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Update docs on system-provided MPI including HDF5 #1706

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Nov 21, 2023
Merged

Update docs on system-provided MPI including HDF5 #1706

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6c314b3
update docs on system-provided MPI including HDF5
JoshuaLampert Nov 4, 2023
1cc618a
fix typo
JoshuaLampert Nov 4, 2023
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Apply suggestions from code review
JoshuaLampert Nov 5, 2023
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put LocalPreferences.toml in code font
JoshuaLampert Nov 5, 2023
ae1f987
Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 5, 2023
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Merge branch 'main' into docs-custom-mpi-hdf5
ranocha Nov 7, 2023
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Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 7, 2023
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add notes when which preferences need to be set
JoshuaLampert Nov 7, 2023
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Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 12, 2023
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Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 19, 2023
6992e07
T8codeMesh does not support MPI yet
JoshuaLampert Nov 19, 2023
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27 changes: 14 additions & 13 deletions docs/src/parallelization.md
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Expand Up @@ -53,23 +53,24 @@ a system-provided MPI installation with Trixi.jl can be found in the following s

### [Using a system-provided MPI installation](@id parallel_system_MPI)

When using Trixi.jl with a system-provided MPI backend the underlying
[`p4est`](https://github.com/cburstedde/p4est) and [`t8code`](https://github.com/DLR-AMR/t8code)
libraries need to be compiled with the same MPI installation. Therefore, you also need to
use system-provided `p4est` and `t8code` installations (for notes on how to install `p4est`
and `t8code` see e.g. [here](https://github.com/cburstedde/p4est/blob/master/README) and
[here](https://github.com/DLR-AMR/t8code/wiki/Installation), use the configure option
When using Trixi.jl with a system-provided MPI backend, the underlying
[`p4est`](https://github.com/cburstedde/p4est), [`t8code`](https://github.com/DLR-AMR/t8code)
and [`hdf5`](https://github.com/HDFGroup/hdf5) libraries need to be compiled with the same MPI
installation. Therefore, you also need to use system-provided `p4est`, `t8code` and `hdf5` installations
(for notes on how to install `p4est` and `t8code` see e.g. [here](https://github.com/cburstedde/p4est/blob/master/README)
and [here](https://github.com/DLR-AMR/t8code/wiki/Installation), use the configure option
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`--enable-mpi`). Note that `t8code` already comes with a `p4est` installation, so it suffices
to install `t8code`. In addition, [P4est.jl](https://github.com/trixi-framework/P4est.jl) and
[T8code.jl](https://github.com/DLR-AMR/T8code.jl) need to be configured to use the custom
installations. Follow the steps described
[here](https://github.com/DLR-AMR/T8code.jl/blob/main/README.md#installation) and
[here](https://github.com/trixi-framework/P4est.jl/blob/main/README.md#installation) for the
configuration. The paths that point to `libp4est.so` (and potentially to `libsc.so`) need to be
to install `t8code`. In addition, [P4est.jl](https://github.com/trixi-framework/P4est.jl),
[T8code.jl](https://github.com/DLR-AMR/T8code.jl) and [HDF5.jl](https://github.com/JuliaIO/HDF5.jl)
need to be configured to use the custom installations. Follow the steps described
[here](https://github.com/DLR-AMR/T8code.jl/blob/main/README.md#installation),
[here](https://github.com/trixi-framework/P4est.jl/blob/main/README.md#installation) and
[here](https://trixi-framework.github.io/Trixi.jl/stable/parallelization/#Using-parallel-input-and-output)
for the configuration. The paths that point to `libp4est.so` (and potentially to `libsc.so`) need to be
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the same for P4est.jl and T8code.jl. This could e.g. be `libp4est.so` that usually can be found
in `lib/` or `local/lib/` in the installation directory of `t8code`.
In total, in your active Julia project you should have a LocalPreferences.toml file with sections
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`[MPIPreferences]`, `[T8code]` and `[P4est]` as well as an entry `MPIPreferences` in your
`[MPIPreferences]`, `[T8code]`, `[P4est]` and `[HDF5]` as well as an entry `MPIPreferences` in your
Project.toml to use a custom MPI installation. A `LocalPreferences.toml` file
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created as described above might look something like the following:
```toml
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