Fix FA2 long-context perf regression (#46693)
Author: ammmanism
Pull request: yes

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## 🔧 Fix ready — root cause confirmed + patched

Traced the regression down to `.item()` removal in **PR #42435**. Three call sites were left returning 0-dim CUDA tensors instead of Python ints for `max_seqlen_in_batch`:

- `_get_unpad_data()`
- `_unpad_input()`
- `prepare_fa_kwargs_from_position_ids()`

These tensors get passed straight into `flash_attn_varlen_func(max_seqlen_q=..., max_seqlen_k=...)`, and on bandwidth-saturated GPUs (🔴 RTX 6000 Pro, 🟡 milder on RTX 4090) with large KV caches, this triggers extra kernel-dispatch/sync overhead per decode step — compounding across thousands of steps into the ~17% slowdown reported here.

**Fix:** restored `.item()` at all three sites, gated behind `is_torchdynamo_compiling()` so `torch.compile` graph capture isn't broken — tensor form is preserved under compile, scalar form used in eager. The downstream `_process_flash_attention_kwargs()` now also converts tensors to ints in eager mode (not just during tracing), ensuring the scalar reaches the flash kernel.

### Verification
- ✅ Regression test asserting scalar type in eager mode: `tests/utils/test_flash_attention_utils.py` (3 tests pass)
- ✅ Standalone microbenchmark isolating the mechanism: `bench_fa2_unpad.py` (runs on CUDA; CPU shows no delta as expected, regression is GPU/bandwidth-specific)
- ✅ Compile-mode guard verified: under `torch.compile` the tensor form is preserved (no graph break); in eager mode a Python `int` is returned
- ✅ `ruff check` / `ruff format --check` clean; `utils/check_copies.py` passes

### Files changed
- `src/transformers/modeling_flash_attention_utils.py` — restore `.item()` with `is_torchdynamo_compiling()` guard in the three call sites + eager-mode conversion in `_process_flash_attention_kwargs`
- `tests/utils/test_flash_attention_utils.py` — regression test for scalar return type
- `bench_fa2_unpad.py` — microbenchmark

Fixes #46693

cc @vasqu @zucchini-nlp @andreasgoulas — building on your investigation and the draft in #47134, this should close the residual gap you flagged. Happy to adjust based on review.

Comments:
Thank you for your contribution 🤗!

## CI Security Gate — automatic approval blocked

This PR was **not** automatically approved for CI because the security gate failed.

**Possible reasons:**
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- A new high-severity security issue was detected in the changed Python files (Bandit check)

See the [workflow run](https://github.com/huggingface/transformers/actions/runs/29032903479) for the exact violations.

A maintainer can review and manually approve CI if a finding is a false positive.

Thank you for your contribution 🤗!

## CI Security Gate — automatic approval blocked

This PR was **not** automatically approved for CI because the security gate failed.

**Possible reasons:**
- The PR touches 50 or more files — only PRs with fewer than 50 changed files are automatically approved
- A changed file is outside the allowed directories (`src/`, `tests/`, `docs/`, `utils/`), has a disallowed extension (only `.py`, `.txt`, `.md` permitted outside `tests/` and `docs/`), or is not `.md`/`.yml` inside `docs/`
- A new high-severity security issue was detected in the changed Python files (Bandit check)

See the [workflow run](https://github.com/huggingface/transformers/actions/runs/29032893688) for the exact violations.

A maintainer can review and manually approve CI if a finding is a false positive.

Hmm afaik, #47134 should suffice. Also there seem to be multiple different fixes being merged into this PR - maybe you built on top of other branches that included different fixes?

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### CI recap

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**Latest run:** [29033386855:2](https://github.com/huggingface/transformers/actions/runs/29093851341)
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> **Code quality check failed**: test jobs were skipped. Fix the code quality issues and push again to run tests.

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@vasqu Good catch, thanks. This branch picked up unrelated commits (tokenizer thread-safety, CI workflow permissions, an unrelated ruff import fix) — looks like it was cut from a stale/dirty local branch rather than clean main. That also explains the security gate trip and the code quality failure.
Re: #47134 — happy to close this in favor of that one if it already covers the fix; otherwise I'll rebuild this branch from clean main with just the FA2 commit + test + benchmark so the diff is scoped correctly (should be ~3 files, not 5+769 lines). Will push the cleaned-up version shortly.