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GeoTransolver: Fix attention and turn off feature broadcasting.#1415

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ktangsali merged 7 commits into2.0.0-rcfrom
geotransolver_attn_fix
Feb 27, 2026
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GeoTransolver: Fix attention and turn off feature broadcasting.#1415
ktangsali merged 7 commits into2.0.0-rcfrom
geotransolver_attn_fix

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@coreyjadams coreyjadams changed the title Fix attention and turn off feature broadcasting. GeoTransolver: Fix attention and turn off feature broadcasting. Feb 24, 2026
@coreyjadams coreyjadams changed the base branch from main to 2.0.0-rc February 24, 2026 18:51
@coreyjadams coreyjadams marked this pull request as ready for review February 24, 2026 18:52
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Rebased into rc for 2.0.0

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greptile-apps Bot commented Feb 24, 2026

Greptile Summary

Fixed critical attention residual connection bug in GeoTransolver and disabled feature broadcasting to match expected tensor shapes.

Key Changes:

  • Fixed residual connection in GALE_block.forward() to add attention output to original input fx instead of normalized input normed_inputs (line 460 in gale.py)
  • Disabled broadcast_global_features in config to avoid broadcasting scalar global features across all spatial points
  • Updated inference script to create scalar tensors with shape () instead of (1,) to match the non-broadcasting mode

Architecture Fix:
The attention fix is critical - the previous code attn[i] + normed_inputs[i] was adding the attention output to the layer-normalized input, which breaks the pre-norm residual architecture. The corrected version attn[i] + fx[i] properly implements: output = Attention(LayerNorm(input)) + input.

Important Files Changed

Filename Overview
physicsnemo/experimental/models/geotransolver/gale.py Fixed residual connection bug in GALE_block - now correctly adds attention output to original input fx instead of normalized input normed_inputs
examples/cfd/external_aerodynamics/transformer_models/src/inference_on_vtk.py Changed scalar parameters from shape (1,) to shape () to match disabled broadcast_global_features mode
examples/cfd/external_aerodynamics/transformer_models/src/conf/geotransolver_surface.yaml Disabled broadcast_global_features flag to avoid broadcasting scalars across all points

Last reviewed commit: 465d9c2

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@ktangsali ktangsali merged commit 6194f04 into 2.0.0-rc Feb 27, 2026
1 check passed
@ktangsali ktangsali deleted the geotransolver_attn_fix branch February 27, 2026 18:12
ktangsali pushed a commit that referenced this pull request Mar 10, 2026
* Fix attention and turn off feature broadcasting.

* Fix scalar loading shapes

* Update volume.yaml

Ensure the volume example works out of the box.

* Fix Geotransolver inference tests
ktangsali pushed a commit that referenced this pull request Mar 10, 2026
* Fix attention and turn off feature broadcasting.

* Fix scalar loading shapes

* Update volume.yaml

Ensure the volume example works out of the box.

* Fix Geotransolver inference tests
ktangsali pushed a commit that referenced this pull request Mar 11, 2026
* Fix attention and turn off feature broadcasting.

* Fix scalar loading shapes

* Update volume.yaml

Ensure the volume example works out of the box.

* Fix Geotransolver inference tests
peterdsharpe added a commit to peterdsharpe/physicsnemo that referenced this pull request Mar 12, 2026
commit fb4f159
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 23:11:04 2026 -0400

    Adds the PhysicsNeMo-Mesh changes required for GLOBE 3D (NVIDIA#1483)

    * Adds the PhysicsNeMo-Mesh changes required for GLOBE 3D

    * Fixes docstring example for compute_cell_normals to reflect correct normal vector output in 2D case.

    * Refactor compute_cell_areas and compute_cell_normals functions to use match-case syntax for improved readability and maintainability.

commit 219aca3
Author: Peter Harrington <48932392+pzharrington@users.noreply.github.com>
Date:   Wed Mar 11 17:23:16 2026 -0700

    Fix window shift in pangu, fengwu (NVIDIA#1492)

    * Fix window shift in pangu, fengwu

    * changelog

commit 26fcdce
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Wed Mar 11 20:20:33 2026 +0000

    fix linting issues

commit ca15f47
Author: Charlelie Laurent <claurent@nvidia.com>
Date:   Wed Mar 11 12:08:12 2026 -0700

    Resolved conflicts in checkpoint.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 95eca0c
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Tue Mar 10 23:27:40 2026 +0000

    remove the conflict block

commit 33d9a7e
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Tue Mar 10 23:22:22 2026 +0000

    update versioins

commit fbfb896
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Mon Mar 9 16:42:38 2026 -0700

    Improved docs for module.py + multiple cleanups in docs (NVIDIA#1478)

    * Improved docs for module.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fix in save_checkpoint and load_checkpoint docstrings

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Addressed PR comments

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Improvements in docs

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Moved down section about static capture in physicsnemo.utils.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    ---------

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 13c6fb4
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Mon Mar 9 11:25:44 2026 -0500

    Update Datapipes API (NVIDIA#1468)

    * Trying again with datapipes check in

    * Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.transforms.rst

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    * Resolve api commits for datapipes

    * Remove old datapipes api

    * Add link to the datapipe docs.

    ---------

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

commit 32f2261
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Fri Mar 6 15:31:53 2026 -0800

    Fix unresolved conflict (NVIDIA#1477)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 9a32517
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Fri Mar 6 15:09:50 2026 -0800

    Diffusion API docs (NVIDIA#1473)

    * New API docs for diffusion

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some fixes in nested API references

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Revert some changes

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some fixes

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some clarifications in introduction.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some clarification in diffusion models.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fixed note sections in preconditioners.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fix some broken short-form refs in losses.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Updated DPSScorePredictor class name in samplers.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Enhance clarity and structure of introduction section

    Refactor introduction section for clarity and readability. Improve formatting and organization of key concepts related to the PhysicsNeMo diffusion framework.

    * Refactor metrics.rst for improved clarity and formatting

    Reformatted the description of the module to use bullet points for clarity. Adjusted wording for consistency and readability.

    * Fix punctuation and enhance clarity in models.rst

    Corrected punctuation and improved clarity in the documentation.

    * Addressed PR comments

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    ---------

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>
    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit d723767
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Mar 5 18:56:46 2026 -0800

    Minor edits to the install guide (NVIDIA#1470)

    * minor edits to the install guide

    * add more details

    * minor doc fix

    * add transolver to the api index

commit 6bb6d04
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Thu Mar 5 12:38:13 2026 -0800

    Fixes and renaming in dps_guidance.py (NVIDIA#1471)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 1e14a56
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Wed Mar 4 15:46:15 2026 -0600

    Update API docs and structure. (NVIDIA#1337)

    * Update API docs and structure.

    * clean-up and re-organization of docs

    * fix based on new api

    * remove unused sections

    * update image paths

    * Update docs/api/models/diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/models/operators.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/models/weather.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.core.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * fix formatting

    ---------

    Co-authored-by: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
    Co-authored-by: Kaustubh Tangsali <ktangsali@nvidia.com>
    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit f22cfbf
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Mon Mar 2 17:56:32 2026 -0500

    Adds PhysicsNeMo-Mesh API Docs (NVIDIA#1461)

    * Adds mesh docs on top of RC branch

    * Update docs/mesh/boundaries.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Apply suggestions from code review

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Refine documentation for mesh geometry functions to clarify usage and API exposure for advanced cases.

    * better subdivision descriptions

    * clearer docs

    ---------

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit 1e9fdd0
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Fri Feb 27 12:12:02 2026 -0600

    GeoTransolver: Fix attention and turn off feature broadcasting. (NVIDIA#1415)

    * Fix attention and turn off feature broadcasting.

    * Fix scalar loading shapes

    * Update volume.yaml

    Ensure the volume example works out of the box.

    * Fix Geotransolver inference tests

commit 4f0a3cb
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Feb 26 15:00:42 2026 -0800

    Wandb fixes (NVIDIA#1458)

    * Add wandb to requirements

    * Modify requirements for trimesh and add wandb

    Updated trimesh version constraint and added wandb.

commit 082cd36
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Feb 26 15:00:16 2026 -0800

    Fixes from SFB builds / testing (NVIDIA#1459)

    * Remove 'perf' extra from physicsnemo installation because NGC containers already include transformer-engine

    * update deterministic settings

commit f6ca818
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Wed Feb 25 13:20:46 2026 -0800

    Fix broken cross-ref links in docstrings (NVIDIA#1454)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 47b8ff0
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 15:21:31 2026 -0400

    Deprecates `physicsnemo.utils.mesh.py` (NVIDIA#1487)

    * Adds DeprecationWarning on module.

    * Changelog update for deprecations

commit 74c91f9
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 14:20:25 2026 -0400

    Adds docstrings to CombinedOptimizer tests. (NVIDIA#1486)
nbren12 pushed a commit to nbren12/modulus that referenced this pull request Mar 24, 2026
…IA#1415)

* Fix attention and turn off feature broadcasting.

* Fix scalar loading shapes

* Update volume.yaml

Ensure the volume example works out of the box.

* Fix Geotransolver inference tests
github-merge-queue Bot pushed a commit that referenced this pull request Apr 15, 2026
* Fix SongUNet with ShardTensor when using zero embedding (#1432)

* Bug fixes for ShardTensor+SongUNet

* Handle dtensor spec in sharded view

* Fix SongUNet with ShardTensor when using zero embedding

* Use buffer for zero embed

---------

Co-authored-by: Peter Harrington <48932392+pzharrington@users.noreply.github.com>
Co-authored-by: Peter Harrington <pharrington@nvidia.com>

* Few fixes (#1434)

* comment out e2grid and makani installs

* fix dtype

* update sfno test

* update version

* some fixes for healpix tests, update to nc install, fix test dir path mismatch

* revert changes to healpix code

* don't change the default path

* fix graphcast doctest, update doctest command to ignore onnx module because of conflict with onnx.utils

* skip pytest for debugging, use floating point comparison for gumbel softmax

* make the test more robust

* bring back pytests

* Bugfix with missing num_steps parameters in CorrDiff generate.py (#1433)

* Bugfix with num_steps parameters in CorrDiff generate.py

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Update examples/weather/corrdiff/conf/base/generation/sampler/stochastic.yaml

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

---------

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>
Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* DSMLoss implementation + minor bugfixes in noise_schedulers.py and pr… (#1430)

* DSMLoss implementation + minor bugfixes in noise_schedulers.py and preconditioners.py

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Bugfix for missing abstract class in noise_schedulers.py

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Grammar improvements

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Added 'reduction' argument to MSEDSMLoss + added new WeightedMSEDSMLoss

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

---------

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Fix dlesym compat map (#1439)

* Fix dlesym compat map

* modafno fix

* format

* Few more misc fixes (#1449)

* add fixes related to dask, dask is needed for healpix datapipes

* update vtk install

* add missing dependency

* add dask dependency

* Apply suggestion from @greptile-apps[bot]

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

---------

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Update requirements.txt (#1448)

Add zarr to datapipe example requirements after it was dropped from core reqs.

* Update requirements.txt (#1447)

The FigConvNet Example needs this preprocessing script, which is how I noticed pyvista and vtk are not listed here as requirements.

* Fix broken cross-ref links in docstrings (#1454)

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Fixes from SFB builds / testing (#1459)

* Remove 'perf' extra from physicsnemo installation because NGC containers already include transformer-engine

* update deterministic settings

* Wandb fixes (#1458)

* Add wandb to requirements

* Modify requirements for trimesh and add wandb

Updated trimesh version constraint and added wandb.

* GeoTransolver: Fix attention and turn off feature broadcasting. (#1415)

* Fix attention and turn off feature broadcasting.

* Fix scalar loading shapes

* Update volume.yaml

Ensure the volume example works out of the box.

* Fix Geotransolver inference tests

* Adds PhysicsNeMo-Mesh API Docs (#1461)

* Adds mesh docs on top of RC branch

* Update docs/mesh/boundaries.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Apply suggestions from code review

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Refine documentation for mesh geometry functions to clarify usage and API exposure for advanced cases.

* better subdivision descriptions

* clearer docs

---------

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update API docs and structure. (#1337)

* Update API docs and structure.

* clean-up and re-organization of docs

* fix based on new api

* remove unused sections

* update image paths

* Update docs/api/models/diffusion.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/models/operators.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/models/weather.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.core.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.diffusion.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.diffusion.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Update docs/api/physicsnemo.utils.rst

Co-authored-by: megnvidia <mmiranda@nvidia.com>

* fix formatting

---------

Co-authored-by: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Co-authored-by: Kaustubh Tangsali <ktangsali@nvidia.com>
Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Fixes and renaming in dps_guidance.py (#1471)

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Minor edits to the install guide (#1470)

* minor edits to the install guide

* add more details

* minor doc fix

* add transolver to the api index

* Diffusion API docs (#1473)

* New API docs for diffusion

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Some fixes in nested API references

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Revert some changes

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Some fixes

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Some clarifications in introduction.rst

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Some clarification in diffusion models.rst

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Fixed note sections in preconditioners.py

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Fix some broken short-form refs in losses.py

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Updated DPSScorePredictor class name in samplers.rst

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Enhance clarity and structure of introduction section

Refactor introduction section for clarity and readability. Improve formatting and organization of key concepts related to the PhysicsNeMo diffusion framework.

* Refactor metrics.rst for improved clarity and formatting

Reformatted the description of the module to use bullet points for clarity. Adjusted wording for consistency and readability.

* Fix punctuation and enhance clarity in models.rst

Corrected punctuation and improved clarity in the documentation.

* Addressed PR comments

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

---------

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>
Co-authored-by: megnvidia <mmiranda@nvidia.com>

* Fix unresolved conflict (#1477)

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* Update Datapipes API (#1468)

* Trying again with datapipes check in

* Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Update docs/api/datapipes/physicsnemo.datapipes.rst

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Update docs/api/datapipes/physicsnemo.datapipes.rst

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Update docs/api/datapipes/physicsnemo.datapipes.rst

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* Update docs/api/datapipes/physicsnemo.datapipes.rst

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* Update docs/api/datapipes/physicsnemo.datapipes.rst

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* Update docs/api/datapipes/physicsnemo.datapipes.transforms.rst

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* Resolve api commits for datapipes

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---------

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* Improved docs for module.py + multiple cleanups in docs (#1478)

* Improved docs for module.py

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* Fix in save_checkpoint and load_checkpoint docstrings

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* Addressed PR comments

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* Improvements in docs

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* Moved down section about static capture in physicsnemo.utils.rst

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

---------

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

* add wip code 1

* first, kinda working setup

* make embeddings configurable

* add eos configs

* add eos configs

* add scripts after succesful 2 stage training. includes updates to gp with different learning rates for different params, matern kernel, test on ood, etc

* add combined transolver and GP run

* add histogram plotting

* add spectral normalization, better consistency, enhanced plotting

* add output scale prior, narrower length scale, embedding normalization

* learn from embedding states

* add files after adding an MLP before the GP

* add files to compare GP head and MLP head

* add files from a good run, KDE plots of Std Dev make sense

* cleanup for pr readiness

* updates after merging main

* add plots and experiment results

* add plots and experiment results

* fix license headers

* remove unwanted files, fix docstring issues

* fix issues with importlinter

* remove changes to base files

* revert some changes to upstream code

* restore normalization.npz from main

* address review comments

* update docstrings and unify the readme

* address rishi's comments

---------

Signed-off-by: Charlelie Laurent <claurent@nvidia.com>
Co-authored-by: Jussi Leinonen <jleinonen@nvidia.com>
Co-authored-by: Peter Harrington <48932392+pzharrington@users.noreply.github.com>
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pull Bot pushed a commit to j3din00b/modulus that referenced this pull request Apr 21, 2026
…eration (NVIDIA#1494)

* Adds the PhysicsNeMo-Mesh changes required for GLOBE 3D

* Add dual-tree traversal algorithm to GLOBE model for O(N) kernel evaluations

- Introduced a new `ClusterTree` class for spatial decomposition, enabling efficient dual-tree traversal.
- Updated `GLOBE` model to utilize the new clustering mechanism, significantly reducing kernel evaluation complexity.
- Enhanced `CHANGELOG.md` to reflect the addition of the dual-tree algorithm and its impact on performance.
- Added comprehensive tests for the `BarnesHutKernel` and `ClusterTree` functionalities to ensure correctness and performance.
- Refactored existing kernel evaluation methods to integrate the new dual-tree approach, improving overall efficiency.

This update is crucial for handling large mesh scales effectively, particularly in scenarios with 800k+ faces.

* Adds DTT-related changes to AirFRANS train.py

* Squashed commit of the following:

commit fb4f159
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 23:11:04 2026 -0400

    Adds the PhysicsNeMo-Mesh changes required for GLOBE 3D (NVIDIA#1483)

    * Adds the PhysicsNeMo-Mesh changes required for GLOBE 3D

    * Fixes docstring example for compute_cell_normals to reflect correct normal vector output in 2D case.

    * Refactor compute_cell_areas and compute_cell_normals functions to use match-case syntax for improved readability and maintainability.

commit 219aca3
Author: Peter Harrington <48932392+pzharrington@users.noreply.github.com>
Date:   Wed Mar 11 17:23:16 2026 -0700

    Fix window shift in pangu, fengwu (NVIDIA#1492)

    * Fix window shift in pangu, fengwu

    * changelog

commit 26fcdce
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Wed Mar 11 20:20:33 2026 +0000

    fix linting issues

commit ca15f47
Author: Charlelie Laurent <claurent@nvidia.com>
Date:   Wed Mar 11 12:08:12 2026 -0700

    Resolved conflicts in checkpoint.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 95eca0c
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Tue Mar 10 23:27:40 2026 +0000

    remove the conflict block

commit 33d9a7e
Author: Kaustubh Tangsali <ktangsali@nvidia.com>
Date:   Tue Mar 10 23:22:22 2026 +0000

    update versioins

commit fbfb896
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Mon Mar 9 16:42:38 2026 -0700

    Improved docs for module.py + multiple cleanups in docs (NVIDIA#1478)

    * Improved docs for module.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fix in save_checkpoint and load_checkpoint docstrings

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Addressed PR comments

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Improvements in docs

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Moved down section about static capture in physicsnemo.utils.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    ---------

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 13c6fb4
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Mon Mar 9 11:25:44 2026 -0500

    Update Datapipes API (NVIDIA#1468)

    * Trying again with datapipes check in

    * Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.cae.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Update docs/api/datapipes/physicsnemo.datapipes.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.rst

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    * Update docs/api/datapipes/physicsnemo.datapipes.transforms.rst

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

    * Resolve api commits for datapipes

    * Remove old datapipes api

    * Add link to the datapipe docs.

    ---------

    Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

commit 32f2261
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Fri Mar 6 15:31:53 2026 -0800

    Fix unresolved conflict (NVIDIA#1477)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 9a32517
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Fri Mar 6 15:09:50 2026 -0800

    Diffusion API docs (NVIDIA#1473)

    * New API docs for diffusion

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some fixes in nested API references

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Revert some changes

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some fixes

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some clarifications in introduction.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Some clarification in diffusion models.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fixed note sections in preconditioners.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Fix some broken short-form refs in losses.py

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Updated DPSScorePredictor class name in samplers.rst

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    * Enhance clarity and structure of introduction section

    Refactor introduction section for clarity and readability. Improve formatting and organization of key concepts related to the PhysicsNeMo diffusion framework.

    * Refactor metrics.rst for improved clarity and formatting

    Reformatted the description of the module to use bullet points for clarity. Adjusted wording for consistency and readability.

    * Fix punctuation and enhance clarity in models.rst

    Corrected punctuation and improved clarity in the documentation.

    * Addressed PR comments

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

    ---------

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>
    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit d723767
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Mar 5 18:56:46 2026 -0800

    Minor edits to the install guide (NVIDIA#1470)

    * minor edits to the install guide

    * add more details

    * minor doc fix

    * add transolver to the api index

commit 6bb6d04
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Thu Mar 5 12:38:13 2026 -0800

    Fixes and renaming in dps_guidance.py (NVIDIA#1471)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 1e14a56
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Wed Mar 4 15:46:15 2026 -0600

    Update API docs and structure. (NVIDIA#1337)

    * Update API docs and structure.

    * clean-up and re-organization of docs

    * fix based on new api

    * remove unused sections

    * update image paths

    * Update docs/api/models/diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/models/operators.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/models/weather.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.core.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.diffusion.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Update docs/api/physicsnemo.utils.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * fix formatting

    ---------

    Co-authored-by: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
    Co-authored-by: Kaustubh Tangsali <ktangsali@nvidia.com>
    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit f22cfbf
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Mon Mar 2 17:56:32 2026 -0500

    Adds PhysicsNeMo-Mesh API Docs (NVIDIA#1461)

    * Adds mesh docs on top of RC branch

    * Update docs/mesh/boundaries.rst

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Apply suggestions from code review

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

    * Refine documentation for mesh geometry functions to clarify usage and API exposure for advanced cases.

    * better subdivision descriptions

    * clearer docs

    ---------

    Co-authored-by: megnvidia <mmiranda@nvidia.com>

commit 1e9fdd0
Author: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Date:   Fri Feb 27 12:12:02 2026 -0600

    GeoTransolver: Fix attention and turn off feature broadcasting. (NVIDIA#1415)

    * Fix attention and turn off feature broadcasting.

    * Fix scalar loading shapes

    * Update volume.yaml

    Ensure the volume example works out of the box.

    * Fix Geotransolver inference tests

commit 4f0a3cb
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Feb 26 15:00:42 2026 -0800

    Wandb fixes (NVIDIA#1458)

    * Add wandb to requirements

    * Modify requirements for trimesh and add wandb

    Updated trimesh version constraint and added wandb.

commit 082cd36
Author: Kaustubh Tangsali <71059996+ktangsali@users.noreply.github.com>
Date:   Thu Feb 26 15:00:16 2026 -0800

    Fixes from SFB builds / testing (NVIDIA#1459)

    * Remove 'perf' extra from physicsnemo installation because NGC containers already include transformer-engine

    * update deterministic settings

commit f6ca818
Author: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Date:   Wed Feb 25 13:20:46 2026 -0800

    Fix broken cross-ref links in docstrings (NVIDIA#1454)

    Signed-off-by: Charlelie Laurent <claurent@nvidia.com>

commit 47b8ff0
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 15:21:31 2026 -0400

    Deprecates `physicsnemo.utils.mesh.py` (NVIDIA#1487)

    * Adds DeprecationWarning on module.

    * Changelog update for deprecations

commit 74c91f9
Author: Peter Sharpe <peterdsharpe@gmail.com>
Date:   Wed Mar 11 14:20:25 2026 -0400

    Adds docstrings to CombinedOptimizer tests. (NVIDIA#1486)

* Grammar fix

* Docstring fix

* Update BarnesHutKernel to use appropriate dtype for zero-valued tensors, ensuring compatibility with AMP autocast settings.

* Update MetaData class in model.py to disable JIT and CUDA graphs for improved compatibility with torch.compile and dynamic input handling.

* Enhance GLOBE model to support cross-boundary condition (BC) interactions. Updated documentation to reflect changes in self-interaction and cross-BC interaction handling. Modified the `GLOBE` class to compute dual interaction plans for all (source BC, destination BC) pairs, improving efficiency in communication layers. Added tests for multi-BC inference to validate functionality.

* Update run.sh script for improved configuration and compatibility

- Introduced variables for output name and directory to enhance flexibility.
- Updated the AIRFRANS_DATA_DIR path for consistency with dataset location.
- Set OMP_NUM_THREADS to 1 to prevent thread oversubscription during data loading.
- Simplified head node retrieval for multi-node training setup.

* Enhance ClusterTree and BarnesHutKernel for improved internal node handling

- Added internal_level_ids and internal_level_offsets to ClusterTree for efficient storage of internal node IDs in CSR-packed level order.
- Introduced internal_nodes_per_level property to retrieve internal node IDs grouped by tree depth.
- Updated _propagate_centroids_bottom_up to utilize cached internal node levels, improving performance.
- Modified BarnesHutKernel to leverage cached level ordering for bottom-up propagation, enhancing efficiency in node strength calculations.
- Adjusted lazy compilation settings for MLP and evaluation pipeline to optimize performance during execution.

* Adds theta and leaf_size forwarding

* Docs fixes, and properly abstracts _ragged.py to deduplicate code.

* Enhance global data handling in MultiscaleKernel by adding a copy operation to prevent unintended modifications.

* Adds ragged arange tests

* Adds traceable ragged_arange variant

* Refactor Kernel class to simplify network evaluation and enhance performance by removing lazy compilation.

* Always use tensorclass, not dataclass

* formatting

* Adds minor type hint annotation

* Adds in option to do far-field 1st-order expansion (default off, toggleable on) + tests

* changelog wording

* formatting

* Refactor inference and training scripts to remove chunk_size parameter from model calls for improved performance and simplicity.

* Switch airfrans to theta 0.0
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