream.StreamOutput;
 import org.elasticsearch.index.shard.ShardId;
@@ -34,15 +36,18 @@ public class RecoveryTranslogOperationsRequest extends TransportRequest {
     private ShardId shardId;
     private List<Translog.Operation> operations;
     private int totalTranslogOps = RecoveryState.Translog.UNKNOWN;
+    private long maxSeenAutoIdTimestampOnPrimary;
 
     public RecoveryTranslogOperationsRequest() {
     }
 
-    RecoveryTranslogOperationsRequest(long recoveryId, ShardId shardId, List<Translog.Operation> operations, int totalTranslogOps) {
+    RecoveryTranslogOperationsRequest(long recoveryId, ShardId shardId, List<Translog.Operation> operations,
+                                      int totalTranslogOps, long maxSeenAutoIdTimestampOnPrimary) {
         this.recoveryId = recoveryId;
         this.shardId = shardId;
         this.operations = operations;
         this.totalTranslogOps = totalTranslogOps;
+        this.maxSeenAutoIdTimestampOnPrimary = maxSeenAutoIdTimestampOnPrimary;
     }
 
     public long recoveryId() {
@@ -61,13 +66,22 @@ public int totalTranslogOps() {
         return totalTranslogOps;
     }
 
+    public long maxSeenAutoIdTimestampOnPrimary() {
+        return maxSeenAutoIdTimestampOnPrimary;
+    }
+
     @Override
     public void readFrom(StreamInput in) throws IOException {
         super.readFrom(in);
         recoveryId = in.readLong();
         shardId = ShardId.readShardId(in);
         operations = Translog.readOperations(in, "recovery");
         totalTranslogOps = in.readVInt();
+        if (in.getVersion().onOrAfter(Version.V_6_5_0)) {
+            maxSeenAutoIdTimestampOnPrimary = in.readZLong();
+        } else {
+            maxSeenAutoIdTimestampOnPrimary = IndexRequest.UNSET_AUTO_GENERATED_TIMESTAMP;
+        }
     }
 
     @Override
@@ -77,5 +91,8 @@ public void writeTo(StreamOutput out) throws IOException {
         shardId.writeTo(out);
         Translog.writeOperations(out, operations);
         out.writeVInt(totalTranslogOps);
+        if (out.getVersion().onOrAfter(Version.V_6_5_0)) {
+            out.writeZLong(maxSeenAutoIdTimestampOnPrimary);
+        }
     }
 }

server/src/main/java/org/elasticsearch/indices/recovery/RemoteRecoveryTargetHandler.java

@@ -110,9 +110,9 @@ public void handoffPrimaryContext(final ReplicationTracker.PrimaryContext primar
     }
 
     @Override
-    public long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps) {
+    public long indexTranslogOperations(List<Translog.Operation> operations, int totalTranslogOps, long maxSeenAutoIdTimestampOnPrimary) {
         final RecoveryTranslogOperationsRequest translogOperationsRequest =
-                new RecoveryTranslogOperationsRequest(recoveryId, shardId, operations, totalTranslogOps);
+                new RecoveryTranslogOperationsRequest(recoveryId, shardId, operations, totalTranslogOps, maxSeenAutoIdTimestampOnPrimary);
         final TransportFuture<RecoveryTranslogOperationsResponse> future = transportService.submitRequest(
                 targetNode,
                 PeerRecoveryTargetService.Actions.TRANSLOG_OPS,