[Bugfix] Fix missing sequence_lengths in qwen3_omni_moe_thinker (#35741)

Signed-off-by: Ye (Charlotte) Qi <yeq@meta.com>

vllm/model_executor/models/qwen3_omni_moe_thinker.py

@@ -648,6 +648,7 @@ class Qwen3_VisionBlock(nn.Module):
         rotary_pos_emb_cos: torch.Tensor,
         rotary_pos_emb_sin: torch.Tensor,
         max_seqlen: torch.Tensor | None,  # Only used for Flash Attention
+        sequence_lengths: torch.Tensor | None,  # Only used for FlashInfer CuDNN backend
     ) -> torch.Tensor:
         x = x + self.attn(
             self.norm1(x),
@@ -655,6 +656,7 @@ class Qwen3_VisionBlock(nn.Module):
             rotary_pos_emb_cos=rotary_pos_emb_cos,
             rotary_pos_emb_sin=rotary_pos_emb_sin,
             max_seqlen=max_seqlen,
+            sequence_lengths=sequence_lengths,
         )
 
         x = x + self.mlp(self.norm2(x))
@@ -975,6 +977,20 @@ class Qwen3Omni_VisionTransformer(nn.Module):
         rotary_pos_emb_sin = rotary_pos_emb_sin.to(hidden_states.device)
         max_seqlen = self.compute_attn_mask_seqlen(cu_seqlens)
 
+        # Recompute cu_seqlens in numpy from grid_thw to avoid GPU->CPU sync
+        grid_thw_np = grid_thw.cpu().numpy()
+        cu_seqlens_np = np.repeat(
+            grid_thw_np[:, 1] * grid_thw_np[:, 2], grid_thw_np[:, 0]
+        ).cumsum(axis=0, dtype=np.int32)
+        cu_seqlens_np = np.concatenate([np.zeros(1, dtype=np.int32), cu_seqlens_np])
+        sequence_lengths = MMEncoderAttention.maybe_compute_sequence_lengths(
+            self.attn_backend, cu_seqlens_np
+        )
+        if sequence_lengths is not None:
+            sequence_lengths = torch.from_numpy(sequence_lengths).to(
+                self.device, non_blocking=True
+            )
+
         hidden_states_list = []
         deepstack_visual_indexes = self.deepstack_visual_indexes
 
@@ -985,6 +1001,7 @@ class Qwen3Omni_VisionTransformer(nn.Module):
                 rotary_pos_emb_cos=rotary_pos_emb_cos,
                 rotary_pos_emb_sin=rotary_pos_emb_sin,
                 max_seqlen=max_seqlen,
+                sequence_lengths=sequence_lengths,
             )
             if (
                 deepstack_visual_indexes is not None