[BugFix] Fix returned logprobs with spec decode + prefill chunking (#29216)

Signed-off-by: Nick Hill <nhill@redhat.com>

tests/v1/sample/test_logprobs.py

@@ -521,8 +521,8 @@ def test_logprobs_mode(logprobs_mode: LogprobsMode):
         pytest.param(
             (
                 "eagle",
-                "meta-llama/Llama-3.1-8B-Instruct",
-                "yuhuili/EAGLE-LLaMA3.1-Instruct-8B",
+                "meta-llama/Llama-3.2-1B-Instruct",
+                "nm-testing/Llama3_2_1B_speculator.eagle3",
             ),
             marks=large_gpu_mark(min_gb=32),
         ),
@@ -541,7 +541,7 @@ def test_spec_decode_logprobs(
     """
     from vllm import LLM
 
-    prompt = "Hello world"
+    prompt = "Hello world " * 50
     sampling_params = SamplingParams(
         temperature=0, logprobs=3, max_tokens=10, ignore_eos=False
     )
@@ -582,6 +582,9 @@ def test_spec_decode_logprobs(
         seed=42,
         logprobs_mode=logprobs_mode,
         gpu_memory_utilization=0.4,
+        # Force prefill chunking
+        enable_chunked_prefill=True,
+        max_num_batched_tokens=32,
     )
     spec_results = spec_llm.generate([prompt], sampling_params)
     # Collect logprobs outputs from spec decode LLM.
@@ -597,6 +600,8 @@ def test_spec_decode_logprobs(
     # Per-token logprobs are expected to be the same.
     assert len(ref_logprobs) == len(spec_logprobs)
     for ref_logprob, spec_logprob in zip(ref_logprobs, spec_logprobs):
-        assert math.isclose(ref_logprob.logprob, spec_logprob.logprob, abs_tol=1e-3)
+        assert math.isclose(
+            ref_logprob.logprob, spec_logprob.logprob, rel_tol=5e-2, abs_tol=1e-1
+        )
         assert ref_logprob.rank == spec_logprob.rank
         assert ref_logprob.decoded_token == spec_logprob.decoded_token