[Bugfix] Fix NemotronH MTP + Chunked Prefill

tests/v1/e2e/test_hybrid_chunked_prefill.py

@@ -0,0 +1,104 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright contributors to the vLLM project
+
+import pytest
+
+from vllm import SamplingParams
+from vllm.platforms import current_platform
+
+from ...utils import large_gpu_mark, multi_gpu_marks
+
+# A trivial request with a short prompt to ensure we run a mixed batch
+SMALL_MESSAGE = [
+    {
+        "role": "user",
+        "content": "The secret beta value is 64. What is the secret beta?",
+    }
+]
+
+# Sample prompt with a bunch of filler in between the critical fact and the request.
+# Both parts need to be processed properly for the model to generate the correct answer
+MESSAGES = [
+    {
+        "role": "user",
+        "content": (
+            "Important: The secret number is 42. "
+            "The sky is green in this hypothetical world. "
+            "Apples grow on trees in the forest. "
+            "Rivers flow through the valleys and mountains. "
+            "Birds sing songs in the early morning light. "
+            "The weather today is sunny with clear skies ahead. "
+            "Flowers bloom in the garden during spring season. "
+            "Now answer with ONLY the number and nothing else: "
+            "What is the secret number plus one?"
+        ),
+    }
+]
+
+
+@pytest.mark.skipif(not current_platform.is_cuda(), reason="CUDA not available")
+@pytest.mark.parametrize(
+    "model_name",
+    [
+        pytest.param("Qwen/Qwen3.5-4B", marks=[large_gpu_mark(min_gb=40)]),
+        pytest.param(
+            "nvidia/NVIDIA-Nemotron-3-Super-120B-A12B-FP8",
+            marks=[large_gpu_mark(min_gb=80)] + multi_gpu_marks(num_gpus=2),
+        ),
+    ],
+)
+@pytest.mark.parametrize("enable_prefix_caching", [False, True])
+def test_mtp_speculative_mixed_batch_short_prefill(
+    vllm_runner, model_name, enable_prefix_caching
+):
+    """Test to ensure MTP speculative decoding correctly handles
+    short prefill chunks that fall below the reorder_batch_threshold."""
+
+    # Set so large that both prefills will be classified as decodes in a mixed batch
+    # note, with prefix caching we require chunk_size >= mamba_block_size
+    chunk_size = 256 if not enable_prefix_caching else 16384
+    num_draft_tokens = 100
+
+    with vllm_runner(
+        model_name,
+        speculative_config={
+            "method": "mtp",
+            "num_speculative_tokens": num_draft_tokens,
+        },
+        max_num_batched_tokens=chunk_size,
+        max_model_len=512,
+        enforce_eager=True,
+        tensor_parallel_size=2,
+        trust_remote_code=True,
+        enable_chunked_prefill=True,
+        enable_prefix_caching=enable_prefix_caching,
+        mamba_cache_mode="align" if enable_prefix_caching else "none",
+    ) as llm:
+        sampling_params = SamplingParams(
+            temperature=0.0,
+            max_tokens=128,
+        )
+
+        # First small message gets prefilled first, under normal conditions since the
+        # batch is not yet mixed. Then the second prefill arrives as a mixed batch, but
+        # is shorter than num_speculative_tokens, so it gets misclassified as a decode
+        # and processed with the wrong state management logic,  causing the critical
+        # fact from the first chunk to be lost and the model to generate nonsense.
+        outputs = llm.get_llm().chat(
+            [SMALL_MESSAGE, MESSAGES],
+            sampling_params,
+            chat_template_kwargs={"enable_thinking": False},
+        )
+
+        responses = []
+        for output in outputs:
+            generated_text = output.outputs[0].text
+            print(f"Generated text: {generated_text!r}")
+            responses.append(generated_text)
+
+        assert "64" in responses[0], (
+            "The first response should contain the correct value of 64."
+        )
+        assert "43" in responses[1], (
+            "The second response should contain the correct value of 42+1=43."
+        )

vllm/model_executor/layers/mamba/ops/mamba_ssm.py

@@ -334,13 +334,13 @@ def selective_state_update(
         dt_bias = dt_bias.unsqueeze(0)
     if out.dim() == 2:
         out = out.unsqueeze(1)
-    if num_accepted_tokens is not None:
-        assert state_batch_indices is not None and state_batch_indices.dim() == 2
-        assert dst_state_batch_indices is None or dst_state_batch_indices.dim() == 2
     if state_batch_indices is not None and state_batch_indices.dim() == 1:
         state_batch_indices = state_batch_indices.unsqueeze(1)
     if dst_state_batch_indices is not None and dst_state_batch_indices.dim() == 1:
         dst_state_batch_indices = dst_state_batch_indices.unsqueeze(1)
+    if num_accepted_tokens is not None:
+        assert state_batch_indices is not None and state_batch_indices.dim() == 2
+        assert dst_state_batch_indices is None or dst_state_batch_indices.dim() == 2
 
     _, nheads, dim, dstate = state.shape
     batch = x.shape[0]

vllm/v1/attention/backends/mamba_attn.py

@@ -414,8 +414,11 @@ def _compute_common_metadata(
             ]
             state_indices_tensor_p = state_indices_tensor_p[:, 0]
 
-        if num_decodes > 0 and self.use_spec_decode:
-            assert num_accepted_tokens is not None
+        # Sometimes even with specdec enabled we get single-token prefill chunks that
+        # should be treated as decodes but don't have num_accepted_tokens set.
+        # These should be fine to process as non-spec decodes since there's only
+        # one token, so no risk of placing accepted tokens in the wrong slot.
+        if num_decodes > 0 and self.use_spec_decode and num_accepted_tokens is not None:
             query_start_loc_d = common_attn_metadata.query_start_loc[: num_decodes + 1]
             num_accepted_tokens = num_accepted_tokens[:num_decodes]
 
@@ -501,9 +504,8 @@ def _update_metadata_for_cudagraph_capture(
             state_indices_tensor_d = self.state_indices_tensor_d[:padded_bs]
             state_indices_tensor_d[metadata.num_decodes :] = PAD_SLOT_ID
 
-            if self.use_spec_decode:
+            if self.use_spec_decode and num_accepted_tokens is not None:
                 assert query_start_loc_d is not None
-                assert num_accepted_tokens is not None
                 query_start_loc_d = query_start_loc_d[: padded_bs + 1]
                 self.decode_num_accepted_tokens[: metadata.num_decodes].copy_(
                     num_accepted_tokens, non_blocking=True

vllm/v1/worker/gpu_model_runner.py

@@ -739,6 +739,19 @@ def __init__(
 
         self.uniform_decode_query_len = 1 + self.num_spec_tokens
 
+        # When spec decode is active, the mamba backend classifies requests
+        # with query_len <= reorder_batch_threshold as "decodes". Prefill
+        # chunks that fall under this threshold get processed via the decode
+        # path, which stores intermediate states at sequential slots. We must
+        # set num_accepted_tokens to the chunk's query_len for those requests
+        # so the next iteration reads from the correct final-state slot.
+        # Prefills that went through the actual prefill path should keep the
+        # default value of 1 (the prefill path stores state at slot 0 only).
+        self.needs_prefill_as_decode_slots: bool = False
+        self.prefill_as_decode_num_tokens = self._make_buffer(
+            self.max_num_reqs, dtype=torch.int32
+        )
+
         # Cudagraph dispatcher for runtime cudagraph dispatching.
         self.cudagraph_dispatcher = CudagraphDispatcher(self.vllm_config)
 
@@ -1355,12 +1368,22 @@ def _update_states_after_model_execute(
             .int()
             .argmax(-1)
         )
+        spec_decode_active = bool(scheduler_output.scheduled_spec_decode_tokens)
+        if self.needs_prefill_as_decode_slots and spec_decode_active:
+            mamba_utils.update_accepted_tokens_for_prefill_as_decode(
+                self.input_batch,
+                self.prefill_as_decode_num_tokens,
+                self.num_accepted_tokens.gpu,
+                scheduler_output,
+                self.reorder_batch_threshold,
+                num_reqs,
+            )
+
         if self.cache_config.mamba_cache_mode == "align":
             for i, num_tokens in enumerate(
                 self.num_accepted_tokens.gpu[:num_reqs].cpu().numpy()
             ):
                 self.input_batch.num_accepted_tokens_cpu[i] = num_tokens
-
             mamba_utils.postprocess_mamba(
                 scheduler_output,
                 self.kv_cache_config,
@@ -2024,6 +2047,8 @@ def _build_attn_group_metadata(
                 else 0
             )
 
+            if isinstance(builder, Mamba2AttentionMetadataBuilder):
+                self.needs_prefill_as_decode_slots = True
             extra_attn_metadata_args = {}
             if use_spec_decode and isinstance(
                 builder, (Mamba2AttentionMetadataBuilder, GDNAttentionMetadataBuilder)

vllm/v1/worker/mamba_utils.py

@@ -266,3 +266,45 @@ def postprocess_mamba(
             if src_block_idx == dest_block_idx:
                 num_accepted_tokens_cpu[i] = 1
     do_mamba_copy_block(copy_bufs)
+
+
+def update_accepted_tokens_for_prefill_as_decode(
+    input_batch: GPUInputBatch,
+    prefill_as_decode_num_tokens: CpuGpuBuffer,
+    num_accepted_tokens_gpu: torch.Tensor,
+    scheduler_output: SchedulerOutput,
+    decode_qlen_threshold: int | None,
+    num_reqs: int,
+):
+    """
+    Adjusts num_accepted_tokens for prefill chunks processed via the decode path.
+    This ensures subsequent iterations read from the correct sequential state slot
+    instead of the default prefill slot 0. Not used by GDN attention, which manually
+    separates short prefills and short decodes when building the attention metadata.
+    """
+    any_is_prefill = False
+    for i in range(num_reqs):
+        num_computed = input_batch.num_computed_tokens_cpu[i]
+        num_prompt = input_batch.num_prompt_tokens[i]
+        is_prefill = num_computed < num_prompt
+        req_id = input_batch.req_ids[i]
+        query_len = scheduler_output.num_scheduled_tokens[req_id]
+
+        if is_prefill:
+            classified_as_decode = (
+                decode_qlen_threshold is not None and query_len <= decode_qlen_threshold
+            )
+            num_tokens = query_len if classified_as_decode else 1
+            any_is_prefill = True
+        else:
+            num_tokens = -1
+        prefill_as_decode_num_tokens.np[i] = num_tokens
+
+    # We can skip the GPU transfer if there aren't any values to update
+    if any_is_prefill:
+        prefill_as_decode_num_tokens.copy_to_gpu(num_reqs)
+        num_accepted_tokens_gpu[:num_reqs] = torch.where(
+            prefill_as_decode_num_tokens.gpu[:num_reqs] != -1,
+            prefill_as_decode_num_tokens.gpu[:num_reqs],
+            num_accepted_tokens_gpu[:num_reqs],
+        )