[Bugfix][Model] Fix DeepSeek-V4.1 microbatch positions and Engram histories

[0z5a]

Fix DeepSeek-V4.1 inputs when a request crosses a microbatch boundary. Reconstruct the history immediately before the microbatch's first actual token, preserve absolute positions when splitting attention metadata, normalize the final boundary to a Python int, refresh captured lookback storage in place, and keep synchronous Engram staging buffers separate per microbatch.

Main sync (2026-09-14): current head 3bd3c4dfb9697ead932a33c542c371cfb72c02b1 merges main at 663d7f679eda78a8d48613dfede8a4b4bcff2b74. The previous feature patch and upstream integration are preserved, with model paths and test imports updated from deepseek_v4_1 to deepseek_v41. Normalized added/removed patch lines are identical. Changed-file pre-commit hooks (.venv/bin/pre-commit run --files for every final PR file), Python parsing and git diff origin/main --check passed. The microbatch input CPU suite passed 7 tests; 2 CUDA cases were skipped. CUDA compilation, GPU execution and full-model evaluations were not rerun; the model/performance evidence below remains historical. AI assistance was used for conflict resolution and validation.

Test Result

Outcome

Item	Recorded details
Change scope	This PR delivers input-correctness fixes.
Performance status	There is no validated full-model DBO E2E throughput improvement to report, and no new DBO model run was performed in the latest H100 batch.

Correctness and regression checks

Validation	Recorded result	Scope
Isolated lookback CPU suite	7 passed, 2 CUDA cases skipped	Actual leaf-module implementation
Attention metadata and real UBatchWrapper thread/graph regressions	32 passed	Earlier H100 integration
Independent history reconstruction	4 workers × 182 slices, all matched	Request boundary, decode and captured-input refresh
Non-DBO full-model control	6/6 QA; 8/8 continuation requests completed	Earlier combined integration
DBO full-model diagnostic	6/6 QA; 5/8 continuations completed, 3/8 HTTP 400 with runtime NaN	Failed; full-model DBO support remains unresolved
Isolated main-branch checks	Changed-file pre-commit and Python parsing passed	No complete-tree GPU rerun
E2E throughput or whole-model memory benefit	Not established	No performance percentage claimed

Diagnostic configuration and limits

Item	Recorded details
Model and hardware	The earlier model diagnostic used official V4.1 Flash revision df42c109f1defefcbfcedbe7d905718a12266e40 on 4×H100 SXM 80 GB, combined with companion changes.
Parallelism and runtime	It used DP2×TP2+EP+SP, DeepEP LL, 32 GiB CPU offload, 1 GiB fixed KV cache and decode/prefill DBO thresholds 1/16.
Observed error	The error was Out of range float values are not JSON compliant: nan.
Additional observation	A shared top-k buffer was also observed being overwritten between source and consumer layers; its causal relationship to the NaNs is unproven.
Unresolved limitation	These failures are not repaired by the input fixes in this PR.

Test commands and scope

Regression and source-check commands

DSV41_SPLIT_REPO="$PWD" .venv/bin/python run_cpu_checks.py \
  tests/v1/worker/test_ubatch_inputs.py
.venv/bin/pre-commit run --files \
  tests/v1/attention/test_attention_splitting.py \
  tests/v1/worker/test_ubatch_inputs.py \
  vllm/models/deepseek_v41/common/engram.py \
  vllm/models/deepseek_v41/nvidia/model.py \
  vllm/v1/worker/gpu_model_runner.py vllm/v1/worker/gpu_ubatch_wrapper.py \
  vllm/v1/worker/ubatch_inputs.py vllm/v1/worker/ubatch_utils.py

The standalone loader preloads the dependency-light leaf modules and executes the existing tests without CUDA model-registry imports. This is the previously recorded isolated check, not a new GPU test.

#56435 changes SP exchange, #56436 changes lookup scheduling and this PR reconstructs per-microbatch inputs/history. No duplicate of this request-boundary reconstruction was found in the earlier scope check. The branch code is unchanged by this description update. Superseded integration-performance tables are omitted; the unresolved full-model limitation remains explicit.

[claude]

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[0z5a]

Contributions from anyone with sufficient GPU capacity are welcome to help fix and validate DeepSeek-V4.1 DBO. The full-model path still has unresolved runtime NaNs. Reproducible GPU E2E results and focused fixes are especially useful; happy to review and cherry-pick contributions with attribution.

[mergify]

This pull request has merge conflicts that must be resolved before it can be
merged. Please rebase the PR, @0z5a.

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, @0z5a.

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, @0z5a.

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