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release-1.6: Backports for 1.6.7 #45319

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merged 34 commits into from
Jul 5, 2022
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@KristofferC KristofferC commented May 16, 2022

Backported PRs:

Need manual backport:

Contains multiple commits, manual intervention needed:

Non-merged PRs with backport label:

DilumAluthge and others added 10 commits May 16, 2022 09:37
…FO` (for e.g. when Git is not available) (#43717)

* `base/version_git.sh`: fix the default value for `Base.GIT_VERSION_INFO` (for e.g. when Git is not available)

* Use single-quotes to avoid the need to backslash-escape the double quotes

(cherry picked from commit 709bc5c)
It also fixes `round(Integer, big(NaN))`.

Solves #44662

(cherry picked from commit ecf3558)
Discovered while running the syntax tests with lines 25-28 of
`jlfrontend.scm` commented out. Turned out we didn't handle `.op`
correctly in neither `check-dotop` nor in `deparse`. This meant we just
got `error: malformed expression` instead of an actually useful error
message.

(cherry picked from commit 9112135)
We were accidentally passing the start of the list instead of the end of
the list, resulting in some values passing through uninitialized.

Fix #42297 regression

(cherry picked from commit 5f2abf6)
…#44972)

* [REPL] remove erroneous space in test
  Introduced by #33805 (74f2de1).
* Revert "Temporarily move the `REPL` test suite to node 1, to buy us time until we fix the underlying bugs (#44961)"
  This reverts commit 322fd70.

(cherry picked from commit fbec395)
(cherry picked from commit c589e0d)
This prior conditional was a fixed constant branch, so this seems more like the intent.

(cherry picked from commit ac51add)
If multiple processes attempt to clean up cache files at the same time, a race condition can result, e.g.
https://buildkite.com/clima/climaatmos-ci/builds/812#6a961e99-e2a1-488b-a116-2a45dee26d38/102-104

(cherry picked from commit d4acead)
@KristofferC KristofferC added the release Release management and versioning. label May 16, 2022
@KristofferC KristofferC changed the title release-1.6: Backports for 1.6.6 release-1.6: Backports for 1.6.7 May 16, 2022
Co-authored-by: Jeff Bezanson <jeff.bezanson@gmail.com>
@jonas-schulze
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f31ef76 should also be backported

N5N3 and others added 3 commits May 23, 2022 11:29
There's no performance change, if the `indices`s of `Rdest` and `Rsrc` are all `NTuple{N,<:AbstractUnitRange}`.

(cherry picked from commit a91be39)
(cherry picked from commit eed2dba)
Otherwise, overrides do not trigger when using `artifact"..."` inside a
submodule.

(cherry picked from commit 9b106ad)
@KristofferC
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@fxcoudert, could you take this branch for a spin to make sure it works ok for your use case?

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@KristofferC I won't have time cause I'm travelling right now (and I've never used the 1.6 branch so far). Sorry. But I appreciate the heads-up.

ViralBShah and others added 6 commits May 23, 2022 16:10
* Apply patch for GMP CVE-2021-43618

* Update checksums

(cherry picked from commit dea9805)
(cherry picked from commit 3d6731b)
Note: this is the first build of the real upstream version 1.2.12 which was
released a few days ago.

(cherry picked from commit 81e7cfc)
(cherry picked from commit 1c10a9e)
Acquiring this lock in many implementations could result in deadlock,
even with an existing reader. Add a TLS check for reentry before, instead
of relying on the implementation specifics, to avoid any issues.

(cherry picked from commit 7df454b)
@KristofferC KristofferC force-pushed the backports-release-1.6 branch from 6e9251a to b6eda9d Compare May 23, 2022 14:11
@JuliaLang JuliaLang deleted a comment from nanosoldier May 29, 2022
@JuliaLang JuliaLang deleted a comment from nanosoldier May 29, 2022
@KristofferC KristofferC force-pushed the backports-release-1.6 branch 2 times, most recently from 789dcc6 to 9561ec5 Compare June 1, 2022 08:13
@jonas-schulze
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@KristofferC please don't forget #39369 🙂

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@nanosoldier runtests(["BestApproximation", "BytePairEncoding", "CoDa", "FastAI", "GBIF", "GaussBP", "GaussianMixtureAlignment", "GeometricFlux", "GraphDatasets", "GraphNeuralNetworks", "HighDimPDE", "LoopThrottle", "MLJText", "PATHSolver", "PsychomotorVigilanceTask", "Scruff", "ShipMMG"], vs = ":release-1.6")

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Your package evaluation job has completed - possible new issues were detected. A full report can be found here.

@KristofferC KristofferC requested a review from a team as a code owner June 14, 2022 06:59
@DilumAluthge DilumAluthge removed the request for review from a team June 14, 2022 11:59
@IanButterworth
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It would be nice but not critical to add JuliaLang/Pkg.jl#3073

@KristofferC KristofferC added the merge me PR is reviewed. Merge when all tests are passing label Jun 15, 2022
@KristofferC KristofferC reopened this Jun 28, 2022
vtjnash and others added 14 commits July 4, 2022 16:29
Apple reintroduced the old bug that we previously worked around in
fad04d3 with a similar patch to this.

This is needed anywhere that we may attempt to stop threads.

Fixes #43578

(cherry picked from commit 2939272)
…sue, since 12.1

Later, we should probably switch to using mach_exc_server generated from
`mig mach_exc.defs`.

(cherry picked from commit 267b124)
* avoid using `@sync_add` on remotecalls

It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which
in turn calls wait() for all the futures synchronously. Not only that is
slightly detrimental for network operations (latencies add up), but in case of
Distributed the call to wait() may actually cause some compilation on remote
processes, which is also wait()ed for. In result, some operations took a great
amount of "serial" processing time if executed on many workers at once.

For me, this closes #44645.

The major change can be illustrated as follows: First add some workers:

```
using Distributed
addprocs(10)
```

and then trigger something that, for example, causes package imports on the
workers:

```
using SomeTinyPackage
```

In my case (importing UnicodePlots on 10 workers), this improves the loading
time over 10 workers from ~11s to ~5.5s.

This is a far bigger issue when worker count gets high. The time of the
processing on each worker is usually around 0.3s, so triggering this problem
even on a relatively small cluster (64 workers) causes a really annoying delay,
and running `@everywhere` for the first time on reasonable clusters (I tested
with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks.

Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s,
and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't
bother to measure that precisely now, sorry) to ~11s.

Related issues:
- Probably fixes #39291.
- #42156 is a kinda complementary -- it removes the most painful source of
  slowness (the 0.3s precompilation on the workers), but the fact that the
  wait()ing is serial remains a problem if the network latencies are high.

May help with #38931

Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com>
(cherry picked from commit 62e0729)
* Fix USE_BINARYBUILDER_OPENBLAS=0 on macOS

We didn't properly move the OpenBLAS -> Objconv dependency chain
over to manifest files.  This was not visible until now because we
rarely build OpenBLAS from source without also building Objconv from
source.

Fixes #42519

* Also update path to `objconv` binary

(cherry picked from commit 6af7584)
Co-authored-by: KristofferC <kristoffer.carlsson@juliacomputing.com>
(cherry picked from commit 86f5501)
Distributed closes and destroys stdin, but some tests attempted to
explicitly use it, leading to test problems. We previously interpreted
this as passing devnull, but this is better to be explicit.

(cherry picked from commit 64a86f9)
This should fix the `Exec format error` problems we've had recently due to us adding some non-x86_64 linux workers to the pool.
* [release-1.6] Backport MbedTLS security patches

A few MbedTLS security patches should be backported to our LTS release.
In the future, we should lock ourselves to MbedTLS LTS releases so that
we can take advantage of their backporting as well.

* Bump mbedtls version and checksums
@KristofferC KristofferC force-pushed the backports-release-1.6 branch from 07de466 to 443c321 Compare July 4, 2022 14:29
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@KristofferC KristofferC merged commit a03fa67 into release-1.6 Jul 5, 2022
@KristofferC KristofferC deleted the backports-release-1.6 branch July 5, 2022 19:57
@DilumAluthge DilumAluthge removed the merge me PR is reviewed. Merge when all tests are passing label Jul 6, 2022
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