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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
49e0299
Apply suggestions from code review
JoshuaLampert Nov 5, 2023
9b00891
put LocalPreferences.toml in code font
JoshuaLampert Nov 5, 2023
ae1f987
Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 5, 2023
077b8f6
Merge branch 'main' into docs-custom-mpi-hdf5
ranocha Nov 7, 2023
bc0b476
Merge branch 'main' into docs-custom-mpi-hdf5
JoshuaLampert Nov 7, 2023
af508a6
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
f857f59
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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33 changes: 17 additions & 16 deletions docs/src/parallelization.md
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Expand Up @@ -53,24 +53,25 @@ 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
`--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
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
`[MPIPreferences]`, `[T8code]` and `[P4est]` as well as an entry `MPIPreferences` in your
Project.toml to use a custom MPI installation. A `LocalPreferences.toml` file
In total, in your active Julia project you should have a `LocalPreferences.toml` file with sections
`[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
created as described above might look something like the following:
```toml
[HDF5]
Expand Down Expand Up @@ -218,7 +219,7 @@ julia> HDF5.API.set_libraries!("/path/to/your/libhdf5.so", "/path/to/your/libhdf
```
For more information see also the
[documentation of HDF5.jl](https://juliaio.github.io/HDF5.jl/stable/mpi/). In total, you should
have a file called LocalPreferences.toml in the project directory that contains a section
have a file called `LocalPreferences.toml` in the project directory that contains a section
`[MPIPreferences]`, a section `[HDF5]` with entries `libhdf5` and `libhdf5_hl`, a section `[P4est]`
with the entry `libp4est` as well as a section `[T8code]` with the entries `libt8`, `libp4est`
and `libsc`.
Expand Down