[Bugfix]: preserve DeepSeek V4 ubatch metadata for DBO prefills

[wangyicong52]

Purpose

Fix a crash on the DeepSeek V4 Flash MLA sparse DBO prefill path.

When long-prefill requests trigger DBO ubatching, split_attn_metadata() rebuilds CommonAttentionMetadata for each ubatch. That rebuild dropped fields needed by the downstream sparse attention paths.

This change:

• preserves positions with attn_metadata.positions[token_slice]
• preserves is_prefilling with attn_metadata.is_prefilling[request_slice]
• makes the DeepSeek sparse indexer use is_prefilling when available, so prefill continuations are not misclassified after ubatch splitting
• adds a regression test to verify that DBO ubatch metadata slicing preserves token-aligned positions and request-aligned is_prefilling.

Issue #43964 is one example of this issue.

Duplicate-work check

Current main at 92bdee05cb4ea5e94c4cce3eb0544f51d6eece8d still drops positions and is_prefilling in _make_metadata_with_slice(). PR #49542 was opened after this PR and overlaps only with the positions fix; it does not preserve is_prefilling or protect the short-prefill classification. Merged PR #51538 changes other DeepSeek V4 sparse-MLA paths but does not fix ubatch metadata slicing.

Test Plan

Testbed

• vLLM image: vllm/vllm-openai:v0.27.1
• Hardware: single node, 8 x NVIDIA H20
• Model: DeepSeek-V4-Flash-0731
• Runtime: DP8 + EP + DBO

vLLM Start Command

CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7 \
VLLM_USE_DEEP_GEMM=1 \
vllm serve "$MODEL" \
  --served-model-name dsv4 \
  --trust-remote-code \
  --tokenizer-mode deepseek_v4 \
  --data-parallel-size 8 \
  --enable-expert-parallel \
  --enable-dbo \
  --dbo-prefill-token-threshold 256 \
  --kv-cache-dtype fp8 \
  --block-size 256 \
  --attention-backend FLASHMLA_SPARSE \
  --attention_config.indexer_kv_dtype=mxfp4 \
  --max-model-len 8192 \
  --max-num-batched-tokens 512 \
  --max-num-seqs 128 \
  --enforce-eager \
  --port 8000

Benchmark

vllm bench serve \
  --backend vllm \
  --base-url http://127.0.0.1:8000 \
  --endpoint /v1/completions \
  --model "$MODEL" \
  --served-model-name dsv4 \
  --dataset-name random \
  --random-input-len 1024 \
  --random-output-len 8 \
  --random-range-ratio '{"input":0.2,"output":0.0}' \
  --num-prompts 64 \
  --request-rate inf \
  --max-concurrency 64 \
  --ignore-eos

Test Result

Baseline

Original v0.27.1 fails during DBO/C128A metadata construction:

AssertionError: positions is required for C128A metadata build
RuntimeError: Worker failed with error 'positions is required for C128A metadata build'

Relevant stack:

vllm/v1/worker/gpu_model_runner.py", line 2603, in _build_attention_metadata
  _build_attn_group_metadata(kv_cache_gid, attn_gid, _cm, ubid)
vllm/models/deepseek_v4/sparse_mla.py", line 220, in build
  c128a_fields = self._build_c128a_metadata(cm, req_id_per_token)
vllm/models/deepseek_v4/sparse_mla.py", line 261, in _build_c128a_metadata
  assert cm.positions is not None, (

With This PR

Service starts successfully:

Application startup complete.

Benchmark result:

Successful requests:                     64
Failed requests:                         0
Total input tokens:                      65790
Total generated tokens:                  512
Request throughput (req/s):              1.05
Output token throughput (tok/s):         8.36

No occurrences of:

positions is required
attention.hpp:346
EngineDeadError

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[wangyicong52]

@njhill @pavanimajety Hello, could you please take a look at this PR when you have time? Thanks a lot!

[mergify]

This pull request has merge conflicts that must be resolved before it can be
merged. Please rebase the PR, @wangyicong52.

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork

[mergify]

This pull request has merge conflicts that must be resolved before it can be
merged. Please rebase the PR, @wangyicong52.

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork