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Update docs on system-provided MPI including HDF5 #1706

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Nov 21, 2023
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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
9b00891
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
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
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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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67 changes: 48 additions & 19 deletions docs/src/parallelization.md
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Expand Up @@ -53,30 +53,43 @@ 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
`--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
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
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. If you want to use `p4est` (via the `P4estMesh`) or `t8code` (via the `T8codeMesh`)
from Trixi.jl, you also need to use system-provided `p4est` or `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
`--enable-mpi`). Otherwise, there will be warnings that no preference is set for P4est.jl and
T8code.jl that can be ignored if you do not use these libraries from Trixi.jl. Note that
`t8code` already comes with a `p4est` installation, so it suffices to install `t8code`.
In order to use system-provided `p4est` and `t8code` installations, [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
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`. Note that the `T8codeMesh`, however,
does not support MPI yet.
The preferences for [HDF5.jl](https://github.com/JuliaIO/HDF5.jl) always need to be set, even if you
do not want to use `HDF5` from Trixi.jl, see also https://github.com/JuliaIO/HDF5.jl/issues/1079.
To set the preferences for HDF5.jl, follow the instructions described
[here](https://trixi-framework.github.io/Trixi.jl/stable/parallelization/#Using-parallel-input-and-output).

In total, in your active Julia project you should have a `LocalPreferences.toml` file with sections
`[MPIPreferences]`, `[T8code]` (only needed if `T8codeMesh` is used), `[P4est]` (only needed if
`P4estMesh` is used), 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]
libhdf5 = "/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so"
libhdf5_hl = "/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so"

[HDF5_jll]
libhdf5_hl_path = "/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so"
libhdf5_path = "/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so"

[MPIPreferences]
__clear__ = ["preloads_env_switch"]
_format = "1.0"
Expand All @@ -97,6 +110,22 @@ libsc = "/home/mschlott/hackathon/libtrixi/t8code/install/lib/libsc.so"
libt8 = "/home/mschlott/hackathon/libtrixi/t8code/install/lib/libt8.so"
```

This file is created with the following sequence of commands:
```julia
julia> using MPIPreferences
julia> MPIPreferences.use_system_binary()
```
Restart the Julia REPL
```julia
julia> using P4est
julia> P4est.set_library_p4est!("/home/mschlott/hackathon/libtrixi/t8code/install/lib/libp4est.so")
julia> P4est.set_library_sc!("/home/mschlott/hackathon/libtrixi/t8code/install/lib/libsc.so")
julia> using T8code
julia> T8code.set_libraries_path!("/home/mschlott/hackathon/libtrixi/t8code/install/lib/")
julia> using HDF5
julia> HDF5.API.set_libraries!("/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so", "/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so")
```
After the preferences are set, restart the Julia REPL again.

### [Usage](@id parallel_usage)

Expand Down Expand Up @@ -218,7 +247,7 @@ 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
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