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Fix _typed_load fast path for Julia 1.10 (currently nightly) #1075

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merged 4 commits into from
May 30, 2023
Merged

Fix _typed_load fast path for Julia 1.10 (currently nightly) #1075

merged 4 commits into from
May 30, 2023

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@mkitti mkitti commented May 30, 2023 •
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Julia master seems to have removed Base._memcpy!. This is to be expected given that this is a private function.

xref: JuliaLang/julia#49550

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mkitti commented May 30, 2023

@t-bltg I believe you are responsible for adding this initially. Can you revisit this?

@mkitti mkitti marked this pull request as ready for review May 30, 2023 02:04
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mkitti commented May 30, 2023

This should fix nightly. I do want to review this piece of code more carefully though.

@mkitti mkitti merged commit 4957fb8 into JuliaIO:master May 30, 2023
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ranocha commented Aug 18, 2023

@mkitti It looks like there is no new release of HDF5.jl including this fix? At least we get

  Got exception outside of a @test
  LoadError: UndefVarError: `_memcpy!` not defined
  Stacktrace:
    [1] _generic_read(::HDF5.Dataset, ::HDF5.Datatype, ::Type{Cstring}, ::Nothing)
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/readwrite.jl:197
    [2] generic_read(::HDF5.Dataset, ::HDF5.Datatype, ::Type{Cstring})
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/readwrite.jl:134
    [3] read(obj::HDF5.Dataset)
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/readwrite.jl:39
    [4] (::Trixi.var"#282#299")(file::HDF5.File)
      @ Trixi ~/work/Trixi.jl/Trixi.jl/src/meshes/mesh_io.jl:308
    [5] (::HDF5.var"#17#18"{HDF5.HDF5Context, @Kwargs{}, Trixi.var"#282#299", HDF5.File})()
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/file.jl:98
    [6] task_local_storage(body::HDF5.var"#17#18"{HDF5.HDF5Context, @Kwargs{}, Trixi.var"#282#299", HDF5.File}, key::Symbol, val::HDF5.HDF5Context)
      @ Base ./task.jl:297
    [7] #h5open#16
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/file.jl:93 [inlined]
    [8] h5open(filename::String, mode::String)
      @ HDF5 ~/.julia/packages/HDF5/aiZLs/src/file.jl:91 [inlined]
...

in our CI runs testing Julia v1.10.0-beta2, see https://github.com/trixi-framework/Trixi.jl/actions/runs/5898667882/job/16000054066?pr=1562#step:7:2270
It would be great to be able to use HDF5.jl on Julia v1.10 once it's released

@ranocha ranocha mentioned this pull request Aug 18, 2023
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mkitti commented Aug 18, 2023

Sorry. I'm working on a breaking release. Targeting Monday in ~96 hours.

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ranocha commented Aug 18, 2023

Great, thanks a lot! I'm looking forward to it

@mkitti mkitti mentioned this pull request Aug 20, 2023
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mkitti commented Aug 20, 2023

I'm planning a 0.16.16 release to fix this sooner than 0.17:
#1098

mkitti added a commit that referenced this pull request Aug 23, 2023
@mkitti @simonbyrne
@musm @stevengj
Port non-breaking changes for 0.16.16 (#1098)
c52831e 
* Fix _typed_load fast path for Julia 1.10 (currently nightly) (#1075)

* Fix _typed_load fast path for Julia 1.10 (currently nightly) by thresholding on `1.10.0-DEV.1390`
* Use `Libc.memcpy` after that threshold

* Add initial support for H5Dchunk_iter (#1031)

* Add initial support for H5Dchunk_iter

* Implement h5d_chunk_iter_helper

* Implement HDF5.get_all_chunk_info

* Make tests pass via HDF5 1.14.0

* Apply formatting

* Test filters with filter_mask via H5Dchunk_iter

* Require functions to return an integer

* Provide index based chunk iteration, rename to HDF5.get_chunk_info_all

* Fix formatting

* Fix documentation

* Fix documentation

* Improve testing

* Always define _get_chunk_info_all_by_iter for documenter

* Update src/datasets.jl

Co-authored-by: Simon Byrne <[email protected]>

* Precompile get_chunk_info_all implementations before benchmarking

* Fix documentation

* Fix tests

* Formatting

---------

Co-authored-by: Simon Byrne <[email protected]>

* Simplify formatter check (#1078)

This will display the diff, and return a non-zero exit code if there are changes

* Fix #1083 maxdims -> max_dims in dataspace documentation (#1085)

* Update light and dark logos for readme (#1087)

* Fixup readme logo links and readme style (#1088)

* Fixup readme logo links and readme style

* Tweak

* Tweak logo centering

* Upload curves directly instead of fonts for logo independence (#1089)

* Allow create_dataset to take a Type and Dataspace, Fix #1084 (#1086)

* Fix #1083 maxdims -> max_dims in dataspace documentation

* Fix #1084, create_dataset with Type and Dataspace

Also expand definitions for dataspace with two positional arguments.
Pin Blosc_jll to 1.21.2 if AVX2 is not detected. See Blosc/c-blosc#371

* Formatter

* Attempt to fix documentation (#1091)

* doc typo: attributes(parent), not attribute(parent) (#1095)

* Fix tests for Julia 1.3

* Fix tests for Julia 1.3, Windows SZIP is broken again

* Use static if block to fix 1.3

* Fix version and formatting

* Fix tests

* Bump version to 0.16.16

* Formatting

---------

Co-authored-by: Simon Byrne <[email protected]>
Co-authored-by: Mustafa M <[email protected]>
Co-authored-by: Steven G. Johnson <[email protected]>
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@mkitti @ranocha