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[None][perf] Avoid paged MSA K/V materialization during prefill - #16857

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[None][perf] Avoid paged MSA K/V materialization during prefill#16857
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@peihu-nv peihu-nv commented Jul 25, 2026

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Summary

  • Added guarded zero-copy MSA sparse prefill for aligned HND paged K/V views that meet SM100 TMA requirements.
  • Kept contiguous materialization for unsupported or unaligned layouts.
  • Replaced the MSA submodule with CMake FetchContent and a pinned patch.
  • Updated wheel staging, extraction, availability checks, attribution, CI, and build documentation.
  • Added patch-state validation and fmha_sm100 package validation.
  • Reported GB200 results: 19.42% lower median prefill latency, 25.57% higher throughput, and removal of 3,648 FP8 copy kernels.
  • Focused GPU tests passed. A full SM100 wheel build was in progress.

Dev Engineer Review

  • The zero-copy path is guarded by stride and alignment checks.
  • Unsupported layouts retain contiguous materialization.
  • require_msa_module() uses direct package imports with a consistent return type.
  • FetchContent, patch application, wheel packaging, extraction, and attribution changes match the new dependency model.
  • Patch handling detects forward, reverse, and inconsistent states.
  • Confirm that staged fmha_sm100 files are available in all supported wheel build paths.
  • Confirm that the pinned MSA source and patch remain reproducible in offline and incremental builds.

QA Engineer Review

  • Added test_msa_paged_kv_preserves_tma_compatible_outer_stride().
  • Added test_msa_paged_hnd_input_materializes_unaligned_outer_stride().
  • Added coverage for HND buffer retrieval, TMA-compatible strides, page-size validation, materialization, and numerical equivalence.
  • No changes to tests/integration/test_lists/ were identified.
  • The new tests are not confirmed in test-db/ or qa/ coverage.
  • Verdict: needs follow-up.

Description

The MSA sparse-prefill path currently calls .contiguous() on paged K/V
views before FMHA. For a valid HND cache view, the tensor is already packed
within each page and satisfies the SM100 TMA requirements; only the outer page
stride is non-contiguous because the cache pool is coalesced. Materializing
the full tensor is unnecessary in that case.

This change adds a guarded zero-copy path to the pinned MSA dependency:

  • preserves a four-dimensional HND paged-cache view when its page size,
    inner row/head strides, base address, and outer page alignment satisfy the
    kernel contract;
  • falls back to the existing contiguous materialization for unsupported
    layouts;
  • manages the pinned MSA source through CMake FetchContent, applies the
    TRT-LLM-owned patch during population, and packages the patched
    fmha_sm100 module in the TensorRT-LLM wheel;
  • removes the MSA git submodule and updates CI checkout, attribution,
    availability checks, and precompiled-wheel extraction for the packaged
    module.

Performance

The matched GB200 1P1D CTX qualification used 8K input tokens, one output
token, concurrency 64, and 1,000 requests. Only the MSA sparse-prefill path
changed.

Metric Baseline Candidate Change
Median prefill _forward_step 660.792 ms 532.481 ms -19.42%
Request throughput 5.984 req/s 7.515 req/s +25.57%

Nsight Systems also showed that the candidate removed 3,648 FP8 copy kernels
and 54.293 GiB of copied data per prefill.

Build design

MSA remains pinned at e2ebe7656649f619af0ad1d457b534283034655e, but is
now declared in 3rdparty/fetch_content.json instead of .gitmodules. CMake
applies msa_strided_paged_kv.patch while populating the source. The wheel
builder then stages the patched fmha_sm100 package for setuptools; invalid
or stale patch state fails the build instead of being silently ignored.

FetchContent downloads MSA from public GitLab during CMake configure, so
uncached builds require outbound GitLab access. The nested MSA CUTLASS submodule
is disabled; wheel staging reuses the existing TRT-LLM CUTLASS dependency.

While updating wheel staging, this also removes a duplicate python -m build
invocation. The remaining invocation preserves EXTRA_WHEEL_BUILD_ARGS,
including the platform argument already merged into that value.

Test Coverage

  • Focused MSA GPU tests on GB200: 3 passed, 1,310 deselected. These cover
    retaining an aligned outer-page stride, materializing an unsupported token
    stride, and bit-identical output and LSE for strided versus packed paged K/V.
  • Matched GB200 1P1D CTX serving A/B: both variants completed 1,000/1,000
    requests with no generation-side performance claim.
  • Changed-file pre-commit and Python syntax checks pass for the follow-up
    packaging fixes.
  • Full SM100 wheel build from the current PR head is in progress.

PR Checklist

Please review the following before submitting your PR:

  • PR description clearly explains what and why. If using CodeRabbit's summary, please make sure it makes sense.

  • PR Follows TRT-LLM CODING GUIDELINES to the best of your knowledge.

  • Test cases are provided for new code paths (see test instructions)

  • If PR introduces API changes, an appropriate PR label is added - either api-compatible or api-breaking. For api-breaking, include BREAKING in the PR title.

  • Any new dependencies have been scanned for license and vulnerabilities

  • CODEOWNERS updated if ownership changes

  • Documentation updated as needed

  • Update tava architecture diagram if there is a significant design change in PR.

  • The reviewers assigned automatically/manually are appropriate for the PR.

  • Please check this after reviewing the above items as appropriate for this PR.

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Signed-off-by: peihengh <259410613+peihu-nv@users.noreply.github.com>
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peihu-nv marked this pull request as ready for review July 27, 2026 23:27
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Walkthrough

Changes

The PR replaces MSA submodule packaging with FetchContent-based staging. It updates wheel extraction and runtime imports. It also adds paged HND KV preparation for MSA sparse attention.

MSA integration

Layer / File(s) Summary
MSA dependency fetching and patching
3rdparty/fetch_content.json, cpp/CMakeLists.txt, 3rdparty/CMakeLists.txt
FetchContent retrieves MSA and applies the paged-KV patch with forward and reverse state checks.
Paged attention layout handling
3rdparty/patches/msa_strided_paged_kv.patch, tests/unittest/_torch/attention/sparse/test_minimax_m3_msa_backend.py
Paged HND inputs preserve aligned packed strides and materialize incompatible layouts. Tests cover page-size validation, stride handling, and output equivalence.
Wheel package staging and checkout integration
scripts/build_wheel.py, setup.py, .gitignore, scripts/attribution/scan/metadata/msa.yml, jenkins/UpdateTestDurations.groovy, docs/source/installation/build-from-source.md
Wheel builds stage fmha_sm100 from fetched content, extract it into the package, update attribution, and remove submodule setup steps.
Runtime MSA package loading
tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_utils.py, tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_availability.py, tensorrt_llm/_torch/attention_backend/fmha/msa_sparse_gqa.py
Runtime checks importability of the packaged fmha_sm100 module and updates missing-package guidance.

Estimated code review effort: 4 (Complex) | ~45 minutes

Sequence Diagram(s)

sequenceDiagram
  participant BuildSystem
  participant FetchContent
  participant WheelBuilder
  participant Runtime
  participant MSAKernel
  BuildSystem->>FetchContent: fetch pinned msa source
  FetchContent->>FetchContent: apply validated patch
  WheelBuilder->>FetchContent: stage fmha_sm100 files
  WheelBuilder->>Runtime: package fmha_sm100
  Runtime->>MSAKernel: import packaged module
Loading

Possibly related PRs

  • NVIDIA/TensorRT-LLM#17284: Extends the same MSA packaging and paged HND stride patch to support non-contiguous sparse block-index strides.

Suggested reviewers: qijune, schetlur-nv

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name Status Explanation Resolution
Docstring Coverage ⚠️ Warning Docstring coverage is 35.71% which is insufficient. The required threshold is 80.00%. Write docstrings for the functions missing them to satisfy the coverage threshold.
✅ Passed checks (4 passed)
Check name Status Explanation
Linked Issues check ✅ Passed Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check ✅ Passed Check skipped because no linked issues were found for this pull request.
Title check ✅ Passed The title clearly identifies the performance change that avoids paged MSA K/V materialization during prefill.
Description check ✅ Passed The description explains the problem, solution, build changes, performance results, test coverage, and checklist status.
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Comment thread scripts/build_wheel.py Outdated
Signed-off-by: Tyler Burt <195370667+tburt-nv@users.noreply.github.com>
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peihu-nv requested a review from a team as a code owner July 28, 2026 17:15

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Actionable comments posted: 1

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)
scripts/build_wheel.py (1)

1147-1158: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Build the wheel once with the complete arguments and environment.

python -m build runs twice. The first invocation uses extra_wheel_build_args but not the MYPYC environment; the second uses the environment but omits extra_wheel_build_args, so EXTRA_WHEEL_BUILD_ARGS can be lost while build time is doubled. Move the environment setup before one invocation and pass extra_wheel_build_args to it.

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/build_wheel.py` around lines 1147 - 1158, Update the wheel-build flow
to perform a single build_run invocation: move the mypyc environment setup
before it, and include both extra_wheel_build_args and plat_name_arg in that
command. Remove the redundant first invocation so the complete arguments and
environment are applied together.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_utils.py`:
- Around line 26-40: Update require_msa_module() to add a precise return
annotation using types.ModuleType, importing the types module as needed.
Preserve the existing deferred import, error handling, and returned fmha_sm100
module.

---

Outside diff comments:
In `@scripts/build_wheel.py`:
- Around line 1147-1158: Update the wheel-build flow to perform a single
build_run invocation: move the mypyc environment setup before it, and include
both extra_wheel_build_args and plat_name_arg in that command. Remove the
redundant first invocation so the complete arguments and environment are applied
together.
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  • Create a new PR with the fixes

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📥 Commits

Reviewing files that changed from the base of the PR and between 411708f and f494551.

📒 Files selected for processing (18)
  • .gitignore
  • .gitmodules
  • 3rdparty/CMakeLists.txt
  • 3rdparty/MSA
  • 3rdparty/fetch_content.json
  • cpp/CMakeLists.txt
  • jenkins/Build.groovy
  • jenkins/BuildDockerImage.groovy
  • jenkins/L0_MergeRequest.groovy
  • jenkins/L0_Test.groovy
  • jenkins/TensorRT_LLM_PLC.groovy
  • jenkins/runPerfSanityTriage.groovy
  • scripts/attribution/scan/metadata/msa.yml
  • scripts/build_wheel.py
  • setup.py
  • tensorrt_llm/_torch/attention_backend/fmha/msa_sparse_gqa.py
  • tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_availability.py
  • tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_utils.py
💤 Files with no reviewable changes (2)
  • .gitmodules
  • 3rdparty/MSA

Comment thread tensorrt_llm/_torch/attention_backend/sparse/minimax_m3/msa_utils.py Outdated
Signed-off-by: peihengh <259410613+peihu-nv@users.noreply.github.com>
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Attention Part LGTM

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I looked at this in depth. The kernel-side change itself is solid: I checked the pinned MSA source and confirmed the compiled kernels mark all non-leading strides dynamic (to_cute_tensor uses mark_layout_dynamic(leading_dim=ndim-1)), so the stride-agnostic compile cache is safe and the outer page stride is honored at runtime. The 16B checks in _prepare_paged_hnd_input match the from_dlpack(assumed_align=16) contract, and _prepare_paged_kv_for_tma at the pin is validation-only, so the view isn't re-materialized downstream. Nice perf win, well evidenced.

My concerns are with the scope and packaging around it:

  • The PR description doesn't mention the CI changes at all: every checkoutSource call site flipped, the submodule removed, precompiled-wheel extraction changed. For a change this invasive the description should cover them, and it should cite a JIRA ticket rather than [None].
  • The FetchContent migration pulls in a second full cutlass tree and adds a full-tree staging copy on every build. That's the small-file pattern that already thrashes networked filesystems (TRTLLM-14628). Details inline.
  • Pre-migration refs become unbuildable through the fixed-branch pipelines, which also matters for bisection. Details inline.

One doc leftover: docs/source/installation/build-from-source.md still tells users to run git submodule update --init --recursive. Since this PR removes the last submodule, drop that line here too.

Comment thread 3rdparty/fetch_content.json
Comment thread 3rdparty/fetch_content.json
Comment thread 3rdparty/CMakeLists.txt Outdated
Comment thread scripts/build_wheel.py Outdated
Comment thread scripts/build_wheel.py
Comment thread jenkins/runPerfSanityTriage.groovy Outdated
Comment thread 3rdparty/patches/msa_strided_paged_kv.patch
Comment thread setup.py
Signed-off-by: peihengh <259410613+peihu-nv@users.noreply.github.com>
…-paged-kv-main

Signed-off-by: peihengh <259410613+peihu-nv@users.noreply.github.com>

# Conflicts:
#	tests/unittest/_torch/attention/sparse/test_minimax_m3_msa_backend.py
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Signed-off-by: peihengh <259410613+peihu-nv@users.noreply.github.com>
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Approving — the comments below are optional touch-ups, not blockers.

The zero-copy guard is conservative and well tested (stride-contract units here, bit-exact strided-vs-packed end-to-end test inside the MSA patch), and the FetchContent migration keeps the exact submodule pin with a reviewable in-tree patch. A few non-blocking points:

  • Ticket: this is a nontrivial perf feature plus a build-system migration under a [None] tag — it deserves a JIRA ticket for tracking.
  • Upstreaming: what's the plan for landing msa_strided_paged_kv.patch in the MSA repo itself so the pin can eventually advance and the patch retire? Worth noting in the PR or a follow-up ticket.
  • Undescribed fix: the consolidation of the duplicated -m build invocation in scripts/build_wheel.py fixes a real pre-existing bug — the second (shipped) build dropped EXTRA_WHEEL_BUILD_ARGS — but the description doesn't mention it. Worth a line so it isn't lost if this PR gets split or reverted.
  • CI coverage: for the record, the new unit tests do run in pre-merge CI — l0_b200.yml enrolls unittest/_torch/attention at directory level and B200 is SM100 — so the auto-generated QA "needs follow-up" note is resolved.

Comment thread scripts/build_wheel.py
Comment thread setup.py
Comment thread jenkins/UpdateTestDurations.groovy
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Thanks again, @brnguyen2 ! Addressed the three follow-ups in 39f01c0979: added the CUTLASS revalidation guard, made older precompiled artifacts fail with a clear error, and documented the submodule checkout flag. All focused validation passed.

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peihu-nv enabled auto-merge (squash) August 6, 2026 05:16
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