Segment Replication - Fix NoSuchFileException errors caused when comp…

…uting metadata snapshot on primary shards. (opensearch-project#4366) * Segment Replication - Fix NoSuchFileException errors caused when computing metadata snapshot on primary shards. This change fixes the errors that occur when computing metadata snapshots on primary shards from the latest in-memory SegmentInfos. The error occurs when a segments_N file that is referenced by the in-memory infos is deleted as part of a concurrent commit. The segments themselves are incref'd by IndexWriter.incRefDeleter but the commit file (Segments_N) is not. This change resolves this by ignoring the segments_N file when computing metadata for CopyState and only sending incref'd segment files to replicas. Signed-off-by: Marc Handalian <handalm@amazon.com> * Fix spotless. Signed-off-by: Marc Handalian <handalm@amazon.com> * Update StoreTests.testCleanupAndPreserveLatestCommitPoint to assert additional segments are deleted. Signed-off-by: Marc Handalian <handalm@amazon.com> * Rename snapshot to metadataMap in CheckpointInfoResponse. Signed-off-by: Marc Handalian <handalm@amazon.com> * Refactor segmentReplicationDiff method to compute off two maps instead of MetadataSnapshots. Signed-off-by: Marc Handalian <handalm@amazon.com> * Fix spotless. Signed-off-by: Marc Handalian <handalm@amazon.com> * Revert catchall in SegmentReplicationSourceService. Signed-off-by: Marc Handalian <handalm@amazon.com> * Revert log lvl change. Signed-off-by: Marc Handalian <handalm@amazon.com> * Fix SegmentReplicationTargetTests Signed-off-by: Marc Handalian <handalm@amazon.com> * Cleanup unused logger. Signed-off-by: Marc Handalian <handalm@amazon.com> Signed-off-by: Marc Handalian <handalm@amazon.com> Co-authored-by: Suraj Singh <surajrider@gmail.com>
pranikum · Sep 25, 2022 · 2bf2590 · 2bf2590
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -42,6 +42,7 @@ Inspired from [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 - Fix flaky random test `NRTReplicationEngineTests.testUpdateSegments` ([#4352](https://github.com/opensearch-project/OpenSearch/pull/4352))
 - [Segment Replication] Extend FileChunkWriter to allow cancel on transport client ([#4386](https://github.com/opensearch-project/OpenSearch/pull/4386))
 - [Segment Replication] Add check to cancel ongoing replication with old primary on onNewCheckpoint on replica ([#4363](https://github.com/opensearch-project/OpenSearch/pull/4363))
+- Fix NoSuchFileExceptions with segment replication when computing primary metadata snapshots ([#4366](https://github.com/opensearch-project/OpenSearch/pull/4366))
 - [Segment Replication] Update flaky testOnNewCheckpointFromNewPrimaryCancelOngoingReplication unit test ([#4414](https://github.com/opensearch-project/OpenSearch/pull/4414))
 - Fixed the `_cat/shards/10_basic.yml` test cases fix.
 

diff --git a/...src/internalClusterTest/java/org/opensearch/indices/replication/SegmentReplicationIT.java b/...src/internalClusterTest/java/org/opensearch/indices/replication/SegmentReplicationIT.java
@@ -9,7 +9,6 @@
 package org.opensearch.indices.replication;
 
 import com.carrotsearch.randomizedtesting.RandomizedTest;
-import org.apache.lucene.index.SegmentInfos;
 import org.junit.BeforeClass;
 import org.opensearch.action.admin.indices.segments.IndexShardSegments;
 import org.opensearch.action.admin.indices.segments.IndicesSegmentResponse;
@@ -586,13 +585,56 @@ private void assertSegmentStats(int numberOfReplicas) throws IOException {
                 ClusterState state = client(internalCluster().getMasterName()).admin().cluster().prepareState().get().getState();
                 final DiscoveryNode replicaNode = state.nodes().resolveNode(replicaShardRouting.currentNodeId());
                 IndexShard indexShard = getIndexShard(replicaNode.getName());
-                final String lastCommitSegmentsFileName = SegmentInfos.getLastCommitSegmentsFileName(indexShard.store().directory());
                 // calls to readCommit will fail if a valid commit point and all its segments are not in the store.
-                SegmentInfos.readCommit(indexShard.store().directory(), lastCommitSegmentsFileName);
+                indexShard.store().readLastCommittedSegmentsInfo();
             }
         }
     }
 
+    public void testDropPrimaryDuringReplication() throws Exception {
+        final Settings settings = Settings.builder()
+            .put(indexSettings())
+            .put(IndexMetadata.SETTING_NUMBER_OF_REPLICAS, 6)
+            .put(IndexMetadata.SETTING_REPLICATION_TYPE, ReplicationType.SEGMENT)
+            .build();
+        final String clusterManagerNode = internalCluster().startClusterManagerOnlyNode();
+        final String primaryNode = internalCluster().startDataOnlyNode(Settings.EMPTY);
+        createIndex(INDEX_NAME, settings);
+        internalCluster().startDataOnlyNodes(6);
+        ensureGreen(INDEX_NAME);
+
+        int initialDocCount = scaledRandomIntBetween(100, 200);
+        try (
+            BackgroundIndexer indexer = new BackgroundIndexer(
+                INDEX_NAME,
+                "_doc",
+                client(),
+                -1,
+                RandomizedTest.scaledRandomIntBetween(2, 5),
+                false,
+                random()
+            )
+        ) {
+            indexer.start(initialDocCount);
+            waitForDocs(initialDocCount, indexer);
+            refresh(INDEX_NAME);
+            // don't wait for replication to complete, stop the primary immediately.
+            internalCluster().stopRandomNode(InternalTestCluster.nameFilter(primaryNode));
+            ensureYellow(INDEX_NAME);
+
+            // start another replica.
+            internalCluster().startDataOnlyNode();
+            ensureGreen(INDEX_NAME);
+
+            // index another doc and refresh - without this the new replica won't catch up.
+            client().prepareIndex(INDEX_NAME).setId("1").setSource("foo", "bar").get();
+
+            flushAndRefresh(INDEX_NAME);
+            waitForReplicaUpdate();
+            assertSegmentStats(6);
+        }
+    }
+
     /**
      * Waits until the replica is caught up to the latest primary segments gen.
      * @throws Exception if assertion fails
@@ -611,10 +653,12 @@ private void waitForReplicaUpdate() throws Exception {
                 final List<ShardSegments> replicaShardSegments = segmentListMap.get(false);
                 // if we don't have any segments yet, proceed.
                 final ShardSegments primaryShardSegments = primaryShardSegmentsList.stream().findFirst().get();
+                logger.debug("Primary Segments: {}", primaryShardSegments.getSegments());
                 if (primaryShardSegments.getSegments().isEmpty() == false) {
                     final Map<String, Segment> latestPrimarySegments = getLatestSegments(primaryShardSegments);
                     final Long latestPrimaryGen = latestPrimarySegments.values().stream().findFirst().map(Segment::getGeneration).get();
                     for (ShardSegments shardSegments : replicaShardSegments) {
+                        logger.debug("Replica {} Segments: {}", shardSegments.getShardRouting(), shardSegments.getSegments());
                         final boolean isReplicaCaughtUpToPrimary = shardSegments.getSegments()
                             .stream()
                             .anyMatch(segment -> segment.getGeneration() == latestPrimaryGen);

diff --git a/server/src/main/java/org/opensearch/index/store/Store.java b/server/src/main/java/org/opensearch/index/store/Store.java
@@ -105,6 +105,7 @@
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -122,6 +123,7 @@
 import static java.util.Collections.emptyMap;
 import static java.util.Collections.unmodifiableMap;
 import static org.opensearch.index.seqno.SequenceNumbers.LOCAL_CHECKPOINT_KEY;
+import static org.opensearch.index.store.Store.MetadataSnapshot.loadMetadata;
 
 /**
  * A Store provides plain access to files written by an opensearch index shard. Each shard
@@ -334,6 +336,51 @@ public MetadataSnapshot getMetadata(SegmentInfos segmentInfos) throws IOExceptio
         return new MetadataSnapshot(segmentInfos, directory, logger);
     }
 
+    /**
+     * Segment Replication method - Fetch a map of StoreFileMetadata for segments, ignoring Segment_N files.
+     * @param segmentInfos {@link SegmentInfos} from which to compute metadata.
+     * @return {@link Map} map file name to {@link StoreFileMetadata}.
+     */
+    public Map<String, StoreFileMetadata> getSegmentMetadataMap(SegmentInfos segmentInfos) throws IOException {
+        assert indexSettings.isSegRepEnabled();
+        return loadMetadata(segmentInfos, directory, logger, true).fileMetadata;
+    }
+
+    /**
+     * Segment Replication method
+     * Returns a diff between the Maps of StoreFileMetadata that can be used for getting list of files to copy over to a replica for segment replication. The returned diff will hold a list of files that are:
+     * <ul>
+     * <li>identical: they exist in both maps and they can be considered the same ie. they don't need to be recovered</li>
+     * <li>different: they exist in both maps but their they are not identical</li>
+     * <li>missing: files that exist in the source but not in the target</li>
+     * </ul>
+     */
+    public static RecoveryDiff segmentReplicationDiff(Map<String, StoreFileMetadata> source, Map<String, StoreFileMetadata> target) {
+        final List<StoreFileMetadata> identical = new ArrayList<>();
+        final List<StoreFileMetadata> different = new ArrayList<>();
+        final List<StoreFileMetadata> missing = new ArrayList<>();
+        for (StoreFileMetadata value : source.values()) {
+            if (value.name().startsWith(IndexFileNames.SEGMENTS)) {
+                continue;
+            }
+            if (target.containsKey(value.name()) == false) {
+                missing.add(value);
+            } else {
+                final StoreFileMetadata fileMetadata = target.get(value.name());
+                if (fileMetadata.isSame(value)) {
+                    identical.add(value);
+                } else {
+                    different.add(value);
+                }
+            }
+        }
+        return new RecoveryDiff(
+            Collections.unmodifiableList(identical),
+            Collections.unmodifiableList(different),
+            Collections.unmodifiableList(missing)
+        );
+    }
+
     /**
      * Renames all the given files from the key of the map to the
      * value of the map. All successfully renamed files are removed from the map in-place.
@@ -709,31 +756,34 @@ public void cleanupAndVerify(String reason, MetadataSnapshot sourceMetadata) thr
     }
 
     /**
-     * This method deletes every file in this store that is not contained in either the remote or local metadata snapshots.
+     * Segment Replication method -
+     * This method deletes every file in this store that is not referenced by the passed in SegmentInfos or
+     * part of the latest on-disk commit point.
      * This method is used for segment replication when the in memory SegmentInfos can be ahead of the on disk segment file.
      * In this case files from both snapshots must be preserved. Verification has been done that all files are present on disk.
      * @param reason         the reason for this cleanup operation logged for each deleted file
-     * @param localSnapshot  The local snapshot from in memory SegmentInfos.
+     * @param infos          {@link SegmentInfos} Files from this infos will be preserved on disk if present.
      * @throws IllegalStateException if the latest snapshot in this store differs from the given one after the cleanup.
      */
-    public void cleanupAndPreserveLatestCommitPoint(String reason, MetadataSnapshot localSnapshot) throws IOException {
+    public void cleanupAndPreserveLatestCommitPoint(String reason, SegmentInfos infos) throws IOException {
+        assert indexSettings.isSegRepEnabled();
         // fetch a snapshot from the latest on disk Segments_N file. This can be behind
         // the passed in local in memory snapshot, so we want to ensure files it references are not removed.
         metadataLock.writeLock().lock();
         try (Lock writeLock = directory.obtainLock(IndexWriter.WRITE_LOCK_NAME)) {
-            cleanupFiles(reason, localSnapshot, getMetadata(readLastCommittedSegmentsInfo()));
+            cleanupFiles(reason, getMetadata(readLastCommittedSegmentsInfo()), infos.files(true));
         } finally {
             metadataLock.writeLock().unlock();
         }
     }
 
-    private void cleanupFiles(String reason, MetadataSnapshot localSnapshot, @Nullable MetadataSnapshot additionalSnapshot)
+    private void cleanupFiles(String reason, MetadataSnapshot localSnapshot, @Nullable Collection<String> additionalFiles)
         throws IOException {
         assert metadataLock.isWriteLockedByCurrentThread();
         for (String existingFile : directory.listAll()) {
             if (Store.isAutogenerated(existingFile)
                 || localSnapshot.contains(existingFile)
-                || (additionalSnapshot != null && additionalSnapshot.contains(existingFile))) {
+                || (additionalFiles != null && additionalFiles.contains(existingFile))) {
                 // don't delete snapshot file, or the checksums file (note, this is extra protection since the Store won't delete
                 // checksum)
                 continue;
@@ -825,17 +875,9 @@ public void commitSegmentInfos(SegmentInfos latestSegmentInfos, long maxSeqNo, l
             userData.put(SequenceNumbers.MAX_SEQ_NO, Long.toString(maxSeqNo));
             latestSegmentInfos.setUserData(userData, true);
             latestSegmentInfos.commit(directory());
-
-            // similar to TrimUnsafeCommits, create a commit with an appending IW, this will delete old commits and ensure all files
-            // associated with the SegmentInfos.commit are fsynced.
-            final List<IndexCommit> existingCommits = DirectoryReader.listCommits(directory);
-            assert existingCommits.isEmpty() == false : "Expected at least one commit but none found";
-            final IndexCommit lastIndexCommit = existingCommits.get(existingCommits.size() - 1);
-            assert latestSegmentInfos.getSegmentsFileName().equals(lastIndexCommit.getSegmentsFileName());
-            try (IndexWriter writer = newAppendingIndexWriter(directory, lastIndexCommit)) {
-                writer.setLiveCommitData(lastIndexCommit.getUserData().entrySet());
-                writer.commit();
-            }
+            directory.sync(latestSegmentInfos.files(true));
+            directory.syncMetaData();
+            cleanupAndPreserveLatestCommitPoint("After commit", latestSegmentInfos);
         } finally {
             metadataLock.writeLock().unlock();
         }
@@ -1033,6 +1075,11 @@ static LoadedMetadata loadMetadata(IndexCommit commit, Directory directory, Logg
         }
 
         static LoadedMetadata loadMetadata(SegmentInfos segmentInfos, Directory directory, Logger logger) throws IOException {
+            return loadMetadata(segmentInfos, directory, logger, false);
+        }
+
+        static LoadedMetadata loadMetadata(SegmentInfos segmentInfos, Directory directory, Logger logger, boolean ignoreSegmentsFile)
+            throws IOException {
             long numDocs = Lucene.getNumDocs(segmentInfos);
             Map<String, String> commitUserDataBuilder = new HashMap<>();
             commitUserDataBuilder.putAll(segmentInfos.getUserData());
@@ -1067,8 +1114,10 @@ static LoadedMetadata loadMetadata(SegmentInfos segmentInfos, Directory director
             if (maxVersion == null) {
                 maxVersion = org.opensearch.Version.CURRENT.minimumIndexCompatibilityVersion().luceneVersion;
             }
-            final String segmentsFile = segmentInfos.getSegmentsFileName();
-            checksumFromLuceneFile(directory, segmentsFile, builder, logger, maxVersion, true);
+            if (ignoreSegmentsFile == false) {
+                final String segmentsFile = segmentInfos.getSegmentsFileName();
+                checksumFromLuceneFile(directory, segmentsFile, builder, logger, maxVersion, true);
+            }
             return new LoadedMetadata(unmodifiableMap(builder), unmodifiableMap(commitUserDataBuilder), numDocs);
         }
 
@@ -1148,7 +1197,6 @@ public Map<String, StoreFileMetadata> asMap() {
          * Helper method used to group store files according to segment and commit.
          *
          * @see MetadataSnapshot#recoveryDiff(MetadataSnapshot)
-         * @see MetadataSnapshot#segmentReplicationDiff(MetadataSnapshot)
          */
         private Iterable<List<StoreFileMetadata>> getGroupedFilesIterable() {
             final Map<String, List<StoreFileMetadata>> perSegment = new HashMap<>();
@@ -1241,51 +1289,6 @@ public RecoveryDiff recoveryDiff(MetadataSnapshot recoveryTargetSnapshot) {
             return recoveryDiff;
         }
 
-        /**
-         * Segment Replication method
-         * Returns a diff between the two snapshots that can be used for getting list of files to copy over to a replica for segment replication. The given snapshot is treated as the
-         * target and this snapshot as the source. The returned diff will hold a list of files that are:
-         * <ul>
-         * <li>identical: they exist in both snapshots and they can be considered the same ie. they don't need to be recovered</li>
-         * <li>different: they exist in both snapshots but their they are not identical</li>
-         * <li>missing: files that exist in the source but not in the target</li>
-         * </ul>
-         */
-        public RecoveryDiff segmentReplicationDiff(MetadataSnapshot recoveryTargetSnapshot) {
-            final List<StoreFileMetadata> identical = new ArrayList<>();
-            final List<StoreFileMetadata> different = new ArrayList<>();
-            final List<StoreFileMetadata> missing = new ArrayList<>();
-            final ArrayList<StoreFileMetadata> identicalFiles = new ArrayList<>();
-            for (List<StoreFileMetadata> segmentFiles : getGroupedFilesIterable()) {
-                identicalFiles.clear();
-                boolean consistent = true;
-                for (StoreFileMetadata meta : segmentFiles) {
-                    StoreFileMetadata storeFileMetadata = recoveryTargetSnapshot.get(meta.name());
-                    if (storeFileMetadata == null) {
-                        // Do not consider missing files as inconsistent in SegRep as replicas may lag while primary updates
-                        // documents and generate new files specific to a segment
-                        missing.add(meta);
-                    } else if (storeFileMetadata.isSame(meta) == false) {
-                        consistent = false;
-                        different.add(meta);
-                    } else {
-                        identicalFiles.add(meta);
-                    }
-                }
-                if (consistent) {
-                    identical.addAll(identicalFiles);
-                } else {
-                    different.addAll(identicalFiles);
-                }
-            }
-            RecoveryDiff recoveryDiff = new RecoveryDiff(
-                Collections.unmodifiableList(identical),
-                Collections.unmodifiableList(different),
-                Collections.unmodifiableList(missing)
-            );
-            return recoveryDiff;
-        }
-
         /**
          * Returns the number of files in this snapshot
          */

diff --git a/server/src/main/java/org/opensearch/indices/replication/CheckpointInfoResponse.java b/server/src/main/java/org/opensearch/indices/replication/CheckpointInfoResponse.java
@@ -10,13 +10,12 @@
 
 import org.opensearch.common.io.stream.StreamInput;
 import org.opensearch.common.io.stream.StreamOutput;
-import org.opensearch.index.store.Store;
 import org.opensearch.index.store.StoreFileMetadata;
 import org.opensearch.indices.replication.checkpoint.ReplicationCheckpoint;
 import org.opensearch.transport.TransportResponse;
 
 import java.io.IOException;
-import java.util.Set;
+import java.util.Map;
 
 /**
  * Response returned from a {@link SegmentReplicationSource} that includes the file metadata, and SegmentInfos
@@ -28,52 +27,41 @@
 public class CheckpointInfoResponse extends TransportResponse {
 
     private final ReplicationCheckpoint checkpoint;
-    private final Store.MetadataSnapshot snapshot;
+    private final Map<String, StoreFileMetadata> metadataMap;
     private final byte[] infosBytes;
-    // pendingDeleteFiles are segments that have been merged away in the latest in memory SegmentInfos
-    // but are still referenced by the latest commit point (Segments_N).
-    private final Set<StoreFileMetadata> pendingDeleteFiles;
 
     public CheckpointInfoResponse(
         final ReplicationCheckpoint checkpoint,
-        final Store.MetadataSnapshot snapshot,
-        final byte[] infosBytes,
-        final Set<StoreFileMetadata> additionalFiles
+        final Map<String, StoreFileMetadata> metadataMap,
+        final byte[] infosBytes
     ) {
         this.checkpoint = checkpoint;
-        this.snapshot = snapshot;
+        this.metadataMap = metadataMap;
         this.infosBytes = infosBytes;
-        this.pendingDeleteFiles = additionalFiles;
     }
 
     public CheckpointInfoResponse(StreamInput in) throws IOException {
         this.checkpoint = new ReplicationCheckpoint(in);
-        this.snapshot = new Store.MetadataSnapshot(in);
+        this.metadataMap = in.readMap(StreamInput::readString, StoreFileMetadata::new);
         this.infosBytes = in.readByteArray();
-        this.pendingDeleteFiles = in.readSet(StoreFileMetadata::new);
     }
 
     @Override
     public void writeTo(StreamOutput out) throws IOException {
         checkpoint.writeTo(out);
-        snapshot.writeTo(out);
+        out.writeMap(metadataMap, StreamOutput::writeString, (valueOut, fc) -> fc.writeTo(valueOut));
         out.writeByteArray(infosBytes);
-        out.writeCollection(pendingDeleteFiles);
     }
 
     public ReplicationCheckpoint getCheckpoint() {
         return checkpoint;
     }
 
-    public Store.MetadataSnapshot getSnapshot() {
-        return snapshot;
+    public Map<String, StoreFileMetadata> getMetadataMap() {
+        return metadataMap;
     }
 
     public byte[] getInfosBytes() {
         return infosBytes;
     }
-
-    public Set<StoreFileMetadata> getPendingDeleteFiles() {
-        return pendingDeleteFiles;
-    }
 }