yacs.CfgNode instead of argparse.Namespace

.gitignore

@@ -2,7 +2,7 @@
 ckp/
 rollout/
 rollouts/
-wandb
+wandb/
 *.out
 datasets
 baselines

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
       - id: check-yaml
       - id: requirements-txt-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.1.8'
+    rev: 'v0.2.2'
     hooks:
       - id: ruff
         args: [ --fix ]

README.md

@@ -72,7 +72,7 @@ pip install --upgrade jax[cuda12_pip]==0.4.20 -f https://storage.googleapis.com/
 ### MacOS
 Currently, only the CPU installation works. You will need to change a few small things to get it going:
 - Clone installation: in `pyproject.toml` change the torch version from `2.1.0+cpu` to `2.1.0`. Then, remove the `poetry.lock` file and run `poetry install --only main`.
-- Configs: You will need to set `f64: False` and `num_workers: 0` in the `configs/` files.
+- Configs: You will need to set `f32: True` and `num_workers: 0` in the `configs/` files.
 
 Although the current [`jax-metal==0.0.5` library](https://pypi.org/project/jax-metal/) supports jax in general, there seems to be a missing feature used by `jax-md` related to padding -> see [this issue](https://github.com/google/jax/issues/16366#issuecomment-1591085071).
 
@@ -81,7 +81,7 @@ Although the current [`jax-metal==0.0.5` library](https://pypi.org/project/jax-m
 A general tutorial is provided in the example notebook "Training GNS on the 2D Taylor Green Vortex" under `./notebooks/tutorial.ipynb` on the [LagrangeBench repository](https://github.com/tumaer/lagrangebench). The notebook covers the basics of LagrangeBench, such as loading a dataset, setting up a case, training a model from scratch and evaluating its performance.
 
 ### Running in a local clone (`main.py`)
-Alternatively, experiments can also be set up with `main.py`, based on extensive YAML config files and cli arguments (check [`configs/`](configs/)). By default, the arguments have priority as: 1) passed cli arguments, 2) YAML config and 3) [`defaults.py`](lagrangebench/defaults.py) (`lagrangebench` defaults).
+Alternatively, experiments can also be set up with `main.py`, based on extensive YAML config files and cli arguments (check [`configs/`](configs/)). By default, the arguments have priority as 1) passed cli arguments, 2) YAML config and 3) [`defaults.py`](lagrangebench/defaults.py) (`lagrangebench` defaults).
 
 When loading a saved model with `--model_dir` the config from the checkpoint is automatically loaded and training is restarted. For more details check the [`experiments/`](experiments/) directory and the [`run.py`](experiments/run.py) file.
 
@@ -127,7 +127,7 @@ The datasets are hosted on Zenodo under the DOI: [10.5281/zenodo.10021925](https
 ### Notebooks
 We provide three notebooks that show LagrangeBench functionalities, namely:
 - [`tutorial.ipynb`](notebooks/tutorial.ipynb) [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tumaer/lagrangebench/blob/main/notebooks/tutorial.ipynb), with a general overview of LagrangeBench library, with training and evaluation of a simple GNS model,
-- [`datasets.ipynb`](notebooks/datasets.ipynb) [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tumaer/lagrangebench/blob/main/notebooks/datasets.ipynb), with more details and visualizations on the datasets, and
+- [`datasets.ipynb`](notebooks/datasets.ipynb) [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tumaer/lagrangebench/blob/main/notebooks/datasets.ipynb), with more details and visualizations of the datasets, and
 - [`gns_data.ipynb`](notebooks/gns_data.ipynb) [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/tumaer/lagrangebench/blob/main/notebooks/gns_data.ipynb), showing how to train models within LagrangeBench on the datasets from the paper [Learning to Simulate Complex Physics with Graph Networks](https://arxiv.org/abs/2002.09405).
 
 ## Directory structure
@@ -165,9 +165,9 @@ Welcome! We highly appreciate [Github issues](https://github.com/tumaer/lagrange
 You can also chat with us on [**Discord**](https://discord.gg/Ds8jRZ78hU).
 
 ### Contributing Guideline
-If you want to contribute to this repository, you will need the dev depencencies, i.e.
+If you want to contribute to this repository, you will need the dev dependencies, i.e.
 install the environment with `poetry install` without the ` --only main` flag.
-Then, we also recommend you to install the pre-commit hooks
+Then, we also recommend you install the pre-commit hooks
 if you don't want to manually run `pre-commit run` before each commit. To sum up:
 
 ```bash
@@ -220,6 +220,6 @@ The associated datasets can be cited as:
 
 
 ### Publications
-The following further publcations are based on the LagrangeBench codebase:
+The following further publications are based on the LagrangeBench codebase:
 
 1. [Learning Lagrangian Fluid Mechanics with E(3)-Equivariant Graph Neural Networks (GSI 2023)](https://arxiv.org/abs/2305.15603), A. P. Toshev, G. Galletti, J. Brandstetter, S. Adami, N. A. Adams

configs/WaterDrop_2d/gns.yaml

@@ -1,6 +1,16 @@
-extends: WaterDrop_2d/base.yaml
+main:
+  data_dir: /tmp/datasets/WaterDrop
 
-model: gns
-num_mp_steps: 10
-latent_dim: 128
-lr_start: 5.e-4
+model: 
+  name: gns
+  num_mp_steps: 10
+  latent_dim: 128
+
+optimizer:
+  lr_start: 5.e-4
+
+logging:
+  wandb_project: waterdrop_2d
+
+neighbors:
+  backend: matscipy

configs/dam_2d/gns.yaml

@@ -1,6 +1,19 @@
-extends: dam_2d/base.yaml
+main:
+  data_dir: datasets/2D_DAM_5740_20kevery100
+
+model: 
+  name: gns
+  num_mp_steps: 10
+  latent_dim: 128
+
+optimizer:
+  lr_start: 5.e-4
+  noise_std: 0.001
+
+logging:
+  wandb_project: dam_2d
+
+neighbors:
+  multiplier: 2.0
+
 
-model: gns
-num_mp_steps: 10
-latent_dim: 128
-lr_start: 5.e-4

configs/dam_2d/segnn.yaml

@@ -1,8 +1,20 @@
-extends: dam_2d/base.yaml
+main:
+  data_dir: datasets/2D_DAM_5740_20kevery100
 
-model: segnn
-num_mp_steps: 10
-latent_dim: 64
-lr_start: 5.e-4
+model: 
+  name: segnn
+  num_mp_steps: 10
+  latent_dim: 64
 
-isotropic_norm: True
+train:
+  isotropic_norm: True
+
+optimizer:
+  lr_start: 5.e-4
+  noise_std: 0.001
+
+logging:
+  wandb_project: dam_2d
+
+neighbors:
+  multiplier: 2.0

configs/ldc_2d/gns.yaml

@@ -1,6 +1,17 @@
-extends: ldc_2d/base.yaml
+main:
+  data_dir: datasets/2D_LDC_2708_10kevery100
 
-model: gns
-num_mp_steps: 10
-latent_dim: 128
-lr_start: 5.e-4
+model: 
+  name: gns
+  num_mp_steps: 10
+  latent_dim: 128
+
+optimizer:
+  lr_start: 5.e-4
+  noise_std: 0.001
+
+logging:
+  wandb_project: ldc_2d
+
+neighbors:
+  multiplier: 2.0

configs/ldc_2d/segnn.yaml

@@ -1,8 +1,20 @@
-extends: ldc_2d/base.yaml
+main:
+  data_dir: datasets/2D_LDC_2708_10kevery100
 
-model: segnn
-num_mp_steps: 10
-latent_dim: 64
-lr_start: 5.e-4
+model: 
+  name: segnn
+  num_mp_steps: 10
+  latent_dim: 64
 
-isotropic_norm: True
+train:
+  isotropic_norm: True
+
+optimizer:
+  lr_start: 5.e-4
+  noise_std: 0.001
+
+logging:
+  wandb_project: ldc_2d
+
+neighbors:
+  multiplier: 2.0

configs/ldc_3d/gns.yaml

@@ -1,6 +1,16 @@
-extends: ldc_3d/base.yaml
+main:
+  data_dir: datasets/3D_LDC_8160_10kevery100
 
-model: gns
-num_mp_steps: 10
-latent_dim: 128
-lr_start: 5.e-4
+model: 
+  name: gns
+  num_mp_steps: 10
+  latent_dim: 128
+
+optimizer:
+  lr_start: 5.e-4
+
+logging:
+  wandb_project: ldc_3d
+
+neighbors:
+  multiplier: 2.0

configs/ldc_3d/segnn.yaml

@@ -1,8 +1,19 @@
-extends: ldc_3d/base.yaml
+main:
+  data_dir: datasets/3D_LDC_8160_10kevery100
 
-model: segnn
-num_mp_steps: 10
-latent_dim: 64
-lr_start: 5.e-4
+model: 
+  name: segnn
+  num_mp_steps: 10
+  latent_dim: 64
 
-isotropic_norm: True
+train:
+  isotropic_norm: True
+
+optimizer:
+  lr_start: 5.e-4
+
+logging:
+  wandb_project: ldc_3d
+
+neighbors:
+  multiplier: 2.0