Only link fd* files during source-only snapshot (#53463)

Source-only snapshots currently create a second full source-only copy of the shard on disk to
support incrementality during upload. Given that stored fields are occupying a substantial part
of a shard's storage, this means that clusters with source-only snapshots can require up to
50% more local storage. Ideally we would only generate source-only parts of the shard for the
things that need to be uploaded (i.e. do incrementality checks on original file instead of
trimmed-down source-only versions), but that requires much bigger changes to the snapshot
infrastructure. This here is an attempt to dramatically cut down on the storage used by the
source-only copy of the shard by soft-linking the stored-fields files (fd*) instead of copying
them.

Relates #50231

Author: ywelsch

x-pack/plugin/core/src/main/java/org/elasticsearch/snapshots/SourceOnlySnapshot.java

@@ -30,25 +30,34 @@
 import org.apache.lucene.search.Scorer;
 import org.apache.lucene.search.Weight;
 import org.apache.lucene.store.Directory;
+import org.apache.lucene.store.FilterDirectory;
 import org.apache.lucene.store.IOContext;
+import org.apache.lucene.store.IndexInput;
 import org.apache.lucene.store.IndexOutput;
 import org.apache.lucene.store.Lock;
 import org.apache.lucene.store.TrackingDirectoryWrapper;
 import org.apache.lucene.util.Bits;
 import org.apache.lucene.util.BytesRef;
 import org.apache.lucene.util.FixedBitSet;
+import org.elasticsearch.common.Strings;
 import org.elasticsearch.common.lucene.Lucene;
 import org.elasticsearch.core.internal.io.IOUtils;
 
 import java.io.ByteArrayOutputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
+import java.nio.file.NoSuchFileException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Supplier;
 
 import static org.apache.lucene.codecs.compressing.CompressingStoredFieldsWriter.FIELDS_EXTENSION;
@@ -60,23 +69,23 @@ public class SourceOnlySnapshot {
 
     private static final String FIELDS_INDEX_EXTENSION = INDEX_EXTENSION_PREFIX + FIELDS_INDEX_EXTENSION_SUFFIX;
     private static final String FIELDS_META_EXTENSION = INDEX_EXTENSION_PREFIX + FIELDS_META_EXTENSION_SUFFIX;
-    private final Directory targetDirectory;
+    private final LinkedFilesDirectory targetDirectory;
     private final Supplier<Query> deleteByQuerySupplier;
 
-    public SourceOnlySnapshot(Directory targetDirectory, Supplier<Query> deleteByQuerySupplier) {
+    public SourceOnlySnapshot(LinkedFilesDirectory targetDirectory, Supplier<Query> deleteByQuerySupplier) {
         this.targetDirectory = targetDirectory;
         this.deleteByQuerySupplier = deleteByQuerySupplier;
     }
 
-    public SourceOnlySnapshot(Directory targetDirectory) {
+    public SourceOnlySnapshot(LinkedFilesDirectory targetDirectory) {
         this(targetDirectory, null);
     }
 
     public synchronized List<String> syncSnapshot(IndexCommit commit) throws IOException {
         long generation;
         Map<BytesRef, SegmentCommitInfo> existingSegments = new HashMap<>();
-        if (Lucene.indexExists(targetDirectory)) {
-            SegmentInfos existingsSegmentInfos = Lucene.readSegmentInfos(targetDirectory);
+        if (Lucene.indexExists(targetDirectory.getWrapped())) {
+            SegmentInfos existingsSegmentInfos = Lucene.readSegmentInfos(targetDirectory.getWrapped());
             for (SegmentCommitInfo info : existingsSegmentInfos) {
                 existingSegments.put(new BytesRef(info.info.getId()), info);
             }
@@ -191,63 +200,78 @@ DirectoryReader wrapReader(DirectoryReader reader) throws IOException {
 
     private SegmentCommitInfo syncSegment(SegmentCommitInfo segmentCommitInfo, LiveDocs liveDocs, FieldInfos fieldInfos,
                                           Map<BytesRef, SegmentCommitInfo> existingSegments, List<String> createdFiles) throws IOException {
-        SegmentInfo si = segmentCommitInfo.info;
-        Codec codec = si.getCodec();
-        final String segmentSuffix = "";
-        SegmentCommitInfo newInfo;
-        final TrackingDirectoryWrapper trackingDir = new TrackingDirectoryWrapper(targetDirectory);
-        BytesRef segmentId = new BytesRef(si.getId());
-        boolean exists = existingSegments.containsKey(segmentId);
-        if (exists == false) {
-            SegmentInfo newSegmentInfo = new SegmentInfo(si.dir, si.getVersion(), si.getMinVersion(), si.name, si.maxDoc(), false,
-                si.getCodec(), si.getDiagnostics(), si.getId(), si.getAttributes(), null);
-            // we drop the sort on purpose since the field we sorted on doesn't exist in the target index anymore.
-            newInfo = new SegmentCommitInfo(newSegmentInfo, 0, 0, -1, -1, -1);
-            List<FieldInfo> fieldInfoCopy = new ArrayList<>(fieldInfos.size());
-            for (FieldInfo fieldInfo : fieldInfos) {
-                fieldInfoCopy.add(new FieldInfo(fieldInfo.name, fieldInfo.number,
-                    false, false, false, IndexOptions.NONE, DocValuesType.NONE, -1, fieldInfo.attributes(), 0, 0, 0,
-                    fieldInfo.isSoftDeletesField()));
-            }
-            FieldInfos newFieldInfos = new FieldInfos(fieldInfoCopy.toArray(new FieldInfo[0]));
-            codec.fieldInfosFormat().write(trackingDir, newSegmentInfo, segmentSuffix, newFieldInfos, IOContext.DEFAULT);
-            newInfo.setFieldInfosFiles(trackingDir.getCreatedFiles());
-            String idxFile = IndexFileNames.segmentFileName(newSegmentInfo.name, segmentSuffix, FIELDS_INDEX_EXTENSION);
-            String dataFile = IndexFileNames.segmentFileName(newSegmentInfo.name, segmentSuffix, FIELDS_EXTENSION);
-            String metaFile = IndexFileNames.segmentFileName(newSegmentInfo.name, segmentSuffix, FIELDS_META_EXTENSION);
-            Directory sourceDir = newSegmentInfo.dir;
+        Directory toClose = null;
+        try {
+            SegmentInfo si = segmentCommitInfo.info;
+            Codec codec = si.getCodec();
+            Directory sourceDir = si.dir;
             if (si.getUseCompoundFile()) {
-                sourceDir = codec.compoundFormat().getCompoundReader(sourceDir, si, IOContext.DEFAULT);
+                sourceDir = new LinkedFilesDirectory.CloseMePleaseWrapper(
+                    codec.compoundFormat().getCompoundReader(sourceDir, si, IOContext.DEFAULT));
+                toClose = sourceDir;
+            }
+            final String segmentSuffix = "";
+            SegmentCommitInfo newInfo;
+            final TrackingDirectoryWrapper trackingDir = new TrackingDirectoryWrapper(targetDirectory);
+            BytesRef segmentId = new BytesRef(si.getId());
+            boolean exists = existingSegments.containsKey(segmentId);
+            if (exists == false) {
+                SegmentInfo newSegmentInfo = new SegmentInfo(targetDirectory, si.getVersion(), si.getMinVersion(), si.name, si.maxDoc(),
+                    false, si.getCodec(), si.getDiagnostics(), si.getId(), si.getAttributes(), null);
+                // we drop the sort on purpose since the field we sorted on doesn't exist in the target index anymore.
+                newInfo = new SegmentCommitInfo(newSegmentInfo, 0, 0, -1, -1, -1);
+                List<FieldInfo> fieldInfoCopy = new ArrayList<>(fieldInfos.size());
+                for (FieldInfo fieldInfo : fieldInfos) {
+                    fieldInfoCopy.add(new FieldInfo(fieldInfo.name, fieldInfo.number,
+                        false, false, false, IndexOptions.NONE, DocValuesType.NONE, -1, fieldInfo.attributes(), 0, 0, 0,
+                        fieldInfo.isSoftDeletesField()));
+                }
+                FieldInfos newFieldInfos = new FieldInfos(fieldInfoCopy.toArray(new FieldInfo[0]));
+                codec.fieldInfosFormat().write(trackingDir, newSegmentInfo, segmentSuffix, newFieldInfos, IOContext.DEFAULT);
+                newInfo.setFieldInfosFiles(trackingDir.getCreatedFiles());
+            } else {
+                newInfo = existingSegments.get(segmentId);
+                assert newInfo.info.getUseCompoundFile() == false;
             }
+
+            // link files for stored fields to target directory
+            final String idxFile = IndexFileNames.segmentFileName(newInfo.info.name, segmentSuffix, FIELDS_INDEX_EXTENSION);
+            final String dataFile = IndexFileNames.segmentFileName(newInfo.info.name, segmentSuffix, FIELDS_EXTENSION);
+            final String metaFile = IndexFileNames.segmentFileName(newInfo.info.name, segmentSuffix, FIELDS_META_EXTENSION);
             trackingDir.copyFrom(sourceDir, idxFile, idxFile, IOContext.DEFAULT);
+            assert targetDirectory.linkedFiles.containsKey(idxFile);
+            assert trackingDir.getCreatedFiles().contains(idxFile);
             trackingDir.copyFrom(sourceDir, dataFile, dataFile, IOContext.DEFAULT);
-             if (Arrays.asList(sourceDir.listAll()).contains(metaFile)) { // only exists for Lucene 8.5+ indices
-                 trackingDir.copyFrom(sourceDir, metaFile, metaFile, IOContext.DEFAULT);
-             }
-            if (sourceDir != newSegmentInfo.dir) {
-                sourceDir.close();
+            assert targetDirectory.linkedFiles.containsKey(dataFile);
+            assert trackingDir.getCreatedFiles().contains(dataFile);
+            if (Arrays.asList(sourceDir.listAll()).contains(metaFile)) { // only exists for Lucene 8.5+ indices
+                trackingDir.copyFrom(sourceDir, metaFile, metaFile, IOContext.DEFAULT);
+                assert targetDirectory.linkedFiles.containsKey(metaFile);
+                assert trackingDir.getCreatedFiles().contains(metaFile);
             }
-        } else {
-            newInfo = existingSegments.get(segmentId);
-            assert newInfo.info.getUseCompoundFile() == false;
-        }
-        if (liveDocs.bits != null && liveDocs.numDeletes != 0 && liveDocs.numDeletes != newInfo.getDelCount()) {
-            if (newInfo.getDelCount() != 0) {
-                assert assertLiveDocs(liveDocs.bits, liveDocs.numDeletes);
+
+            if (liveDocs.bits != null && liveDocs.numDeletes != 0 && liveDocs.numDeletes != newInfo.getDelCount()) {
+                assert newInfo.getDelCount() == 0 || assertLiveDocs(liveDocs.bits, liveDocs.numDeletes);
+                codec.liveDocsFormat().writeLiveDocs(liveDocs.bits, trackingDir, newInfo, liveDocs.numDeletes - newInfo.getDelCount(),
+                    IOContext.DEFAULT);
+                SegmentCommitInfo info = new SegmentCommitInfo(newInfo.info, liveDocs.numDeletes, 0, newInfo.getNextDelGen(), -1, -1);
+                info.setFieldInfosFiles(newInfo.getFieldInfosFiles());
+                info.info.setFiles(trackingDir.getCreatedFiles());
+                newInfo = info;
             }
-            codec.liveDocsFormat().writeLiveDocs(liveDocs.bits, trackingDir, newInfo, liveDocs.numDeletes - newInfo.getDelCount(),
-                IOContext.DEFAULT);
-            SegmentCommitInfo info = new SegmentCommitInfo(newInfo.info, liveDocs.numDeletes, 0, newInfo.getNextDelGen(), -1, -1);
-            info.setFieldInfosFiles(newInfo.getFieldInfosFiles());
-            info.info.setFiles(trackingDir.getCreatedFiles());
-            newInfo = info;
-        }
-        if (exists == false) {
-            newInfo.info.setFiles(trackingDir.getCreatedFiles());
-            codec.segmentInfoFormat().write(trackingDir, newInfo.info, IOContext.DEFAULT);
+            if (exists == false) {
+                newInfo.info.setFiles(trackingDir.getCreatedFiles());
+                codec.segmentInfoFormat().write(trackingDir, newInfo.info, IOContext.DEFAULT);
+            }
+            final Set<String> createdFilesForThisSegment = trackingDir.getCreatedFiles();
+            createdFilesForThisSegment.remove(idxFile);
+            createdFilesForThisSegment.remove(dataFile);
+            createdFilesForThisSegment.remove(metaFile);
+            createdFiles.addAll(createdFilesForThisSegment);
+            return newInfo;
+        } finally {
+            IOUtils.close(toClose);
         }
-        createdFiles.addAll(trackingDir.getCreatedFiles());
-        return newInfo;
     }
 
     private boolean assertLiveDocs(Bits liveDocs, int deletes) {
@@ -270,4 +294,163 @@ private static class LiveDocs {
             this.bits = bits;
         }
     }
+
+    public static class LinkedFilesDirectory extends Directory {
+
+        private final Directory wrapped;
+        private final Map<String, Directory> linkedFiles = new HashMap<>();
+
+        public LinkedFilesDirectory(Directory wrapped) {
+            this.wrapped = wrapped;
+        }
+
+        public Directory getWrapped() {
+            return wrapped;
+        }
+
+        @Override
+        public String[] listAll() throws IOException {
+            Set<String> files = new HashSet<>();
+            Collections.addAll(files, wrapped.listAll());
+            files.addAll(linkedFiles.keySet());
+            String[] result = files.toArray(Strings.EMPTY_ARRAY);
+            Arrays.sort(result);
+            return result;
+        }
+
+        @Override
+        public void deleteFile(String name) throws IOException {
+            final Directory directory = linkedFiles.remove(name);
+            if (directory == null) {
+                wrapped.deleteFile(name);
+            } else {
+                try (directory) {
+                    wrapped.deleteFile(name);
+                } catch (NoSuchFileException | FileNotFoundException e) {
+                    // ignore
+                }
+            }
+        }
+
+        @Override
+        public long fileLength(String name) throws IOException {
+            final Directory linkedDir = linkedFiles.get(name);
+            if (linkedDir != null) {
+                return linkedDir.fileLength(name);
+            } else {
+                return wrapped.fileLength(name);
+            }
+        }
+
+        @Override
+        public IndexOutput createOutput(String name, IOContext context) throws IOException {
+            if (linkedFiles.containsKey(name)) {
+                throw new IllegalArgumentException("file cannot be created as linked file with name " + name + " already exists");
+            } else {
+                return wrapped.createOutput(name, context);
+            }
+        }
+
+        @Override
+        public IndexOutput createTempOutput(String prefix, String suffix, IOContext context) throws IOException {
+            return wrapped.createTempOutput(prefix, suffix, context);
+        }
+
+        @Override
+        public void sync(Collection<String> names) throws IOException {
+            final List<String> primaryNames = new ArrayList<>();
+
+            for (String name : names) {
+                if (linkedFiles.containsKey(name) == false) {
+                    primaryNames.add(name);
+                }
+            }
+
+            if (primaryNames.isEmpty() == false) {
+                wrapped.sync(primaryNames);
+            }
+        }
+
+        @Override
+        public void syncMetaData() throws IOException {
+            wrapped.syncMetaData();
+        }
+
+        @Override
+        public void rename(String source, String dest) throws IOException {
+            if (linkedFiles.containsKey(source) || linkedFiles.containsKey(dest)) {
+                throw new IllegalArgumentException("file cannot be renamed as linked file with name " + source + " or " + dest +
+                    " already exists");
+            } else {
+                wrapped.rename(source, dest);
+            }
+        }
+
+        @Override
+        public IndexInput openInput(String name, IOContext context) throws IOException {
+            final Directory linkedDir = linkedFiles.get(name);
+            if (linkedDir != null) {
+                return linkedDir.openInput(name, context);
+            } else {
+                return wrapped.openInput(name, context);
+            }
+        }
+
+        @Override
+        public Lock obtainLock(String name) throws IOException {
+            return wrapped.obtainLock(name);
+        }
+
+        @Override
+        public void close() throws IOException {
+            IOUtils.close(() -> IOUtils.close(linkedFiles.values()), linkedFiles::clear, wrapped);
+        }
+
+        @Override
+        public void copyFrom(Directory from, String src, String dest, IOContext context) throws IOException {
+            if (src.equals(dest) == false) {
+                throw new IllegalArgumentException();
+            } else {
+                final Directory previous;
+                if (from instanceof CloseMePleaseWrapper) {
+                    ((CloseMePleaseWrapper) from).incRef();
+                    previous = linkedFiles.put(src, from);
+                } else {
+                    previous = linkedFiles.put(src, new FilterDirectory(from) {
+                        @Override
+                        public void close() {
+                            // ignore
+                        }
+                    });
+                }
+                IOUtils.close(previous);
+            }
+        }
+
+        static class CloseMePleaseWrapper extends FilterDirectory {
+
+            private final AtomicInteger refCount = new AtomicInteger(1);
+
+            CloseMePleaseWrapper(Directory in) {
+                super(in);
+            }
+
+            public void incRef() {
+                int ref = refCount.incrementAndGet();
+                assert ref > 1;
+            }
+
+            @Override
+            public void close() throws IOException {
+                if (refCount.decrementAndGet() == 0) {
+                    in.close();
+                }
+            }
+        }
+
+        @Override
+        public Set<String> getPendingDeletions() throws IOException {
+            return wrapped.getPendingDeletions();
+        }
+    }
 }

x-pack/plugin/core/src/main/java/org/elasticsearch/snapshots/SourceOnlySnapshotRepository.java

@@ -138,17 +138,18 @@ public void snapshotShard(Store store, MapperService mapperService, SnapshotId s
         Path snapPath = dataPath.resolve(SNAPSHOT_DIR_NAME);
         final List<Closeable> toClose = new ArrayList<>(3);
         try {
-            FSDirectory directory = new SimpleFSDirectory(snapPath);
-            toClose.add(directory);
-            Store tempStore = new Store(store.shardId(), store.indexSettings(), directory, new ShardLock(store.shardId()) {
+            SourceOnlySnapshot.LinkedFilesDirectory overlayDir = new SourceOnlySnapshot.LinkedFilesDirectory(
+                new SimpleFSDirectory(snapPath));
+            toClose.add(overlayDir);
+            Store tempStore = new Store(store.shardId(), store.indexSettings(), overlayDir, new ShardLock(store.shardId()) {
                 @Override
                 protected void closeInternal() {
                     // do nothing;
                 }
             }, Store.OnClose.EMPTY);
             Supplier<Query> querySupplier = mapperService.hasNested() ? Queries::newNestedFilter : null;
             // SourceOnlySnapshot will take care of soft- and hard-deletes no special casing needed here
-            SourceOnlySnapshot snapshot = new SourceOnlySnapshot(tempStore.directory(), querySupplier);
+            SourceOnlySnapshot snapshot = new SourceOnlySnapshot(overlayDir, querySupplier);
             snapshot.syncSnapshot(snapshotIndexCommit);
             // we will use the lucene doc ID as the seq ID so we set the local checkpoint to maxDoc with a new index UUID
             SegmentInfos segmentInfos = tempStore.readLastCommittedSegmentsInfo();