Add fix for evo2 generate/inference by jwilber · Pull Request #14027 · NVIDIA-NeMo/NeMo

jwilber · 2025-06-26T05:36:18Z

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What does this PR do ?

Fixes Evo 2 inference issue where state wasn't correctly accumulating during generate.

Background:
Documented issue example: NVIDIA/bionemo-framework#890

Collection: [Note which collection this PR will affect]
GPT/hyena

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Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

nemo/collections/llm/gpt/model/megatron/hyena/hyena_utils.py

+        # x1, x2, v all of shape torch.Size([1, 4096, 63])
+        u = torch.cat([x2, x1, v], dim=1) # torch.Size([1, 12288, 63])
+        L = u.shape[-1]
+        poles = rearrange(self.filter.p, "d n -> d n 1") # n = 16


farhadrgh

Left some comments, LGTM

nemo/collections/llm/gpt/model/megatron/hyena/hyena_mixer.py

nemo/collections/llm/gpt/model/megatron/hyena/engine.py

Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

nemo/collections/llm/gpt/model/megatron/hyena/hyena_mixer.py

nemo/collections/llm/gpt/model/megatron/hyena/hyena_utils.py

Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

nemo/collections/llm/gpt/model/megatron/hyena/hyena_utils.py

+        update_filter_state("inner_fir", state=fir_state)
+        return rearrange(y, "b l d -> b d l")  # b l d
+
+    def forward(self, x1, x2, v, _hyena_use_cp=True, inference_context=None):


Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

Signed-off-by: jwilber <jwilber@users.noreply.github.com>

Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

Signed-off-by: jwilber <jwilber@users.noreply.github.com>

nemo/collections/llm/gpt/model/megatron/hyena/hyena_utils.py

jstjohn

Approved with some cosmetic comments and one code block diff to verify.

Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

Signed-off-by: jwilber <jwilber@users.noreply.github.com>

Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

Signed-off-by: jwilber <jwilber@users.noreply.github.com>

chtruong814 · 2025-07-11T16:57:10Z

Although the code coverage is below the targeted patch change, we will go ahead and merge this given the need to handle a support request. This has a minimal impact for the coverage of the llm collection overall.

* Add fix for evo2 generate/inference Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add Farhad's suggested refactor Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Remove unused and truism code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add inference_context conditional check to use new ops Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add hyena operator tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add doc strings for flake8 Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * remove unnecessary assignments Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * invoke original forward for non-inference calls Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Fix reset issue Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * add docstring Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Remove test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add tests for hyena operator Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * simplify context manager in tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused import in test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add env vars for test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * mark tests gpu only Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> --------- Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Signed-off-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Co-authored-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Charlie Truong <chtruong@nvidia.com> Signed-off-by: Amir Hussein <amhussein@nvidia.com>

* Add fix for evo2 generate/inference Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add Farhad's suggested refactor Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Remove unused and truism code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add inference_context conditional check to use new ops Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add hyena operator tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add doc strings for flake8 Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * remove unnecessary assignments Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * invoke original forward for non-inference calls Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Fix reset issue Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * add docstring Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Remove test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add tests for hyena operator Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * simplify context manager in tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused import in test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add env vars for test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * mark tests gpu only Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> --------- Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Signed-off-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Co-authored-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Charlie Truong <chtruong@nvidia.com>

* Add fix for evo2 generate/inference Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add Farhad's suggested refactor Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Remove unused and truism code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add inference_context conditional check to use new ops Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add hyena operator tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add doc strings for flake8 Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * remove unnecessary assignments Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * invoke original forward for non-inference calls Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Fix reset issue Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * add docstring Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Remove test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add tests for hyena operator Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * simplify context manager in tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused import in test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add env vars for test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * mark tests gpu only Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> --------- Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Signed-off-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Co-authored-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Charlie Truong <chtruong@nvidia.com> Signed-off-by: Amir Hussein <amhussein@nvidia.com>

* Add fix for evo2 generate/inference Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add Farhad's suggested refactor Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Remove unused and truism code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add inference_context conditional check to use new ops Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add hyena operator tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add doc strings for flake8 Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * remove unnecessary assignments Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * invoke original forward for non-inference calls Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Fix reset issue Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * add docstring Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Remove test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add tests for hyena operator Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * simplify context manager in tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused import in test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add env vars for test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * mark tests gpu only Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> --------- Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Signed-off-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Co-authored-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Charlie Truong <chtruong@nvidia.com>

* Add fix for evo2 generate/inference Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add Farhad's suggested refactor Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Remove unused and truism code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add inference_context conditional check to use new ops Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add hyena operator tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused code Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * add doc strings for flake8 Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * remove unnecessary assignments Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * invoke original forward for non-inference calls Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Fix reset issue Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * add docstring Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * Remove test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add tests for hyena operator Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> * lint Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * simplify context manager in tests Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * remove unused import in test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Add env vars for test Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * mark tests gpu only Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> * Apply isort and black reformatting Signed-off-by: jwilber <jwilber@users.noreply.github.com> --------- Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Signed-off-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com> Co-authored-by: jwilber <jwilber@users.noreply.github.com> Co-authored-by: Charlie Truong <chtruong@nvidia.com> Signed-off-by: Guyue Huang <guyueh@nvidia.com>

Add fix for evo2 generate/inference

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Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

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Jared Wilber added 2 commits June 26, 2025 13:19

Add Farhad's suggested refactor

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lint

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Jared Wilber added 2 commits June 30, 2025 13:49

Remove unused and truism code

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add inference_context conditional check to use new ops

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Jared Wilber and others added 9 commits July 1, 2025 13:36

add hyena operator tests

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lint

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remove unused code

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add doc strings for flake8

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Merge branch 'main' into jwilber/fix-evo2-generate

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Apply isort and black reformatting

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remove unnecessary assignments

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invoke original forward for non-inference calls

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Apply isort and black reformatting

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Fix reset issue

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jwilber dismissed jstjohn’s stale review via 2d3692b July 3, 2025 22:57

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Apply isort and black reformatting

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Merge branch 'main' into jwilber/fix-evo2-generate

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add docstring

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Add env vars for test

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Signed-off-by: Jared Wilber <jwilber@login-eos01.eos.clusters.nvidia.com>

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mark tests gpu only

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Apply isort and black reformatting

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Merge branch 'main' into jwilber/fix-evo2-generate

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Merge branch 'main' into jwilber/fix-evo2-generate

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chtruong814 merged commit 15dc5cb into NVIDIA-NeMo:main Jul 11, 2025
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Add fix for evo2 generate/inference#14027

Add fix for evo2 generate/inference#14027
chtruong814 merged 35 commits intoNVIDIA-NeMo:mainfrom
jwilber:jwilber/fix-evo2-generate

jwilber commented Jun 26, 2025 •

edited

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jwilber commented Jun 26, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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jwilber commented Jun 26, 2025 •

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