mosaic-bench 0.1.0__tar.gz

mosaic_bench-0.1.0/.gitignore

@@ -0,0 +1,57 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+*.egg
+dist/
+build/
+*.so
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Quarto
+_site/
+.quarto/
+docs/solvers.qmd
+
+# LaTeX
+*.aux
+*.bbl
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.out
+*.synctex.gz
+*.pdf
+
+# Benchmark results (default output of `mosaic run`)
+mosaic-results/
+
+# Tesseract build artifacts
+*.whl
+
+# Misc
+.env
+.claude/
+uv.lock
+
+/.quarto/
+
+# Version file (auto-generated)
+mosaic/_version.py

mosaic_bench-0.1.0/LICENSE

@@ -0,0 +1,200 @@
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mosaic_bench-0.1.0/PKG-INFO

@@ -0,0 +1,278 @@
+Metadata-Version: 2.4
+Name: mosaic-bench
+Version: 0.1.0
+Summary: A benchmark suite for differentiable physics solvers
+Project-URL: Homepage, https://github.com/pasteurlabs/mosaic
+Project-URL: Documentation, https://docs.pasteurlabs.ai/projects/mosaic/latest
+Author-email: "The Mosaic team @ Pasteur Labs + OSS contributors" <info@simulation.science>
+License: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: docker>=6
+Requires-Dist: filelock>=3
+Requires-Dist: jax[cpu]
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: nvidia-ml-py
+Requires-Dist: optax
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: pyyaml
+Requires-Dist: rich>=13.0
+Requires-Dist: tesseract-core[runtime]>=1.9.0
+Requires-Dist: tesseract-jax
+Requires-Dist: typer>=0.12
+Provides-Extra: dev
+Requires-Dist: mosaic-shared; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pyyaml; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Description-Content-Type: text/markdown
+
+![logo](logo.png)
+
+# Mosaic: a benchmark suite for differentiable physics solvers
+
+Mosaic measures gradient quality, computational cost, and solver compatibility across 14 differentiable physics solvers in 4 domains. Each solver is packaged as a [Tesseract](https://github.com/pasteurlabs/tesseract-core) container exposing a uniform `apply` / `vjp` interface, enabling cross-solver comparison regardless of language or AD backend.
+
+### Why Mosaic?
+
+Differentiable physics solvers unlock gradient-based optimization for topology optimization, aerodynamic design, optimal control, and solver-in-the-loop ML. But the practical cost of obtaining correct gradients is largely undocumented: solvers span multiple languages and AD frameworks, runtime overhead varies by orders of magnitude, and subtle numerical issues (ill-conditioned Jacobians, chaotic divergence, floating-point truncation) can silently corrupt gradients. Mosaic provides a standardized, solver-agnostic evaluation that surfaces these practically relevant differences so practitioners can make informed choices.
+
+<p align="center"><img src="visual_abstract.png" width="100%" alt="Overview of Mosaic: diverse solver backends are wrapped behind a uniform containerized interface (Tesseract), enabling cross-solver comparison on shared benchmark tasks across different physical domains."></p>
+
+| ID     | Domain                     | Optimization task              | Solvers                                                |
+| :----- | :------------------------- | :----------------------------- | :----------------------------------------------------- |
+| **H**  | Heat transfer              | Conductivity inversion         | deal.II, FEniCS, Firedrake, JAX-FEM, torch-fem         |
+| **S**  | Structural mechanics       | Compliance minimization (SIMP) | deal.II, FEniCS, Firedrake, JAX-FEM, TopOpt.jl         |
+| **F2** | Incompressible fluids (2D) | Inflow optimization (drag)     | JAX-CFD, PhiFlow, INS.jl, XLB, PICT, Warp-NS, OpenFOAM |
+| **F3** | 3D Navier-Stokes           | Initial condition recovery     | PhiFlow, XLB, PICT, Warp-NS, Exponax, INS.jl, OpenFOAM |
+
+### 📊 [Browse the latest benchmark results →](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_ns_grid.html)
+
+Per-domain pages with every plot, solver rankings, and the full evaluation protocol, refreshed on each release:
+[Navier–Stokes 2D](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_ns_grid.html) ·
+[Navier–Stokes 3D](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_ns_3d_grid.html) ·
+[Structural mechanics](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_structural_mesh.html) ·
+[Heat transfer](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_thermal_mesh.html)
+
+---
+
+> **Paper reproduction:** if you're here to reproduce the results from [our paper](https://arxiv.org/abs/XXXX.XXXXX), see the [`v0.1+paper-repro`](https://github.com/pasteurlabs/mosaic/tree/v0.1+paper-repro) tag which contains the figure-generation code, pinned dependencies, and step-by-step instructions.
+
+**Jump to your use case:**
+
+- [Browse the results](https://docs.pasteurlabs.ai/projects/mosaic/latest/docs/results_ns_grid.html) — see how the solvers compare, no setup required
+- [Run the benchmarks](#run-the-benchmarks) — run solvers and inspect results
+- [Use Tesseracts in your own code](#use-tesseracts-in-your-own-code) — researcher building on Mosaic solvers
+- [Contribute](#contribute) — add a solver, tune a configuration, or extend to a new domain
+
+---
+
+## Run the benchmarks
+
+Requires Python >= 3.10, Docker, and (for GPU solvers) the [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html).
+
+> **Platform note:** We strongly recommend **Linux with Docker Engine** for the best experience. Docker Desktop on macOS and Windows runs containers inside a VM, which adds significant overhead to solver execution and can surface ARM-related compatibility issues on Apple Silicon. If you're on macOS or Windows, consider using a Linux VM or WSL 2 with Docker Engine installed natively inside it.
+
+```bash
+git clone https://github.com/pasteurlabs/mosaic && cd mosaic
+uv sync          # or: pip install -e .
+mosaic run       # builds containers, runs experiments, generates plots
+```
+
+A single-problem run with `--debug` (reduced grid sizes) finishes in minutes and is a good way to verify your setup:
+
+```bash
+$ mosaic run -p thermal-mesh --suites forward --debug
+──────────────────────────── problem: thermal-mesh ─────────────────────────────
+──────────────────────────────────── build ─────────────────────────────────────
+  deal.II          → dealii_heat_thermal_mesh:latest     (3.6s)
+  FEniCS           → fenics_heat_thermal_mesh:latest     (3.2s)
+  Firedrake        → firedrake_heat_thermal_mesh:latest  (2.4s)
+  JAX-FEM          → jax_fem_thermal_mesh:latest         (5.1s)
+  torch-fem        → torch_fem_thermal_mesh:latest       (4.8s)
+───────────────────────────────   suite: forward ───────────────────────────────
+  5 experiment(s) queued, 5 solver(s) registered
+────────────────────────── experiment: baseline [1/5] ──────────────────────────
+  deal.II done in 0.8s
+  FEniCS done in 1.2s
+  Firedrake done in 1.5s
+  JAX-FEM done in 2.3s
+  torch-fem done in 1.1s
+...
+─────────────────────────────────── summary ────────────────────────────────────
+┏━━━━━━━━━━━━━━┳━━━━━━━━━┓
+┃ problem      ┃ forward ┃
+┡━━━━━━━━━━━━━━╇━━━━━━━━━┩
+│ thermal-mesh │   ok    │
+└──────────────┴─────────┘
+```
+
+### Inspect results
+
+```bash
+mosaic status                        # per-experiment completion table
+mosaic status -p ns-grid -f          # single domain with failure reasons
+mosaic status --format md > report.md
+mosaic status --format json > snap.json
+```
+
+### Pick which solvers run
+
+`-s` (alias `--solvers`) takes either a flat CSV applied as a union
+across every problem, or a per-problem map for finer control:
+
+```bash
+# Flat CSV — each problem keeps only the listed solvers that exist
+# there; problems with zero matches are skipped.
+mosaic run -s OpenFOAM,XLB,deal.II,JAX-FEM
+
+# Per-problem map — explicit picks per domain.
+mosaic run -s "ns-grid=XLB,jax-cfd;structural-mesh=Firedrake,JAX-FEM"
+```
+
+### Re-run a subset
+
+After an initial pass, `mosaic run --only <state[,…]>` re-executes only
+the cells currently in the given state and leaves fresh-ok cells alone.
+Useful for iterating on a single solver or recovering from a partial
+failure without redoing everything.
+
+```bash
+mosaic run --only failed              # re-run only failed cells
+mosaic run --only failed,stale        # plus anything the harness/source has invalidated
+mosaic run --only missing             # first-time runs only
+mosaic run -s PhiFlow --only excluded # re-check after dropping an exclusion
+```
+
+States: `failed`, `anom`, `missing`, `stale`, `excluded`. Combinable
+with `-p / --suites / -e / -s` for finer scoping.
+
+---
+
+## Use Tesseracts in your own code
+
+Every solver in Mosaic is a standalone [Tesseract](https://github.com/pasteurlabs/tesseract-core) that you can call from your own research code — no benchmark harness required.
+
+### Install
+
+```bash
+# Shared schemas (only deps: pydantic + tesseract-core)
+pip install -e mosaic/mosaic_shared
+
+# For containerised usage (recommended): also install tesseract-jax
+pip install tesseract-core tesseract-jax jax
+```
+
+### Option A: Local (no Docker)
+
+Fastest for prototyping. Requires the solver's native Python dependencies.
+
+```python
+import numpy as np
+from tesseract_core import Tesseract
+from mosaic_shared.problems.navier_stokes_grid.schemas import make_vortex_ic
+
+ic = make_vortex_ic(N=64, seed=42)
+inputs = {"v0": ic, "viscosity": np.array([0.01], dtype=np.float32), "steps": 50}
+
+t = Tesseract.from_tesseract_api(
+    "mosaic/tesseracts/navier-stokes-grid/exponax/tesseract_api.py"
+)
+outputs = t.apply(inputs)
+```
+
+### Option B: Via container (requires Docker, fully isolated)
+
+Works for every solver regardless of language. Build the image once, then use it from JAX:
+
+```bash
+$ tesseract build mosaic/tesseracts/navier-stokes-grid/exponax
+```
+
+```python
+import jax
+import jax.numpy as jnp
+from tesseract_core import Tesseract
+from tesseract_jax import apply_tesseract
+from mosaic_shared.problems.navier_stokes_grid.schemas import make_vortex_ic
+
+ic = make_vortex_ic(N=64, seed=42)
+inputs = {"v0": ic, "viscosity": jnp.array([0.01]), "steps": 50}
+
+with Tesseract.from_image("exponax_navier_stokes_grid:latest") as t:
+    outputs = apply_tesseract(t, inputs)
+    grad_v0 = jax.grad(lambda v0: jnp.mean(
+        apply_tesseract(t, {**inputs, "v0": v0})["result"] ** 2
+    ))(inputs["v0"])
+```
+
+See [Standalone Usage](docs/standalone.qmd) for the full guide (GPU usage, mesh-based solvers, common gotchas) and the [Solver Reference](docs/solvers.qmd) for the per-solver catalog with image names.
+
+### Programmatic API
+
+Mosaic also exposes a Python API for running evaluations without the CLI:
+
+```python
+from mosaic import get_config, PROBLEMS
+
+cfg = get_config("ns-grid")           # Problem for 2-D Navier-Stokes
+print(cfg.solver_names)               # available solver backends
+
+# Each (suite, experiment) is registered on the Problem as an Experiment
+# closure. Invoke one directly with a {solver_name: image_tag} mapping:
+tags = {s.name: s.image_tag for s in cfg.solvers}
+results = cfg.experiments["gradient/fd_check"].fn(cfg, tags)
+```
+
+Available top-level imports: `PROBLEMS`, `get_config`, `Problem`, `SolverSpec`, `IcSpec`, and the shared suite-kernel modules `forward`, `gradient`, `cost`, `optimization` (from `mosaic.benchmarks.problems.shared`).
+
+---
+
+## Contribute
+
+Mosaic is designed to grow with the community. There are three ways in, roughly ordered by scope:
+
+- **Tune an existing solver** — improve an out-of-the-box configuration. Snapshot `mosaic status --format json` before/after and include the diff in your PR. See [CONTRIBUTING.md](CONTRIBUTING.md#tuning-an-existing-solver) for the full workflow.
+- **Add a solver** to an existing domain — three files under `mosaic/tesseracts/<domain>/<solver-name>/`. Walkthrough: [Add a Solver tutorial](docs/tutorial-add-solver.qmd).
+- **Add a benchmark domain** — scaffold with `mosaic new-domain <name> --from-template <template>`. Walkthrough: [Add a Domain tutorial](docs/tutorial-add-domain.qmd).
+
+[CONTRIBUTING.md](CONTRIBUTING.md) covers code style, the PR workflow, and how to build the docs locally. For questions and support, visit the [Tesseract Forum](https://si-tesseract.discourse.group/).
+
+## Documentation
+
+- [Getting Started](docs/getting-started.qmd) — prerequisites, installation, first benchmark
+- [Use Mosaic solvers elsewhere](docs/standalone.qmd) — using individual Tesseracts in your own code
+- [Architecture](docs/architecture.qmd) — Tesseract interface, data structures, evaluation protocol
+- [Solver Reference](docs/solvers.qmd) — per-solver documentation with numerical methods, AD strategies, and known limitations
+- [Add a Solver](docs/tutorial-add-solver.qmd) — step-by-step tutorial with a complete working example
+- [Add a Domain](docs/tutorial-add-domain.qmd) — end-to-end walkthrough for a new physics domain
+
+## Project structure
+
+```
+mosaic/
+  benchmarks/             # evaluation harness (Python package: mosaic.benchmarks)
+    cli.py                # command-line interface
+    core/                 # runner, config, hardware detection, solver auto-discovery
+    problems/             # per-domain packages (ns-grid, ns-3d-grid, structural-mesh, thermal-mesh)
+      shared/             # cross-domain suite kernels (forward, gradient, cost, optimization) + plots
+    plots/                # plotting infrastructure
+  templates/              # task templates for scaffolding new domains
+  tesseracts/             # solver backends (each is a Tesseract container)
+    mosaic_shared/     # shared Tesseract interface schemas (also pip-installable)
+      problems/           # per-domain input/output schemas
+      utils/              # comparison metrics, plotting utilities
+    navier-stokes-grid/   # JAX-CFD, PhiFlow, XLB, PICT, Warp-NS, etc.
+    structural-mesh/      # deal.II, FEniCS, Firedrake, JAX-FEM, TopOpt.jl
+    thermal-mesh/         # deal.II, FEniCS, Firedrake, JAX-FEM, torch-fem
+  tests/                  # unit tests (run with pytest)
+docs/                     # Quarto documentation site
+```
+
+## License
+
+Apache 2.0. Individual solver backends retain their upstream licenses, documented per solver in the repository.