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[release-1.9] Backports for Julia 1.9 #50977

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merged 31 commits into from
Nov 7, 2023
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IanButterworth
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@IanButterworth IanButterworth commented Aug 19, 2023

Backported PRs:

Need manual backport:

Contains multiple commits, manual intervention needed:

Non-merged PRs with backport label:

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NHDaly commented Aug 23, 2023

@IanButterworth: Is it common to add Fixes #... to this backport PR?

I wanted to add:

Fixes #50831

since backporting #48720 should close that issue.

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NHDaly commented Aug 23, 2023

Oh and actually, wait, huh, #48720 isn't in the list in this PR anymore. I see that it was at some point, since you tagged it and removed the label?:
Screenshot 2023-08-23 at 12 02 53 PM

But it's not there now. Did you end up backing it out?

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@NHDaly it's in the queue for 1.9.3 already, see https://github.com/JuliaLang/julia/commits/release-1.9

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I'll rebase this as 1.9.3 has been tagged on release-1.9 now and it would be confusing if these commits came before that

DilumAluthgeBot and others added 8 commits August 24, 2023 21:03
…3fa4 (#50976)

Co-authored-by: Dilum Aluthge <dilum@aluthge.com>
fix inference of PackageSpec constructor in presence of imprecise input types (#3585)
If two processes attempt to recursively delete a directory at the same
time, then we can end up in a state where the initial `isdir` is `true`,
but by the time it actually deletes the directory it is already gone.
e.g.
-
https://buildkite.com/clima/climacore-ci/builds/2460#0189d254-76a9-474b-ad25-e5b16440d629/140-142
which is triggered by

https://github.com/cjdoris/PackageExtensionCompat.jl/blob/636eb5a14ddf9134d004c93f598515903af26443/src/PackageExtensionCompat.jl#L59

-
https://buildkite.com/clima/climacore-ci/builds/2457#0189c7fe-8872-40c5-9106-da2e621ff55a/139-150
which is triggered by

https://github.com/JuliaGPU/GPUCompiler.jl/blob/06e670657d7ceebc1845d7c9534a8352c33490de/src/rtlib.jl#L152

I've been conservative and only applied this when `force=true`, but
perhaps it should apply generally?

(cherry picked from commit cbd3c89)
Without this, the task created by a `Channel` will run in the threadpool
of the creating task; in the REPL, this could be the interactive
threadpool.

On 1.8, without threadpools:
```julia
% julia +1.8 -t 8
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.8.5 (2023-01-08)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> for _ in 1:10
           Channel{Int}(1; spawn=true) do _
               Core.print("threadid=$(Threads.threadid())\n")
           end
       end

threadid=2
threadid=5
threadid=2
threadid=2
threadid=1
threadid=6
threadid=7
threadid=8
threadid=3
threadid=4
```

On 1.9, with no interactive threads:
```julia
% julia +1.9 -t 8
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.9.2 (2023-07-05)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> for _ in 1:10
           Channel{Int}(1; spawn=true) do _
               Core.print("threadid=$(Threads.threadid())\n")
           end
       end

threadid=4
threadid=4
threadid=4
threadid=2
threadid=3
threadid=1
threadid=7
threadid=5
threadid=8
threadid=6
```
On 1.9, with an interactive thread:
```julia
% julia +1.9 -t 7,1
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.9.2 (2023-07-05)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> for _ in 1:10
           Channel{Int}(1; spawn=true) do _
               Core.print("threadid=$(Threads.threadid())\n")
           end
       end
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
```

With this PR, the `:default` threadpool is used instead.
```julia
% julia +master -t7,1
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.11.0-DEV.244 (2023-08-09)
 _/ |\__'_|_|_|\__'_|  |  Commit d99f249* (0 days old master)
|__/                   |

julia> for _ in 1:10
           Channel{Int}(1; spawn=true) do _
               Core.print("threadid=$(Threads.threadid())\n")
           end
       end

threadid=7
threadid=6
threadid=7
threadid=7
threadid=6
threadid=3
threadid=5
threadid=2
threadid=4
threadid=8
```
And, the behavior can be overridden.
```julia
% julia +master -t7,1
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.11.0-DEV.244 (2023-08-09)
 _/ |\__'_|_|_|\__'_|  |  Commit d99f249* (0 days old master)
|__/                   |

julia> for _ in 1:10
           Channel{Int}(1; spawn=true, threadpool=:interactive) do _
               Core.print("threadid=$(Threads.threadid())\n")
           end
       end
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
threadid=1
```

---------

Co-authored-by: Nathan Daly <NHDaly@gmail.com>
(cherry picked from commit 555cd23)
Ensure that `isapprox` gives correct results when comparing an integer
with another integer or with a float. For comparison between integers,
the fix only works when keeping default values for `rtol` and `norm`,
and with `atol < 1`.

It is not possible to handle the (atypical) case where `norm !== abs`,
but that's OK since the user is responsible for providing a safe
function.

It would be possible to handle the case where `rtol > 0` or `atol >= 1`,
but with complex code which would check for overflow and handle all
possible corner cases; it would work only for types defined in Base and
would not be extensible by packages. So I'm not sure that's worth it. At
least with PR fixes the most common case.

Fixes #50380.

(cherry picked from commit 5f03a18)
Update the docs for `Task` to mention
the fact that they default to sticky.

Co-authored-by: Gabriel Baraldi <baraldigabriel@gmail.com>
(cherry picked from commit 5466d3d)
Trying for cross-compile and disabling CSL and realized both of those
configurations were broken now.

(cherry picked from commit d080fe6)
…ba42 (#50979)

Co-authored-by: Dilum Aluthge <dilum@aluthge.com>
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NHDaly commented Aug 29, 2023

Aha. Thanks! I had been assuming we'd close/merge the PR and create a new one for each patch release. Sorry for the noise!

…857f (#51473)

Co-authored-by: Dilum Aluthge <dilum@aluthge.com>
@IanButterworth
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There's quite a lot of Pkg fixes lined up here. Maybe worth going for 1.9.4 soon? @KristofferC

3a39ca33e precompile: stop swallowing internal errors (#3584)
0537ed0a9 Don't mutate project.deps during project write (#3591)
31a192e4c Update manifest entry of project for non-local manifests (#3579)
46cc38566 fix inference of PackageSpec constructor in presence of imprecise input types (#3585)
55afe117e Remove mentions of “home project” in documentation and comments (#3547)
353bd0bbe precompilation: `warnings` -> `output` (#3575)
204977740 precompile: also consider sysimage modules that activate extensions (#3572)
d0d5dda4d handle git cli errors as pkgerrors (#3538)
50a492698 Give examples of using `julia_args`, `test_args` (#2673)
9054ac588 Clarify "Providing global configuration options" in docs (#1800)
b50c2d229 sort compat entries in `pkg> compat` (#3605)
1e42aa6df status: expand 2 symbol upgrade note to highlight *may* be upgradable (#3576)

kpamnany and others added 12 commits September 30, 2023 17:12
`unsafe_trunc(UInt, -1.0)` is unspecified behavior but worked fine on
apple and AMD so we didn't notice??? This has been very broken since 1.7.

(cherry picked from commit 61ebaf6)
Co-authored-by: Gabriel Baraldi <baraldigabriel@gmail.com>
Co-authored-by: Dilum Aluthge <dilum@aluthge.com>
(cherry picked from commit 8be469e)
…or in distributed message processing (#51019)

There is a use of `oldstate` on line 244 which has the possibility of
being undefined. This bug seems to have been introduced in
40c622b#diff-39fa44ff86c5b38bd6b9e7f60733b25724a9efd9221ca38f776ed3f3ab01dec2.
I don't have a repro for this but this PR reverts back to the situation
where `oldstate` is defined at the topmost level of the catch block as
it was before the offending commit.

(cherry picked from commit 777b784)
This can cause segfaults when exiting julia.

Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com>
(cherry picked from commit b3741c0)
The guard instruction for unreachables and other crashes in aarch64 is
`brk`, in macos there isn't a distinction between a brk for a breakpoint
and one for a crash, as an attempt we check the value of `pc` when the
signal is triggered, if it is
`brk #0x1` we say that it is a crash and go into the sigdie_handler.

We should probably do the same in aarch64 linux, though I haven't dug
too deep into what values it uses for traps, and if what compiler used
matters, on apple I assumed we use clang/LLVM

It might be possible to test this by calling some inline assembly.

This means that something like
#51267 actually crashes with
```c
[16908] signal (5): Trace/BPT trap: 5
in expression starting at /Users/gabrielbaraldi/julia/test.jl:2
_collect at ./array.jl:768
collect at ./array.jl:757
top-level scope at /Users/gabrielbaraldi/julia/test.jl:5
_jl_invoke at /Users/gabrielbaraldi/julia/src/gf.c:2892
jl_toplevel_eval_flex at /Users/gabrielbaraldi/julia/src/toplevel.c:925
jl_toplevel_eval_flex at /Users/gabrielbaraldi/julia/src/toplevel.c:877
ijl_toplevel_eval at /Users/gabrielbaraldi/julia/src/toplevel.c:943 [inlined]
ijl_toplevel_eval_in at /Users/gabrielbaraldi/julia/src/toplevel.c:985
eval at ./boot.jl:383 [inlined]
include_string at ./loading.jl:2070
_jl_invoke at /Users/gabrielbaraldi/julia/src/gf.c:2873
ijl_apply_generic at /Users/gabrielbaraldi/julia/src/gf.c:3074
_include at ./loading.jl:2130
include at ./Base.jl:494
jfptr_include_46486 at /Users/gabrielbaraldi/julia/usr/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/gabrielbaraldi/julia/src/gf.c:2873
ijl_apply_generic at /Users/gabrielbaraldi/julia/src/gf.c:3074
exec_options at ./client.jl:317
_start at ./client.jl:552
jfptr__start_83179 at /Users/gabrielbaraldi/julia/usr/lib/julia/sys.dylib (unknown line)
_jl_invoke at /Users/gabrielbaraldi/julia/src/gf.c:2873
ijl_apply_generic at /Users/gabrielbaraldi/julia/src/gf.c:3074
jl_apply at /Users/gabrielbaraldi/julia/src/./julia.h:1970 [inlined]
true_main at /Users/gabrielbaraldi/julia/src/jlapi.c:582
jl_repl_entrypoint at /Users/gabrielbaraldi/julia/src/jlapi.c:731
Allocations: 570978 (Pool: 570031; Big: 947); GC: 1
fish: Job 1, './julia test.jl' terminated by signal SIGTRAP (Trace or breakpoint trap)
```
instead of hanging silently

---------

Co-authored-by: Jameson Nash <vtjnash@gmail.com>
(cherry picked from commit d51ad06)
deps/curl: Remove "without-ssl" because of configure error

(cherry picked from commit 3254e62)
@IanButterworth IanButterworth marked this pull request as ready for review October 16, 2023 17:31
@KristofferC KristofferC force-pushed the backports-release-1.9 branch 2 times, most recently from 3352ca7 to 4f07359 Compare October 17, 2023 11:58
@KristofferC KristofferC force-pushed the backports-release-1.9 branch from 4f07359 to 926a060 Compare October 18, 2023 17:25
KristofferC and others added 2 commits October 20, 2023 15:33
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@nanosoldier runtests()

We're now using libssh2 v1.11.0 which includes the two patches we were
carrying. The patches need to be dropped in order to build with
`USE_BINARYBUILDER=0`. (This was my bad, I should have made this change
as part of #50826, which updated libssh2 to v1.11.0.)

(cherry picked from commit 315ff53)
@IanButterworth
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PkgEval didnt run/report back?
cc. @maleadt

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maleadt commented Oct 30, 2023

There was an outage due to a revoked AWS key.

@nanosoldier runtests()

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The package evaluation job you requested has completed - possible new issues were detected.
The full report is available.

This shouldn't be needed because `ldd` should do it itself.

(cherry picked from commit 5b34cdf)
@KristofferC KristofferC force-pushed the backports-release-1.9 branch from f6ff2aa to 1a09ea5 Compare November 1, 2023 12:45
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@nanosoldier runtests(["Conda", "CausalityTools", "CitableImage", "ParameterizedFunctions", "TensND", "MomentClosure", "PlutoStaticHTML", "MCPTrajectoryGameSolver", "FastBroadcast", "NeuronBuilder", "Trixi", "ConstrainedSystems", "ChargeTransport", "JumpProblemLibrary", "SkeelBerzins", "Electrum", "HOODESolver", "FastAI", "SymbolicNumericIntegration", "IterativeLearningControl", "SpiDy", "SMLMMetrics", "Catalyst", "MTKHelpers", "JumpProcesses", "Intervals", "UCIData", "GpABC", "CharacteristicInvFourier", "RegularizedProblems", "RxEnvironments", "Yunir", "PALEOaqchem", "HarmonicBalance", "ScatteringOptics", "AllocArrays", "ODEProblemLibrary", "SchwarzChristoffel", "HclinicBifurcationKit", "PALEOocean", "MinimallyDisruptiveCurves", "GlobalSensitivity", "Nonconvex", "ComplexityMeasures", "IRKGaussLegendre", "Chamber", "SymPy", "MiseEnPage", "Simplices", "NeuroAnalysis", "Aerosol", "NumCME", "ModelPredictiveControl", "PyMBAR", "ReactionNetworkImporters", "MINDFulMakie", "SBMLToolkit", "Bactos", "MathML", "ReactionSensitivity", "ManifoldDiff", "PRONTO", "PowerSimulationsDynamics"])

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The package evaluation job you requested has completed - possible new issues were detected.
The full report is available.

…dispatch (#51995)

The artifacts dict is not lowered to ensure_artifact_installed which
causes to load the ".toml" during runtime for lazy artifacts

(cherry picked from commit 9bc6994)
@KristofferC KristofferC merged commit bc55f44 into release-1.9 Nov 7, 2023
2 of 5 checks passed
@KristofferC KristofferC deleted the backports-release-1.9 branch November 7, 2023 09:09
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