fix for bug when fused pq is used with no hierarchy

jvector-base/src/main/java/io/github/jbellis/jvector/graph/disk/CompactWriter.java

@@ -61,13 +61,17 @@ final class CompactWriter implements AutoCloseable {
     private final ProductQuantization pq;
     private final int baseDegree;
     private final int maxOrdinal;
+    private final int entryNode;
     private final ThreadLocal<ByteBuffer> bufferPerThread;
     private final ThreadLocal<ByteSequence<?>> zeroPQ;
     private final boolean fusedPQEnabled;
     private final Path outputPath;
     private final List<CommonHeader.LayerInfo> configuredLayerInfo;
     private final List<Integer> configuredLayerDegrees;
     private final List<UpperLayerFeatureRecord> level1FeatureRecords;
+    // PQ code for the entry node, required when hierarchy is disabled (no level 1).
+    // Mirrors what AbstractGraphIndexWriter.writeSparseLevels writes in the no-hierarchy branch.
+    private ByteSequence<?> entryNodePqCode;
 
     CompactWriter(Path outputPath,
                   int maxOrdinal,
@@ -91,7 +95,9 @@ final class CompactWriter implements AutoCloseable {
         this.baseDegree = layerDegrees.get(0);
         this.pq = pq;
         this.maxOrdinal = maxOrdinal;
+        this.entryNode = entryNode;
         this.level1FeatureRecords = new ArrayList<>();
+        this.entryNodePqCode = null;
 
         Map<FeatureId, Feature> featureMap = new LinkedHashMap<>();
         InlineVectors inlineVectorFeature = new InlineVectors(dimension);
@@ -134,10 +140,21 @@ public void writeHeader() throws IOException {
     }
 
     void writeFooter() throws IOException {
-        if (fusedPQEnabled && version == 6 && !level1FeatureRecords.isEmpty()) {
-            for (UpperLayerFeatureRecord record : level1FeatureRecords) {
-                writer.writeInt(record.ordinal);
-                vectorTypeSupport.writeByteSequence(writer, record.pqCode);
+        if (fusedPQEnabled && version == 6) {
+            if (!level1FeatureRecords.isEmpty()) {
+                // Hierarchy is enabled: write PQ source feature for every level-1 node.
+                // Mirrors AbstractGraphIndexWriter.writeSparseLevels (getMaxLevel >= 1 branch).
+                for (UpperLayerFeatureRecord record : level1FeatureRecords) {
+                    writer.writeInt(record.ordinal);
+                    vectorTypeSupport.writeByteSequence(writer, record.pqCode);
+                }
+            } else if (entryNodePqCode != null) {
+                // No hierarchy: write the entry node's own PQ code so that
+                // OnDiskGraphIndex.loadInMemoryFeatures can populate hierarchyCachedFeatures
+                // and GraphSearcher.initializeInternal can score the entry point.
+                // Mirrors AbstractGraphIndexWriter.writeSparseLevels (getMaxLevel == 0 branch).
+                writer.writeInt(entryNode);
+                vectorTypeSupport.writeByteSequence(writer, entryNodePqCode);
             }
         }
         long headerOffset = writer.position();
@@ -157,6 +174,10 @@ public Path getOutputPath() {
         return outputPath;
     }
 
+    public void setEntryNodePqCode(ByteSequence<?> code) {
+        this.entryNodePqCode = code;
+    }
+
     public void writeUpperLayerNode(int level, int ordinal, int[] neighbors, ByteSequence<?> level1PqCode) throws IOException {
         writer.writeInt(ordinal);
         writer.writeInt(neighbors.length);

jvector-base/src/main/java/io/github/jbellis/jvector/graph/disk/OnDiskGraphIndexCompactor.java

@@ -223,13 +223,31 @@ public void compact(Path outputPath) throws FileNotFoundException {
         }
 
         List<CommonHeader.LayerInfo> layerInfo = computeLayerInfoFromSources();
-        int entryNode = resolveEntryNode();
+        int[] entryNodeSource = resolveEntryNodeSource(); // {sourceIdx, originalOrdinal}
+        int entryNode = remappers.get(entryNodeSource[0]).oldToNew(entryNodeSource[1]);
 
         log.info("Writing compacted graph : {} total nodes, maxOrdinal={}, dimension={}, degree={}",
                 numTotalNodes, maxOrdinal, dimension, maxDegrees.get(0));
         try (CompactWriter writer = new CompactWriter(outputPath, maxOrdinal, numTotalNodes, 0, layerInfo, entryNode, dimension, maxDegrees, pq, pqLength, fusedPQEnabled)) {
             writer.writeHeader();
             compactLevels(writer, similarityFunction, fusedPQEnabled, compressedPrecision, pq);
+
+            // When FusedPQ is enabled and there is no hierarchy (only L0), the reader expects
+            // to find the entry node's own PQ code written after the L0 block, just as
+            // AbstractGraphIndexWriter.writeSparseLevels does in its getMaxLevel == 0 branch.
+            // Without it, loadInMemoryFeatures reads garbage and hierarchyCachedFeatures is
+            // missing the entry node, causing "Node X is not in the hierarchy" on first search.
+            if (fusedPQEnabled && maxDegrees.size() == 1) {
+                try (var entryView = sources.get(entryNodeSource[0]).getView()) {
+                    var entryVec = vectorTypeSupport.createFloatVector(dimension);
+                    entryView.getVectorInto(entryNodeSource[1], entryVec, 0);
+                    var entryPqCode = vectorTypeSupport.createByteSequence(pq.getSubspaceCount());
+                    entryPqCode.zero();
+                    pq.encodeTo(entryVec, entryPqCode);
+                    writer.setEntryNodePqCode(entryPqCode);
+                }
+            }
+
             writer.writeFooter();
             log.info("Compaction complete: {}", outputPath);
         } catch (IOException | ExecutionException | InterruptedException e) {
@@ -240,12 +258,13 @@ public void compact(Path outputPath) throws FileNotFoundException {
     }
 
     /**
-     * Resolves the entry node for the compacted graph. The chosen node must exist at maxLevel
-     * (since the on-disk format sets entryNode.level = maxLevel). Prefers the designated entry
-     * node of any source whose maxLevel equals the global maxLevel; if all such entry nodes
-     * are deleted, falls back to the first live node at maxLevel across all sources.
+     * Returns {sourceIdx, originalOrdinal} for the entry node of the compacted graph.
+     * The chosen node must exist at maxLevel (since the on-disk format sets entryNode.level =
+     * maxLevel). Prefers the designated entry node of any source whose maxLevel equals the global
+     * maxLevel; if all such entry nodes are deleted, falls back to the first live node at maxLevel
+     * across all sources.
      */
-    private int resolveEntryNode() {
+    private int[] resolveEntryNodeSource() {
         int maxLevel = sources.stream().mapToInt(OnDiskGraphIndex::getMaxLevel).max().orElse(0);
 
         // The on-disk format sets entryNode.level = layerInfo.size() - 1 (i.e. maxLevel).
@@ -256,7 +275,7 @@ private int resolveEntryNode() {
             if (sources.get(s).getMaxLevel() == maxLevel) {
                 int originalEntry = sources.get(s).getView().entryNode().node;
                 if (liveNodes.get(s).get(originalEntry)) {
-                    return remappers.get(s).oldToNew(originalEntry);
+                    return new int[]{s, originalEntry};
                 }
             }
         }
@@ -268,7 +287,7 @@ private int resolveEntryNode() {
             while (it.hasNext()) {
                 int node = it.next();
                 if (liveNodes.get(s).get(node)) {
-                    return remappers.get(s).oldToNew(node);
+                    return new int[]{s, node};
                 }
             }
         }