diff --git a/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java b/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
--- a/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
@@ -6,6 +6,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.RandomAccessFile;
 import java.io.Writer;
 import java.util.zip.GZIPInputStream;
 
@@ -15,14 +16,16 @@
 import it.unimi.dsi.fastutil.longs.LongBigArrays;
 import it.unimi.dsi.fastutil.longs.LongBigList;
 import it.unimi.dsi.fastutil.objects.Object2LongFunction;
-import it.unimi.dsi.fastutil.objects.ObjectBigArrays;
 import it.unimi.dsi.io.FastBufferedReader;
 import it.unimi.dsi.io.LineIterator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import org.softwareheritage.graph.Graph;
 import org.softwareheritage.graph.Node;
 import org.softwareheritage.graph.SwhId;
 import org.softwareheritage.graph.backend.NodeTypesMap;
+import org.softwareheritage.graph.utils.Timing;
 
 /**
  * Pre-processing steps (such as dumping mapping files on disk) before running the graph service.
@@ -33,6 +36,9 @@
  */
 
 public class Setup {
+  /** Timings logger */
+  private static final Logger logger = LoggerFactory.getLogger(Setup.class);
+
   public static void main(String[] args) throws IOException {
     if (args.length != 2) {
       System.err.println("Expected parameters: <nodes.csv.gz path> <compressed graph path>");
@@ -42,12 +48,10 @@
     String nodesPath = args[0];
     String graphPath = args[1];
 
-    System.out.println("Pre-computing node id maps...");
-    long startTime = System.nanoTime();
+    long startTime = Timing.start();
     precomputeNodeIdMap(nodesPath, graphPath);
-    long endTime = System.nanoTime();
-    double duration = (double) (endTime - startTime) / 1_000_000_000;
-    System.out.println("Done in: " + duration + " seconds");
+    float duration = Timing.stop(startTime);
+    logger.debug("Finished mapping files dumping, took " + duration + " seconds in total.");
   }
 
   /**
@@ -82,9 +86,8 @@
     LineIterator swhIdIterator = new LineIterator(buffer);
 
     try (Writer swhToNodeMap = new BufferedWriter(new FileWriter(graphPath + Graph.PID_TO_NODE));
-         Writer nodeToSwhMap = new BufferedWriter(new FileWriter(graphPath + Graph.NODE_TO_PID))) {
-      // nodeToSwhMap needs to write SWH id in order of node id, so use a temporary array
-      Object[][] nodeToSwhId = ObjectBigArrays.newBigArray(nbIds);
+         RandomAccessFile nodeToSwhMap = new RandomAccessFile(graphPath + Graph.NODE_TO_PID, "rw")) {
+      // RandomAccessFile is necessary for nodeToSwhMap to write SWH id in order of node id
 
       // To effectively run edge restriction during graph traversals, we store node id (long) -> SWH
       // type map. This is represented as a bitmap using minimum number of bits per Node.Type.
@@ -94,6 +97,7 @@
           LongArrayBitVector.ofLength(nbBitsPerNodeType * nbIds);
       LongBigList nodeTypesMap = nodeTypesBitVector.asLongBigList(nbBitsPerNodeType);
 
+      long startTime = Timing.start();
       for (long iNode = 0; iNode < nbIds && swhIdIterator.hasNext(); iNode++) {
         String strSwhId = swhIdIterator.next().toString();
         long mphId = mphMap.getLong(strSwhId);
@@ -103,18 +107,21 @@
         String line = strSwhId + " " + paddedNodeId + "\n";
         swhToNodeMap.write(line);
 
-        ObjectBigArrays.set(nodeToSwhId, nodeId, strSwhId);
+        nodeToSwhMap.seek((NodeIdMap.SWH_ID_LENGTH + 1) * nodeId);
+        nodeToSwhMap.writeBytes(strSwhId + "\n");
 
         SwhId swhId = new SwhId(strSwhId);
         nodeTypesMap.set(nodeId, swhId.getType().ordinal());
+
+        if (iNode % 10_000_000 == 0) {
+          long percentage = iNode * 100 / nbIds;
+          long duration = (long) Timing.stop(startTime);
+          logger.debug("{}% done in {} seconds.", percentage, duration);
+          startTime = Timing.start();
+        }
       }
 
       BinIO.storeObject(nodeTypesMap, graphPath + Graph.NODE_TO_TYPE);
-
-      for (long iNode = 0; iNode < nbIds; iNode++) {
-        String line = ObjectBigArrays.get(nodeToSwhId, iNode).toString() + "\n";
-        nodeToSwhMap.write(line);
-      }
     }
   }
 }