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Extending DOLFINx with checkpointing functionality

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# ADIOS4DOLFINx - A framework for checkpointing in DOLFINx

![MIT](https://img.shields.io/github/license/jorgensd/adios4dolfinx)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06451/status.svg)](https://doi.org/10.21105/joss.06451)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/adios4dolfinx/badges/version.svg)](https://anaconda.org/conda-forge/adios4dolfinx)

ADIOS4DOLFINx is an extension for [DOLFINx](https://github.com/FEniCS/dolfinx/) to checkpoint meshes, meshtags and functions using [ADIOS 2](https://adios2.readthedocs.io/en/latest/).

The code uses the ADIOS2 Python-wrappers to write DOLFINx objects to file, supporting N-to-M (_recoverable_) and N-to-N (_snapshot_) checkpointing.
See: [Checkpointing in DOLFINx - FEniCS 23](https://jsdokken.com/checkpointing-presentation/#/) or the examples in the [Documentation](https://jsdokken.com/adios4dolfinx/) for more information.

For scalability, the code uses [MPI Neighbourhood collectives](https://www.mpi-forum.org/docs/mpi-3.1/mpi31-report/node200.htm) for communication across processes.

## Statement of Need

As the usage of high performance computing clusters increases, more and more large-scale, long-running simulations are deployed.
The need for storing intermediate solutions from such simulations are crucial, as the HPC system might crash, or the simulation might crash or exceed the alloted computational budget.
Having a checkpoint of related variables, such as the solutions to partial differential equations (PDEs) is therefore essential.
The `adios4dolfinx` library extends the [DOLFINx](https://github.com/FEniCS/dolfinx/) computational framework for solving PDEs with checkpointing functionality, such that immediate solutions and mesh information can be stored and re-used in another simulation.

## Installation

Compatibility with DOLFINx:

- ADIOS4DOLFINx v0.11.0 is compatible with DOLFINx v0.11.x
- ADIOS4DOLFINx v0.10.0 is compatible with DOLFINx v0.10.x
- ADIOS4DOLFINx v0.9.6 is compatible with DOLFINx v0.9.x
- ADIOS4DOLFINx v0.8.1 is compatible with DOLFINx v0.8.x
- ADIOS4DOLFINx v0.7.3 is compatible with DOLFINx v0.7.x

### Dependencies

The library depends on the Python-interface of [DOLFINx](https://github.com/) and an MPI-build of [ADIOS2](https://adios2.readthedocs.io/en/latest/setting_up/setting_up.html#as-package).
Therefore `ADIOS2` should not be install through PYPI/pip, but has to be installed through Conda, Spack or from source.

> [!IMPORTANT]  
> ADIOS2<2.10.2 does not work properly with `numpy>=2.0.0`. Everyone is advised to use the newest version of ADIOS2.
> This is for instance available through `conda` or the `ghcr.io/fenics/dolfinx/dolfinx:nightly` Docker-image.

### Spack

ADIOS4DOLFINx is a [spack package](https://packages.spack.io/package.html?name=py-adios4dolfinx)
which can be installed with

```bash
spack add py-adios4dolfinx ^py-fenics-dolfinx+petsc4py+slepc4py
spack concretize
spack install
```

once you have downloaded spack and set up a new environment, as described in [Spack: Installation notes](https://github.com/spack/spack?tab=readme-ov-file#installation).
To ensure that the spack packages are up to date, please call

```bash
spack repo update builtin
```

prior to concretizing.

### Docker

An MPI build of ADIOS2 is installed in the official DOLFINx containers, and thus there are no additional dependencies required to install `adios4dolfinx`
on top of DOLFINx in these images.

Create a Docker container, named for instance `dolfinx-checkpoint`.
Use the `nightly` tag to get the main branch of DOLFINx, or `stable` to get the latest stable release

```bash
docker run -ti -v $(pwd):/root/shared -w /root/shared --name=dolfinx-checkpoint ghcr.io/fenics/dolfinx/dolfinx:nightly
```

For the latest version compatible with nightly (with the ability to run the test suite), use

```bash
python3 -m pip install adios4dolfinx[test]@git+https://github.com/jorgensd/adios4dolfinx@main
```

If you are using the `stable` image, you can install `adios4dolfinx` from [PYPI](https://pypi.org/project/adios4dolfinx/) with

```bash
python3 -m pip install adios4dolfinx[test]
```

This docker container can be opened with

```bash
docker container start -i dolfinx-checkpoint
```

at a later instance

### Conda

> [!NOTE]  
> Conda supports the stable release of DOLFINx, and thus the appropriate version should be installed, see the section above for more details.

Following is a minimal recipe of how to install adios4dolfinx, given that you have conda installed on your system.

```bash
conda create -n dolfinx-checkpoint python=3.10
conda activate dolfinx-checkpoint
conda install -c conda-forge adios4dolfinx
```

> [!NOTE]
> Remember to download the appropriate version of `adios4dolfinx` from Github [adios4dolfinx: Releases](https://github.com/jorgensd/adios4dolfinx/releases)

To run the test suite, you should also install `ipyparallel`, `pytest` and `coverage`, which can all be installed with conda

```bash
conda install -c conda-forge ipyparallel pytest coverage
```

## Functionality

### DOLFINx

- Reading and writing meshes, using `adios4dolfinx.read/write_mesh`
- Reading and writing meshtags associated to meshes `adios4dolfinx.read/write_meshtags`
- Reading checkpoints for any element (serial and parallel, arbitrary number of functions and timesteps per file). Use `adios4dolfinx.read/write_function`.
- Writing standalone function checkpoints relating to "original meshes", i.e. meshes read from `XDMFFile`. Use `adios4dolfinx.write_function_on_input_mesh` for this.
- Store mesh partitioning and re-read the mesh with this information, avoiding calling SCOTCH, Kahip or Parmetis.

> [!IMPORTANT]  
> For checkpoints written with `write_function` to be valid, you first have to store the mesh with `write_mesh` to the checkpoint file.

> [!IMPORTANT]  
> A checkpoint file supports multiple functions and multiple time steps, as long as the functions are associated with the same mesh

> [!IMPORTANT]  
> Only one mesh per file is allowed

## Example Usage

The repository contains many documented examples of usage, in the `docs`-folder, including

- [Reading and writing mesh checkpoints](./docs/writing_mesh_checkpoint.py)
- [Storing mesh partitioning data](./docs/partitioned_mesh.py)
- [Writing mesh-tags to a checkpoint](./docs/meshtags.py)
- [Reading and writing function checkpoints](./docs/writing_functions_checkpoint.py)
- [Checkpoint on input mesh](./docs/original_checkpoint.py)
  Further examples can be found at [ADIOS4DOLFINx examples](https://jsdokken.com/adios4dolfinx/)

### Backwards compatibility

> [!WARNING]
> If you are using v0.7.2, you are advised to upgrade to v0.7.3, as it contains som crucial fixes for openmpi.

### Legacy DOLFIN

Only checkpoints for `Lagrange` or `DG` functions are supported from legacy DOLFIN

- Reading meshes from the DOLFIN HDF5File-format
- Reading checkpoints from the DOLFIN HDF5File-format (one checkpoint per file only)
- Reading checkpoints from the DOLFIN XDMFFile-format (one checkpoint per file only, and only uses the `.h5` file)

See the [API](./docs/api) for more information.

## Testing

This library uses `pytest` for testing.
To execute the tests, one should first install the library and its dependencies, as listed above.
Then, can execute all tests by calling

```bash
python3 -m pytest .
```

### Testing against data from legacy dolfin

Some tests check the capability of reading data created with the legacy version of DOLFIN.
To create this dataset, start a docker container with legacy DOLFIN, for instance:

```bash
docker run -ti -v $(pwd):/root/shared -w /root/s
hared --rm ghcr.io/scientificcomputing/fenics:2024-02-19
```

Then, inside this container, call

```bash
python3 ./tests/create_legacy_data.py --output-dir=legacy
```

### Testing against data from older versions of ADIOS4DOLFINx

Some tests check the capability to read data generated by `adios4dolfinx<0.7.2`.
To generate data for these tests use the following commands:

```bash
docker run -ti -v $(pwd):/root/shared -w /root/shared --rm ghcr.io/fenics/dolfinx/dolfinx:v0.7.3
```

Then, inside the container, call

```bash
python3 -m pip install adios4dolfinx==0.7.1
python3 ./tests/create_legacy_checkpoint.py --output-dir=legacy_checkpoint
```

## Long term plan

The long term plan is to get this library merged into DOLFINx (rewritten in C++ with appropriate Python-bindings).

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