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[JAX] Fix test_layer to support fused attention and adjust test encoder tolerance to account for minor diff (#2563)

Fix failing unit tests
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

Update copyright to include 2026
Signed-off-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

* Fix incorrect calculation of segment pos from segment ids for thd cases and load balanced cases in from_segment_ids_and_pos. Enforce passing of segment_pos for THD cases and lod balanced cases
Signed-off-by: Kshitij Lakhani <klakhani@nvidia.com>

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* Correct the assert condition
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* Modify fused attn tests to pass new args to from_segment_ids_and_pos()
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* Calculate seg ids before pos
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* 1. Change the signature for from_segment_ids_and_pos()
2. Add support for THD in from_segment_ids_and_pos()
3. Assert if load balanced segment_ids is passed to generate a segment_pos
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* Pass keyword-only args by name
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* nit: Fix typo to use seg_ids instead of segment_ids
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* nit: Fix comments
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* Modify the function call to differentiate between load balancing and actually reordered segment_ids and segment_pos
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* Fix the is_segment_ids_reordered to be set only when CP and load balancing
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* Fix comments for from_segment_ids_and_pos()
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* Code clean up

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Fix lint errors
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* [PyTorch] Fuse permute+pad and unpermute+unpad ops for FP8 optimization

1.Fused `moe_permute_with_probs` + `Fp8Padding` and fused `moe_unpermute` + `Fp8Unpadding`,
  that can remove the explicit padding/unpadding of moe expert, improved performance and reduced peak gpu memory usage.
2.Add tests of fused permute/pad and unpermute/unpad.
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* [PyTorch/Common] Fuse permute+pad and unpermute+unpad support with_merging_probs
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* [PyTorch]format code
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* [Common]perf expert_idx loaded once
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* fix: pad_offsets can be None
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* add padding + merging probs bwd support. Not tested
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* Fix garbage initialized act grad
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* all test passing for jax permutation + pad
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* change tokens_per_experts APIs to num_out_tokens with conservative allocation of worst case padding for output buffer
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* change test permutation to reduce test time
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* triggering PR refresh
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* format code
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* Remove some tests cases from pytorch side. Add a separate toekn_dispatch test for sanity in case combine accidentally undo an error on dispatch in the roundtrip test. Add distinction between L0 and L2 in test cases in jax
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* format code
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* remove chance for inefficiency in moving between CPU and GPU, remove redundant primitive using a new static bool for padding, add assert for align size
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* fix lint in jax
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* account for both jax newer and older than version 0.8.2. Adjusted gpu triton binding accordingly
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* format code
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* fix typo
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* branch off of initial permutation jax-triton PR
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* Set 0 as the size of dummy tensors to reduce memory usage.
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* Correct setting of permuted_probs_stride_token, unpermuted_probs_stride_token and unpermuted_probs_stride_expert in unpermutation
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* Implement primitives, wrapper, test for wrapper, edit trit
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* Change implemementation of VJP functions to match correct pattern. Deduce some static scalar args from shapes of inputs. Accept B, S instead of num_tokens. Change test to use value_and_grad to test vjp funcs properly
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* formatting
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* fix pylint
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* fix test to compare to the correct reference impl. relax 1 tol for grad compare, fix lint the rightway
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* fix test_permutation to use value_and_grad for reference impl, tighten tols, and add unpermute with probs for token combine bwd rule
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* added forgotten file in prev commit
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* format
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* merge with_probs to without_probs
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* add aserts and fix lint
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* Add generic stripe_height support for load balancing
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* Fix imports in test for deprecated jax.experimental.pjit
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* Add test case for stripe_height greater than 1. Add stripe_height arg to reordering methods
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* Add Striped 1 and 4 test cases. Refactor the Load Balancing test case. Fix the incorrect shape in striping inverser reordering
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* Modify test code for CP + AG + THD + stripe height greater than 1
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* Add stripe_height arg to fused attn and fused attn fwd API. Add appropriate mask checks for AG+THD+CP and pick BRCM to be executed per rank. Add Fused Attn Primitive for CP + THD +AG + Striping. Add a method to reorder and all gather segment ids and offsets for kv
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* Add comments in primitive registration process
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* Add support for calculating q and kv seqlens and offsets per rank for CP+THD+AG+SW+Striped>1 primitive
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* Augment jax primitive register code comments
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* Fix the array sizes and padding values returned for seqlens and offsets to fit what the fused attn primitive non cp computation
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* Add support in new primitive for softmax_offset related changes. Put in missing primitive registering line in again. Increase the seqoffsets arrays lengths by 1
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* Add new set of helper functions for seqlens and seqoffsets fo AG+THD+CP+Stripe>1 which accounts for batching and seq offsets size b+1
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* Add backward primitive for CP+THD+AG+Striped>1
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* Modify tests for backward primitive for CP+THD+AG+Striped>1
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* Move stripe_height along with other static args in fused_attn_bwd rule. Fix typo in CP+AG+TH+Striped>1 primitive
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* Add test for CP+THD+AG+Striped>1
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* Fix missing var
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* Add SWA tests for AG+Striped>1+CP+THD+SWA
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* Restoring test code
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* Remove assert preventing SWA code path in CP+AG+Striped primitive
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* Parametrize num_segments_per_seq in tests
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* Clean up test code
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Clean up debug statements
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* Rename stripe_height to stripe_size
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* Code clean up and add additional comments
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nit: Apply suggestions from code review
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Fix type on fused attn tests
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* Fix seqoffsets length to be passed onto FusedAttn primitive as it is b and not b+1 needed by cuDNN
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* Skip THD test cases for CP + AG + Dual chunk. Skip BSHD cases for CP + AG + Striped>1. Correct the layout and shapr parameters passed to the tests
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* nit: Correct the ID for the test dist fused attn tests to account for cp*2 which is done under the hood
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* Set num_segments_per_seq defaults to None instead of 0
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* Augment comments. Add ValueError for stripe_size=0
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* Test only 1 num_segments_per_seq combination for CP+AG+THD+Striped>1+SWA instead of 2. Modify the num segments and window size to easily to debug values
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* Remove incorrectly added file
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* Explicitly pass zero sized arrays for seg ids and pos in the CP + AG + Striped primitive rather than using the seqlens or the offsets as placeholders
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* Add a deep dive doc for CP+THD+AG+Stripe>1+SWA regarding design considerations and decisions
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Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

* Add L1 entry for NORM_INPUT_SHAPES that was missing
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

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Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

* rm cudaGraph compatible trait from GroupedGEMM and groupedQuantize
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

* add grouped_gemm jitting in the unit test
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

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Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

* rm batch_dim, sequence_dim, sequence_parallel_output
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

* rm lhs_quantized_colwise and rhs_quantized_colwise
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

* rm unnecessary transpose_batch_sequence arg from some modules
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

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Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

* Pytest timings
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

* Reduce softmax test shape sizes
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

* Switch softmax tests to use shardy by default
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

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Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>