fix for parallel write overwriting inline writes

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

@@ -21,7 +21,12 @@
 import io.github.jbellis.jvector.graph.disk.feature.Feature;
 import io.github.jbellis.jvector.graph.disk.feature.FeatureId;
 
+import java.io.IOException;
+import java.io.UncheckedIOException;
 import java.nio.ByteBuffer;
+import java.nio.channels.FileChannel;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -46,6 +51,7 @@ class NodeRecordTask implements Callable<List<NodeRecordTask.Result>> {
     private final int recordSize;
     private final long baseOffset;   // Base file offset for L0 (offsets calculated per-ordinal)
     private final ByteBuffer buffer;
+    private final Path filePath;
 
     /**
      * Result of building a node record.
@@ -71,7 +77,8 @@ static class Result {
                    Map<FeatureId, IntFunction<Feature.State>> featureStateSuppliers,
                    int recordSize,
                    long baseOffset,
-                   ByteBuffer buffer) {
+                   ByteBuffer buffer,
+                   Path filePath) {
         this.startOrdinal = startOrdinal;
         this.endOrdinal = endOrdinal;
         this.ordinalMapper = ordinalMapper;
@@ -82,6 +89,7 @@ static class Result {
         this.recordSize = recordSize;
         this.baseOffset = baseOffset;
         this.buffer = buffer;
+        this.filePath = filePath;
     }
 
     @Override
@@ -125,16 +133,28 @@ public List<Result> call() throws Exception {
                 }
 
                 // Write inline features
+                long featureOffset = fileOffset + Integer.BYTES; // After the ordinal
                 for (var feature : inlineFeatures) {
                     var supplier = featureStateSuppliers.get(feature.id());
                     if (supplier == null) {
-                        // Write zeros for missing supplier
-                        for (int i = 0; i < feature.featureSize(); i++) {
-                            writer.writeByte(0);
+                        // Read existing data from file to preserve what was written by writeInline()
+                        try (var channel = FileChannel.open(filePath, StandardOpenOption.READ)) {
+                            ByteBuffer readBuffer = ByteBuffer.allocate(feature.featureSize());
+                            int bytesRead = channel.read(readBuffer, featureOffset);
+                            if (bytesRead != feature.featureSize()) {
+                                throw new IOException(String.format(
+                                        "Expected to read %d bytes but got %d at offset %d",
+                                        feature.featureSize(), bytesRead, featureOffset));
+                            }
+                            readBuffer.flip();
+                            writer.write(readBuffer.array(), 0, feature.featureSize());
+                        } catch (IOException e) {
+                            throw new UncheckedIOException(e);
                         }
                     } else {
                         feature.writeInline(writer, supplier.apply(originalOrdinal));
                     }
+                    featureOffset += feature.featureSize();
                 }
 
                 // Write neighbors

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

@@ -211,7 +211,8 @@ public void writeL0Records(OrdinalMapper ordinalMapper,
                         featureStateSuppliers,
                         recordSize,
                         baseOffset,               // Base offset (task calculates per-ordinal offsets)
-                        buffer
+                        buffer,
+                        filePath
                 );
 
                 return task.call();

jvector-examples/yaml-configs/autoDefault.yml

@@ -1,12 +1,12 @@
 version: 6
 
-dataset: cohere-english-v3-100k
+dataset: default
 
 construction:
   outDegree: [32]
   efConstruction: [100]
   neighborOverflow: [1.2f]
-  addHierarchy: [Yes]
+  addHierarchy: [Yes, No]
   refineFinalGraph: [Yes]
   fusedGraph: [No]
   compression:
@@ -18,12 +18,12 @@ construction:
         centerData: No
         anisotropicThreshold: -1.0 # optional parameter. By default, anisotropicThreshold=-1 (i.e., no anisotropy)
   reranking:
-    - NVQ
+    - FP
   useSavedIndexIfExists: Yes
 
 search:
   topKOverquery:
-    10: [1.0]
+    10: [1.0, 2.0, 5.0]
   useSearchPruning: [Yes]
   compression:
     - type: PQ

jvector-examples/yaml-configs/default.yml

@@ -8,7 +8,7 @@ construction:
   neighborOverflow: [1.2f]
   addHierarchy: [Yes]
   refineFinalGraph: [Yes]
-  fusedGraph: [No]
+  fusedGraph: [Yes, No]
   compression:
     - type: PQ
       parameters:
@@ -18,7 +18,7 @@ construction:
         centerData: No
         anisotropicThreshold: -1.0 # optional parameter. By default, anisotropicThreshold=-1 (i.e., no anisotropy)
   reranking:
-    - NVQ
+    - FP
   useSavedIndexIfExists: Yes
 
 search: