adios4dolfinx 0.8.0.dev0__tar.gz → 0.8.1.post0__tar.gz

adios4dolfinx-0.8.1.post0/PKG-INFO

@@ -0,0 +1,208 @@
+Metadata-Version: 2.1
+Name: adios4dolfinx
+Version: 0.8.1.post0
+Summary: Checkpointing functionality for DOLFINx meshes/functions with ADIOS2
+Author-email: "Jørgen S. Dokken" <dokken@simula.no>
+License: Copyright 2023 Jørgen S. Dokken
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+        
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fenics-dolfinx>=0.8.0
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: ipyparallel; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: jupyter-book; extra == "docs"
+Requires-Dist: ipyparallel; extra == "docs"
+Requires-Dist: ipywidgets; extra == "docs"
+Provides-Extra: all
+Requires-Dist: adios4dolfinx[dev,docs,test]; extra == "all"
+
+# ADIOS4DOLFINx - A framework for checkpointing in DOLFINx
+
+![MIT](https://img.shields.io/github/license/jorgensd/adios4dolfinx)
+[![status](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25/status.svg)](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25)
+[![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 v0.8.1 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.
+
+### 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 adviced 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).

adios4dolfinx-0.8.1.post0/README.md

@@ -0,0 +1,176 @@
+# ADIOS4DOLFINx - A framework for checkpointing in DOLFINx
+
+![MIT](https://img.shields.io/github/license/jorgensd/adios4dolfinx)
+[![status](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25/status.svg)](https://joss.theoj.org/papers/7866cb142db8a803e32d79a109573d25)
+[![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 v0.8.1 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.
+
+### 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 adviced 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).

{adios4dolfinx-0.8.0.dev0 → adios4dolfinx-0.8.1.post0}/pyproject.toml

@@ -3,12 +3,12 @@ requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
 name = "adios4dolfinx"
-version = "0.8.0.dev0"
+version = "0.8.1.post0"
 description = "Checkpointing functionality for DOLFINx meshes/functions with ADIOS2"
 authors = [{ name = "Jørgen S. Dokken", email = "dokken@simula.no" }]
 license = { file = "LICENSE" }
 readme = "README.md"
-dependencies = ["fenics-dolfinx>=0.8.0.dev0"]
+dependencies = ["fenics-dolfinx>=0.8.0"]
 
 [project.optional-dependencies]
 test = ["pytest", "coverage", "ipyparallel"]

{adios4dolfinx-0.8.0.dev0 → adios4dolfinx-0.8.1.post0}/src/adios4dolfinx/adios2_helpers.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from contextlib import contextmanager
 from pathlib import Path
-from typing import NamedTuple
+from typing import NamedTuple, Union
 
 from mpi4py import MPI
 
@@ -44,7 +44,7 @@ class AdiosFile(NamedTuple):
 @contextmanager
 def ADIOSFile(
     adios: adios2.ADIOS,
-    filename: Path | str,
+    filename: Union[Path, str],
     engine: str,
     mode: adios2.Mode,
     io_name: str,
@@ -62,7 +62,7 @@ def ADIOSFile(
 def read_cell_perms(
     adios: adios2.ADIOS,
     comm: MPI.Intracomm,
-    filename: Path | str,
+    filename: Union[Path, str],
     variable: str,
     num_cells_global: np.int64,
     engine: str,
@@ -126,12 +126,12 @@ def read_cell_perms(
 def read_adjacency_list(
     adios: adios2.ADIOS,
     comm: MPI.Intracomm,
-    filename: Path | str,
+    filename: Union[Path, str],
     dofmap: str,
     dofmap_offsets: str,
     num_cells_global: np.int64,
     engine: str,
-) -> dolfinx.cpp.graph.AdjacencyList_int64 | dolfinx.cpp.graph.AdjacencyList_int32:
+) -> Union[dolfinx.cpp.graph.AdjacencyList_int64, dolfinx.cpp.graph.AdjacencyList_int32]:
     """
     Read an adjacency-list from an ADIOS file with given communicator.
     The adjancency list is split in to a flat array (data) and its corresponding offset.
@@ -205,7 +205,7 @@ def read_adjacency_list(
 
 def read_array(
     adios: adios2.ADIOS,
-    filename: Path | str,
+    filename: Union[Path, str],
     array_name: str,
     engine: str,
     comm: MPI.Intracomm,

{adios4dolfinx-0.8.0.dev0 → adios4dolfinx-0.8.1.post0}/src/adios4dolfinx/checkpointing.py

@@ -6,6 +6,7 @@
 
 from __future__ import annotations
 
+import typing
 from pathlib import Path
 
 from mpi4py import MPI
@@ -30,13 +31,20 @@ from .comm_helpers import (
     send_dofs_and_recv_values,
 )
 from .structures import FunctionData, MeshData
-from .utils import compute_dofmap_pos, compute_local_range, index_owner, unroll_dofmap
+from .utils import (
+    compute_dofmap_pos,
+    compute_local_range,
+    index_owner,
+    unroll_dofmap,
+    unroll_insert_position,
+)
 from .writers import write_function as _internal_function_writer
 from .writers import write_mesh as _internal_mesh_writer
 
 adios2 = resolve_adios_scope(adios2)
 
 __all__ = [
+    "read_mesh_data",
     "read_mesh",
     "write_function",
     "read_function",
@@ -49,7 +57,7 @@ __all__ = [
 
 
 def write_attributes(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     comm: MPI.Intracomm,
     name: str,
     attributes: dict[str, np.ndarray],
@@ -64,6 +72,7 @@ def write_attributes(
         attributes: Dictionary of attributes to write to file
         engine: ADIOS2 engine to use
     """
+
     adios = adios2.ADIOS(comm)
     with ADIOSFile(
         adios=adios,
@@ -82,7 +91,7 @@ def write_attributes(
 
 
 def read_attributes(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     comm: MPI.Intracomm,
     name: str,
     engine: str = "BP4",
@@ -97,7 +106,6 @@ def read_attributes(
     Returns:
         The attributes
     """
-
     adios = adios2.ADIOS(comm)
     with ADIOSFile(
         adios=adios,
@@ -117,11 +125,11 @@ def read_attributes(
 
 
 def write_meshtags(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     mesh: dolfinx.mesh.Mesh,
     meshtags: dolfinx.mesh.MeshTags,
     engine: str = "BP4",
-    meshtag_name: str | None = None,
+    meshtag_name: typing.Optional[str] = None,
 ):
     """
     Write meshtags associated with input mesh to file.
@@ -196,7 +204,7 @@ def write_meshtags(
 
 
 def read_meshtags(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     mesh: dolfinx.mesh.Mesh,
     meshtag_name: str,
     engine: str = "BP4",
@@ -276,8 +284,8 @@ def read_meshtags(
         adios_file.file.PerformGets()
         adios_file.file.EndStep()
 
-    local_entities, local_values = dolfinx.cpp.io.distribute_entity_data(
-        mesh._cpp_object, int(dim), mesh_entities, tag_values
+    local_entities, local_values = dolfinx.io.distribute_entity_data(
+        mesh, int(dim), mesh_entities.astype(np.int32), tag_values
     )
     mesh.topology.create_connectivity(dim, 0)
     mesh.topology.create_connectivity(dim, mesh.topology.dim)
@@ -293,12 +301,12 @@ def read_meshtags(
 
 
 def read_function(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     u: dolfinx.fem.Function,
     engine: str = "BP4",
     time: float = 0.0,
     legacy: bool = False,
-    name: str | None = None,
+    name: typing.Optional[str] = None,
 ):
     """
     Read checkpoint from file and fill it into `u`.
@@ -376,18 +384,27 @@ def read_function(
         input_perms = read_cell_perms(
             adios, comm, filename, "CellPermutations", num_cells_global, engine
         )
+        # Start by sorting data array by cell permutation
+        num_dofs_per_cell = input_dofmap.offsets[1:] - input_dofmap.offsets[:-1]
+        assert np.allclose(num_dofs_per_cell, num_dofs_per_cell[0])
+
+        # Sort dofmap by input local cell index
+        input_perms_sorted = input_perms[input_local_cell_index]
+        unrolled_dofmap_position = unroll_insert_position(
+            input_local_cell_index, num_dofs_per_cell[0]
+        )
+        dofmap_sorted_by_input = recv_array[unrolled_dofmap_position]
 
         # First invert input data to reference element then transform to current mesh
-        for i, l_cell in enumerate(input_local_cell_index):
-            start, end = input_dofmap.offsets[l_cell : l_cell + 2]
-            # FIXME: Tempoary cast uint32 to integer as transformations
-            # doesn't support uint32 with the switch to nanobind
-            element.pre_apply_transpose_dof_transformation(
-                recv_array[int(start) : int(end)], int(input_perms[l_cell]), bs
-            )
-            element.pre_apply_inverse_transpose_dof_transformation(
-                recv_array[int(start) : int(end)], int(inc_perms[i]), bs
-            )
+        element.Tt_apply(dofmap_sorted_by_input, input_perms_sorted, bs)
+        element.Tt_inv_apply(dofmap_sorted_by_input, inc_perms, bs)
+        # Compute invert permutation
+        inverted_perm = np.empty_like(unrolled_dofmap_position)
+        inverted_perm[unrolled_dofmap_position] = np.arange(
+            len(unrolled_dofmap_position), dtype=inverted_perm.dtype
+        )
+        recv_array = dofmap_sorted_by_input[inverted_perm]
+
     # ------------------Step 6----------------------------------------
     # For each dof owned by a process, find the local position in the dofmap.
     V = u.function_space
@@ -419,17 +436,17 @@ def read_function(
     u.x.scatter_forward()
 
 
-def read_mesh(
-    filename: Path | str,
+def read_mesh_data(
+    filename: typing.Union[Path, str],
     comm: MPI.Intracomm,
     engine: str = "BP4",
     ghost_mode: dolfinx.mesh.GhostMode = dolfinx.mesh.GhostMode.shared_facet,
     time: float = 0.0,
     legacy: bool = False,
     read_from_partition: bool = False,
-) -> dolfinx.mesh.Mesh:
+) -> tuple[np.ndarray, np.ndarray, ufl.Mesh, typing.Callable]:
     """
-    Read an ADIOS2 mesh into DOLFINx.
+    Read an ADIOS2 mesh data for use with DOLFINx.
 
     Args:
         filename: Path to input file
@@ -441,7 +458,7 @@ def read_mesh(
         legacy: If checkpoint was made prior to time-dependent mesh-writer set to True
         read_from_partition: Read mesh with partition from file
     Returns:
-        The distributed mesh
+        The mesh topology, geometry, UFL domain and partition function
     """
     adios = adios2.ADIOS(comm)
 
@@ -552,7 +569,45 @@ def read_mesh(
     else:
         partitioner = dolfinx.cpp.mesh.create_cell_partitioner(ghost_mode)
 
-    return dolfinx.mesh.create_mesh(comm, mesh_topology, mesh_geometry, domain, partitioner)
+    return mesh_topology, mesh_geometry, domain, partitioner
+
+
+def read_mesh(
+    filename: typing.Union[Path, str],
+    comm: MPI.Intracomm,
+    engine: str = "BP4",
+    ghost_mode: dolfinx.mesh.GhostMode = dolfinx.mesh.GhostMode.shared_facet,
+    time: float = 0.0,
+    legacy: bool = False,
+    read_from_partition: bool = False,
+) -> dolfinx.mesh.Mesh:
+    """
+    Read an ADIOS2 mesh into DOLFINx.
+
+    Args:
+        filename: Path to input file
+        comm: The MPI communciator to distribute the mesh over
+        engine: ADIOS engine to use for reading (BP4, BP5 or HDF5)
+        ghost_mode: Ghost mode to use for mesh. If `read_from_partition`
+            is set to `True` this option is ignored.
+        time: Time stamp associated with mesh
+        legacy: If checkpoint was made prior to time-dependent mesh-writer set to True
+        read_from_partition: Read mesh with partition from file
+    Returns:
+        The distributed mesh
+    """
+    return dolfinx.mesh.create_mesh(
+        comm,
+        *read_mesh_data(
+            filename,
+            comm,
+            engine=engine,
+            ghost_mode=ghost_mode,
+            time=time,
+            legacy=legacy,
+            read_from_partition=read_from_partition,
+        ),
+    )
 
 
 def write_mesh(
@@ -654,12 +709,12 @@ def write_mesh(
 
 
 def write_function(
-    filename: Path | str,
+    filename: typing.Union[Path, str],
     u: dolfinx.fem.Function,
     engine: str = "BP4",
     mode: adios2.Mode = adios2.Mode.Append,
     time: float = 0.0,
-    name: str | None = None,
+    name: typing.Optional[str] = None,
 ):
     """
     Write function checkpoint to file.