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feat(compile): CustomKernel and GatherQMM implement output_shapes for shapeless compile#3485

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feat(compile): CustomKernel and GatherQMM implement output_shapes for shapeless compile#3485
dexwritescode wants to merge 7 commits intoml-explore:mainfrom
dexwritescode:fix/custom-kernel-output-shapes

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@dexwritescode dexwritescode commented May 5, 2026

Problem

mx::compile(shapeless=true) calls Primitive::output_shapes() on every
node when re-tracing a compiled function after input shapes change. Two
primitives were missing this override, causing compiled functions that
contain them to throw at runtime:

[Primitive::output_shapes] CustomKernel cannot infer output shapes
[Primitive::output_shapes] GatherQMM cannot infer output shapes

This makes it impossible to use mx::compile on models that combine custom
Metal kernels with gather-quantized-matmul — for example, hybrid SSM+attention
MoE models (like Qwen3 MoE) where the SSM step uses a custom Metal kernel and
the MoE routing uses gather_qmm.

Fix

CustomKernel (mlx/fast_primitives.h, mlx/backend/metal/custom_kernel.cpp, mlx/backend/cuda/custom_kernel.cpp)

The output shapes are already provided by the caller at creation time via
metal_kernel()(inputs, output_shapes, ...) and passed to array::make_arrays.
They just weren't stored on the primitive.

Add an optional output_shapes constructor parameter (default {} — backward
compatible), store in output_shapes_ member, override output_shapes() to
return it. Falls through to the base-class throw when empty (legacy path).

GatherQMM (mlx/primitives.h)

The output shape is fully inferrable from the stored fields and input shapes:

out_shape = lhs_indices.shape() + [x.shape(-2), w_outer_dims]

where w_outer_dims = transpose ? w.shape(-2) : w.shape(-1) * 32 / bits.

Input layout differs by quantization mode: Affine mode has biases at index 3,
pushing lhs_indices to index 4; other modes have lhs_indices at index 3.

Testing

Verified by enabling mx::compile(shapeless=true) on a 94-layer hybrid
SSM+attention MoE model (Qwen3.6-35B-A3B-4bit) where the GatedDeltaNet SSM
step uses a custom Metal kernel and the MoE routing uses gather_qmm.
Previously crashed on re-trace; with this fix the compiled graph is reused
correctly across decode steps.

`mx::compile(shapeless=true)` calls `Primitive::output_shapes()` on
every node when re-tracing a compiled function with changed input
shapes. `CustomKernel` never implemented this override, so any
compiled function containing a `metal_kernel` / `custom_kernel` call
would throw:

  [Primitive::output_shapes] CustomKernel cannot infer output shapes

The output shapes are already provided by the caller at creation time
via `metal_kernel()(inputs, output_shapes, ...)` and passed to
`array::make_arrays`. They just weren't stored on the primitive.

Fix: add an optional `output_shapes` parameter to the `CustomKernel`
constructor (default `{}` for backward compatibility), store it in a
new `output_shapes_` member, and override `output_shapes()` to return
it. If the field is empty (legacy construction path), fall through to
the base-class throw as before.

Update both Metal and CUDA call sites to copy the shapes before
`std::move`-ing them into `array::make_arrays` and pass the copy to
the constructor.
output_shapes() is called on every primitive during shapeless=true
retracing. GatherQMM was missing this override, causing compile to
throw when any graph containing gather_qmm was retraced.

The output shape is fully inferrable from inputs and stored fields:
  out_shape = lhs_indices.shape() + [x.shape(-2), w_outer_dims]
where w_outer_dims = transpose ? w.shape(-2) : w.shape(-1)*32/bits.

Input layout differs by mode: Affine has biases at index 3 (pushing
indices to 4/5); other modes have indices at 3/4.
@dexwritescode dexwritescode changed the title feat(compile): CustomKernel stores and returns output shapes feat(compile): CustomKernel and GatherQMM implement output_shapes for shapeless compile May 5, 2026
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The change overall looks good to me, can you add some simple tests?

Comment thread mlx/backend/cuda/custom_kernel.cpp Outdated
Comment thread mlx/primitives.h Outdated
Address review feedback from zcbenz:

- output_shapes is a const& in the lambda parameter, so std::move(output_shapes)
  compiles but silently copies rather than moves. Remove the misleading std::move
  in both metal and cuda backends — make_arrays receives a plain copy.
- Fix one extra space in the GatherQMM input layout comment to correctly align
  lhs_idx under the Affine layout line.
…rQMM

Verify that mx.compile(shapeless=True) correctly re-traces functions
containing mx.fast.metal_kernel (CustomKernel) and mx.gather_qmm
(GatherQMM) when input shapes change between calls.

Both tests fail before the fix with the respective 'cannot infer output
shapes' error and pass after output_shapes() is implemented.
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Added two tests to python/tests/test_compile.py:

  • test_shapeless_compile_custom_kernel — compiles a metal_kernel passthrough with shapeless=True, then calls it with a larger shape. Fails before the fix with CustomKernel cannot infer output shapes.
  • test_shapeless_compile_gather_qmm — compiles a gather_qmm call with shapeless=True, then calls it with a different M dimension. Fails before the fix with GatherQMM cannot infer output shapes.

Also addressed the two inline comments (removed std::move on const ref in both Metal and CUDA backends, fixed comment alignment in primitives.h).

@dexwritescode dexwritescode requested a review from zcbenz May 6, 2026 23:45
Remove the intermediate output_shapes_copy and pass output_shapes
directly to the CustomKernel constructor, which takes it by value.
cklxx added a commit to cklxx/arle that referenced this pull request May 7, 2026
…:async_eval encoder

Adds INFER_CPP_PHASE_TIMING=1 stderr probes around the two C++ FFI hot
paths so we can split "Rust async_kick = 23ms" into its components:

- crates/mlx-sys/src/mlx_qwen35_model.cpp:2541 — `forward_build_us`
  around `m->forward(inputs)` (lazy graph build).
- crates/mlx-sys/src/mlx_bridge.cpp:2072 — `async_eval_call_us`
  around the actual `mx::async_eval(arrs)` call (encoder + commit
  work).

Cached env probe (one atomic read after first call); zero prod cost
when env unset. file-static helper in each TU to avoid header churn.

Bench (Qwen3.6 35B-A3B-4bit, c=4 + c=8):

  forward_build_us  c=4 p50 = 1509μs  ← lazy graph build is FAST
  forward_build_us  c=8 p50 = 1793μs

  async_eval_call_us count=82 p50 = 24992μs  ← here's the 25ms
  (count=82 = logits + new_sampled + 80 packed_kv_flat slabs)

→ Hypothesis confirmed (per MLX async_eval research subagent this
date): mx::async_eval does graph traversal + Metal command-buffer
encoding SYNCHRONOUSLY on the calling thread. Only GPU completion is
async. For a 40-layer MoE forward (~600-1000 primitives at c=4-8),
the ~25ms is real CPU encoder work — NOT GPU compute. Confirmed by
mlx/transforms.cpp eval_impl(... async=true) which only skips the
final wait, never offloads encoding.

Erratum: AGENTS.md narrows the previous "MLX_MAX_OPS_PER_BUFFER=200
recommended for any Metal bench at c≥8" recommendation. That was
Qwen3.5-dense-specific and benched as wash-or-loss on Qwen3.6 MoE per
docs/experience/wins/2026-05-07-bench-qwen36-baseline.md. Removed
from default guidance; downgraded to "per-workload matched-A/B
tunable". Auto-wired-limit (default since 180e48b) is the canonical
Metal serving knob.

Wins entry:
docs/experience/wins/2026-05-07-bench-qwen36-encode-bottleneck.md
captures the localization, the implications (mx::compile blocked on
ml-explore/mlx#3485, multi-thread encode blocked by #3078), and four
viable next levers ranked S/M.

644 infer tests pass; clippy --features metal -- -D warnings clean.
Bench: doc + instrumentation only; no hot-path behavior change when
env unset (default).
lhs_indices shape (8,) cannot broadcast with the auto-generated
rhs_indices arange(num_experts) shape (4,), causing the second
shapeless compile call to fail during graph update.

Fix by keeping both indices fixed at shape (num_experts,) and varying
only the M dimension via x.shape = (num_experts, M, K).
grid=(x.size, 1, 1) is captured as a fixed tuple at trace time.
On the second shapeless-compile call (x.size=8) the primitive still
holds grid=(4,1,1), so only 4 of 8 output elements are written and
array_equal fails.

The test goal is to verify output_shapes prevents a throw and
returns the correct shape — not value correctness, which would
require the grid to be updated dynamically (out of scope).
@dexwritescode
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Hey @zcbenz, I've pushed a change to fix a test that failed. Would appreciate if you can trigger the CI run. Thanks!

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