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HF login in JAX examples
Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>

* Initial API change
Signed-off-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

* Change all imports and api
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Signed-off-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

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* Review
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Signed-off-by: Jeremy Berchtold <jberchtold@nvidia.com>
Co-authored-by: Phuong Nguyen <phuonguyen@nvidia.com>

* clean up sharding
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

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

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* add mesh_resource into fp8_autocast in test_helper.py
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---------
Signed-off-by: Phuong Nguyen <phuonguyen@nvidia.com>

tighten encoder test tols
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* Support flax sharding constraints
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* Add warning for deprecated TE logical axes
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* Update examples
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---------
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started GemmPrimitive, abstract done
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gemm custom op working with BF16, needs testing for FP8/MXFP8
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converted TE GEMM API to use ScaledTensor and added os ENV flag to use TE GEMM under general gemm() call
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BF16 tests passing, FP8 tests should be passing but contracting_dims has a scoping issue
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fp8 tests passing for E4M3, getting CUBLAS_STATUS_NOT_SUPPORTED for E5M2
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updated GEMM API to use separate LHS and RHS quantizers instead of a QuantizerSet
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new GemmPrimitive passing all Dense tests
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import cleanup and reverted code chunk movement
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removed unused .transpose() implementations from ScaledTensors
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all custom call tests passing on Hopper, GEMM-related tests cover both GemmPrimitive and native JAX impl
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removed direct calls to GemmPrimitive.enabled() from outside of cpp_extensions
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removed unused changes to ScaledTensor classes and debug prints
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* minor unit test cleanup
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* FP8 tests passing on Blackwell but MXFP8 outputs NaN
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* MXFP8 issue traced to scale factor padding with NaNs instead of zeros
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* fix bug on rhs_scale_inv usage
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* segfault fixed, passing all unittests on Blackwell
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* fix for fuseddense tests
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* fixed GemmPrimitive custom partitioning to match jax.nn.scaled_matmul
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all unit tests passing on H100x8 node
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linting fixes
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fixed batch dimension numbers
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fixed FP8 scale sharding rule when there are no FP8 scales
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added error message for unsupported Shardy partitioner
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fixed test tolerances for FP8 cases
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fixed shardy test skip cases
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* moved reshape of encoder output in encoder examples to make custom partitioning rules work correctly
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* added helper functions for padding and unpadding block scales, changed GemmPrimitive to accept unpadded scales and pad them after sharding
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* updated shardy rules for all custom ops to decouple block scale rules from their tensors
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* fixed linting errors
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* changed unit test use_jax_gemm option to be a context to preserve external custom op settings, tightened multi-GPU encoder test tolerances, changed gemm() API to use contracting_dims and batched_dims separately instead of dimension_numbers
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* fixed datasets version for JAX examples
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* reverting modification to force_1x_quantization decision
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Use keyword args for jit in_shardings and out_shardings
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* fix model parallel encoder to be properly sharded
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* Add experimental Shardy support.

Production use is not yet recommended.

---------
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* scaling enum abstract

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---------
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* rename QuantizeAxis to QuantizeLayout, get_layout to get_data_layout, q_axis to q_layout

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---------
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* refactor + mxfp8

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flax module with compute dtype inferred from the inputs
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* fixes L1 test

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* Skip encoder tests on V100

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* Make test_layer be able to run on both Flax >=0.7.1 and <=0.7.0
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Update Flax version
Signed-off-by: Tim Moon <tmoon@nvidia.com>

---------
Signed-off-by: Ming Huang <mingh@nvidia.com>
Signed-off-by: Tian Zheng (Engrg-Hardware 1) <tizheng@nvidia.com>
Signed-off-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Signed-off-by: Tim Moon <tmoon@nvidia.com>
Co-authored-by: Tian Zheng <tizheng@nvidia.com>
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Co-authored-by: Tim Moon <tmoon@nvidia.com>

* Fully remove attn_type and set self_attn_mask_type default to 'causal'
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Fix tests with new arguments
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Explicit self_attn_mask_type for examples
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Update transformer_engine/jax/flax/transformer.py
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Signed-off-by: zlsh80826 <rewang@nvidia.com>

* Update transformer_engine/jax/flax/transformer.py
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Signed-off-by: zlsh80826 <rewang@nvidia.com>

---------
Signed-off-by: Reese Wang <rewang@nvidia.com>
Signed-off-by: zlsh80826 <rewang@nvidia.com>
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

* Enable fused attention dropout
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Cast the uint32 key/counter to int64
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Update dropout support in fused attention docs
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Revise devPtrCuSeqlen* to align the naming
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Support different Jax PRNG impls
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Revert CastAsync since it is not used
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Implement is_training for 16-bit fused attn
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Add fused attn with dropout sanity unit tests
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Enhance the comments readability and rng_state checker
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Change the attention dropout shape to align other frameworks
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Make encoder tests deterministic
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Change the default seed for the jax encoder tests
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Maintain offset in TE
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Enhance the resource safety
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Revert rng_state type to allow only i64
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Handle the corner case for elts_per_threads calculation
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Populate rng state by kernels
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Rename rng_state as seed in cpp_extensions
Signed-off-by: Reese Wang <rewang@nvidia.com>

* Update the attention dropout comment
Signed-off-by: Reese Wang <rewang@nvidia.com>

---------
Signed-off-by: Reese Wang <rewang@nvidia.com>
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

* Adding JAX/Praxis modules and dependencies.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Adding UTs to JAX/Praxis modules.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Remove praxis as a dependency due to not strictly needed
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Repalce is_fp8_supported to is_fp8_available
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Make Praxis as an optional dependency.

1. Removed 'from . import praxis' in __init__.py.
    1.1 Noted, keep 'from . import flax' for deprecated warning.
2. Changed te.flax to te_flax in examples and README.rst.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Adding a workaround to FP8 training on Praxis.
Signed-off-by: Ming Huang <mingh@nvidia.com>

---------
Signed-off-by: Ming Huang <mingh@nvidia.com>

* add mp example
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* refactor
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* update doc-string
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* better FP8 checker
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* update readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* replace te.* with te.flax* to remove deprecated warning
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* remove nouse os.environ
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* remove nouse
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix typo
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/README.md
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/README.md
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/README.md
Co-authored-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/README.md
Co-authored-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/test_multiprocessing_encoder.py
Co-authored-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* remove cuda-python
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* adjust readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update examples/jax/encoder/README.md
Signed-off-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix cpp lint

fix issue of "Could not find a newline character at the end of the file."
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix AssertionError: 1 GPU per process
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* replace tfds with datasets

The Flax application crash if it use TensorFlow Dataset (tfds) in NVIDIA JAX container.
The tfds is very useful for downloading well-knwon dataset (e.g., MNIST, GLUE) and commonly used by TF/JAX community.
However, it seems like that it is NOT compatible with NVIDIA TensorFlow in NVIDIA JAX container and somehow affects JAX.
It triggers random errors at JAX initialization depending on different versions, and make CI unstable.
Thus, this commit replaces tfds with "huggingface datasets" to download needed datasets.
See "nvbugs 4039266" for more details.
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix input sharding

Unlike SPMD mode, in multiprocessing mode, the input tensor must be sharded manually.
Using DP=4, TP=2 as an example, the device mesh looks like:

mesh.device_ids = [[0, 1],
                   [2, 3],
                   [4, 5],
                   [6, 7]]

Assume that the process ID is mapped to GPU ID.
The process 0 and process 1 are grouped for model parallelism,
process 2 and process 3 are grouped together too, and so on.

The process 0 and process 1 need to share the same micro-batch in the training step,
process 0 and process 2, 4, and 6 have different micro-batch.

Thus, `shard_array_wrapper` partitions inputs to 4 parts (and setup
needed arguments for jax.make_array_from_single_device_arrays).
The process 0 and process 1 take the first quarter,
process 2 and process 3 take the second quarter, and so on.
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* refactor UT for multiprocess example

Use Python `multiprocessing` to test the multiprocessing example,
if the system has multiple GPU. 1 GPU per process.

Because `jax.distributed.initialize` must be called before any other JAX or Flax API,
GPU info cannot be queried by calling jax.local_devices() in TestEncoder.
Thus, `unittest_query_gpu()` forks another process to query number of GPUs and
FP8 capability.
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* remove nouse arg `--num-gpu`

JAX doesn't have an API to setup number of GPU used in SPMD mode.
The only way is to use `CUDA_VISIBLE_DEVICES` for now.
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix typo
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix ut
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* simplify the mask setting
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* increase batch-size for multigpu example

The batch-size 64 is too small to be partitioned for 8xH100.
If batch-size is 64, the GEMM shape is 256x8192x8 per GPU.
The 8 is too small for FP8 GEMM kernel, and
cuBLASLt will throw "Failed to query heuristics".
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix downloading mnist error

To download MNIST via `huggingface datasets`, it requires Pillow.
Otherwise, it throws `An error occurred while generating the
dataset`
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

---------
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>
Signed-off-by: Jeng Bai-Cheng <jeng1220@users.noreply.github.com>
Signed-off-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>
Signed-off-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>
Co-authored-by: Tim Moon <4406448+timmoon10@users.noreply.github.com>

* Adjust Module Structure.

1. Collect Flax related modules to a sub-folder, flax.
2. Add a function to unify scale_init for zero-centered-gamma LN.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Make changes be compatible to previous versions.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Adapt jax/examples to the new module structure.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Update jax/docs and Add deprecated warning.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Update README
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Adding deprecated_wrapper
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Adding deprecated warning to flax modules which imported via transformer_engine.jax
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Fix CI errors and update docs.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Removing unnecessary deprecated warning in docs.
Signed-off-by: Ming Huang <mingh@nvidia.com>

* Implementing __iter__ to DeprecatedEnum.
Signed-off-by: Ming Huang <mingh@nvidia.com>

---------
Signed-off-by: Ming Huang <mingh@nvidia.com>
Co-authored-by: Kirthi Shankar Sivamani <ksivamani@nvidia.com>

* refactor JAX examples
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix doc-string
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* add dp example
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* refactor
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* fix params_axes_pspec
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Add model parallel example and refactor
Update readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* align code and readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* update verification
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* add mask
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* num_gpu is configurable
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* update readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* update readme
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* solvepylint issue
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* ignore markdown and txt file from license check
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* Update README.md
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

* add flax into requirements.txt
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>

---------
Signed-off-by: Ryan Jeng <rjeng@nvidia.com>