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Switch to Preferences for using system hdf5 #1037

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simonbyrne opened this issue Jan 19, 2023 · 8 comments · Fixed by #1061
Closed

Switch to Preferences for using system hdf5 #1037

simonbyrne opened this issue Jan 19, 2023 · 8 comments · Fixed by #1061

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@simonbyrne
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Technically this is already possible, by overriding the HDF5_jll paths, e.g. https://github.com/CliMA/ClimaCore.jl/blob/3e250b1f75d3bd3f4f7353cb9c1892e318b9e809/.buildkite/JuliaProject.toml

However I'm not sure that this will work on systems where JLL's aren't already available.
@simonbyrne
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Unfortunately setting the HDF5_jll paths can then break other packages, like NetCDF_jll.

@mkitti
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mkitti commented Mar 19, 2023

How so?

@simonbyrne
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Because the library in NetCDF_jll is linked against the library name which includes the version number, and this may not be the same as on the system:
https://buildkite.com/clima/climacore-ci/builds/1880#0186f6b7-490c-4439-8c42-ef21dc99fbed/986-1211

@mkitti
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mkitti commented Mar 19, 2023

Ah yes. That situation is particularly confusing. Would a symlink work? Is there another solution that works better?

@mkitti
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mkitti commented Mar 19, 2023

I'm this particular case perhaps you should just rebuild the NetCDF and HDF5 JLLs... then maintain a fork.

@mkitti
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mkitti commented Mar 19, 2023

Also have we considered using Preferences.jl separately from the JLL override mechanism?

@JoshuaLampert
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What's the status of this issue? It would indeed be nice to switch to Preferences.

@JoshuaLampert JoshuaLampert mentioned this issue Apr 17, 2023
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@simonbyrne
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Also have we considered using Preferences.jl separately from the JLL override mechanism?

This is probably the easiest option for now. PRs welcome?

@JoshuaLampert JoshuaLampert mentioned this issue Apr 19, 2023
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Use Preferences for using custom hdf5 library JoshuaLampert/HDF5.jl
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@simonbyrne @mkitti @JoshuaLampert