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Few more misc fixes#1449

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ktangsali merged 5 commits intoNVIDIA:2.0.0-rcfrom
ktangsali:few-more-fixes
Feb 25, 2026
Merged

Few more misc fixes#1449
ktangsali merged 5 commits intoNVIDIA:2.0.0-rcfrom
ktangsali:few-more-fixes

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PhysicsNeMo Pull Request

Description

Fixes for bugs found during QA testing.

Checklist

Dependencies

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greptile-apps bot commented Feb 24, 2026

Greptile Summary

This PR addresses several dependency and configuration issues found during QA testing.

Key changes:

  • Simplified VTK installation in Dockerfile by removing custom ARM64 wheel handling since VTK 9.6.0+ now provides official aarch64 wheels
  • Added dask to datapipes-extras dependencies (required for xarray chunking operations used in healpix datapipes)
  • Added @requires_module("dask") decorators to healpix tests to ensure tests are skipped when dask is unavailable
  • Added imageio dependency to mhd_pino example requirements

Issues found:

  • Package name ImageIO should be lowercase imageio in requirements.txt
  • Missing newline at end of requirements.txt file

Important Files Changed

Filename Overview
Dockerfile Simplified VTK installation by removing custom ARM64 wheel logic since VTK 9.6.0 now ships official aarch64 wheels
examples/cfd/mhd_pino/requirements.txt Added ImageIO dependency but package name should be lowercase imageio, missing newline at EOF
pyproject.toml Added dask to datapipes-extras dependencies, required for xarray chunking operations in healpix datapipes

Last reviewed commit: 14cbebc

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5 files reviewed, 2 comments

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Comment thread examples/cfd/mhd_pino/requirements.txt Outdated
Comment thread examples/cfd/mhd_pino/requirements.txt Outdated
ktangsali and others added 2 commits February 24, 2026 23:56
Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
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LGTM! We're gonna have a couple of these after dropping dask, zarr, h5py, etc as core deps and moving them to optional. It's a good move IMO but I made a small mess, so thank you for fixing this.

@ktangsali ktangsali merged commit 269dc18 into NVIDIA:2.0.0-rc Feb 25, 2026
@ktangsali ktangsali deleted the few-more-fixes branch February 25, 2026 01:54
ktangsali added a commit that referenced this pull request Feb 25, 2026
* 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>
nbren12 pushed a commit to nbren12/modulus that referenced this pull request Mar 24, 2026
* 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>
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

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

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>

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

* 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>
Co-authored-by: Peter Harrington <pharrington@nvidia.com>
Co-authored-by: Charlelie Laurent <84199758+CharlelieLrt@users.noreply.github.com>
Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
Co-authored-by: Corey adams <6619961+coreyjadams@users.noreply.github.com>
Co-authored-by: Peter Sharpe <peterdsharpe@gmail.com>
Co-authored-by: megnvidia <mmiranda@nvidia.com>
Co-authored-by: root <root@eos0065.eos.clusters.nvidia.com>
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