Offset PE nodes in cube_view to avoid overlapping routers

PE nodes are shifted 1.2mm above (top half) or below (bottom half)
their assigned router position. PE size reduced to 1.4x0.7mm.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/kernbench/topology/builder.py

@@ -946,13 +946,17 @@ def _build_cube_view(spec: dict) -> ViewGraph:
     ) if mesh_data else {}
 
     pe_idx = 0
+    pe_offset_y = 1.2  # mm offset to avoid overlapping router node
     for corner in corners:
+        is_top = corner in ("NW", "NE")
         for ci in range(pe_per_corner):
             pid = f"pe{pe_idx}"
             px, py = corner_pos[corner][ci]
+            # Offset PE above (top) or below (bottom) its router
+            py_view = py - pe_offset_y if is_top else py + pe_offset_y
             nodes[pid] = Node(
                 id=pid, kind="pe", impl="",
-                attrs={"corner": corner}, pos_mm=(px, py),
+                attrs={"corner": corner}, pos_mm=(px, py_view),
                 label=f"PE{pe_idx}",
             )
             pe_idx += 1

src/kernbench/topology/visualizer.py

@@ -157,7 +157,7 @@ def _compute_node_sizes(
         w_mm, h_mm = _KIND_SIZE.get(node.kind, (_DEFAULT_NODE_W, _DEFAULT_NODE_H))
         # For cube view, use smaller PE nodes
         if view.name == "cube" and node.kind == "pe":
-            w_mm, h_mm = 1.8, 1.0
+            w_mm, h_mm = 1.4, 0.7
         if view.name == "pe":
             w_mm, h_mm = 2.5, 1.4
         sizes[nid] = (w_mm * scale, h_mm * scale)