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Bump OpenBLAS 0.3.9 #35113

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merged 13 commits into from
May 6, 2020
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haampie
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@haampie haampie commented Mar 15, 2020

Following @ViralBShah's comment in the linear algebra channel on Slack, it might be the right time to bump OpenBLAS to 3.9.0 for the Julia 1.5 release.

  • Remove Keno's Windows patch since it has been incorporated into OpenBLAS already
  • Forward the USE_BLAS_FFLAGS to OPENBLAS_FFLAGS. This addresses an issue where OpenBLAS does not build LAPACK with -fdefault-integer-8 and causes a segfault when running the OpenBLAS tests during the build (ref INTERFACE64 builds segfault with kernel_regress:skx_avx OpenMathLib/OpenBLAS#2429)
  • Add the -frecursive -fno-optimize-sibling-calls flags to USE_BLAS_FFLAGS. I'm not 100% sure why this would be necessary, but read INTERFACE64 builds segfault with kernel_regress:skx_avx OpenMathLib/OpenBLAS#2429 where they include those flags. Actually, I'm inclined to drop this... from the comments there they mention that -frecursive cannot hurt but does not seem to be mandatory, and -fno-optimize-sibling-calls sounds very unrelated. The important bit is passing -fdefault-integer-8 to LAPACK I figure.

Todo:

New todo:

@haampie haampie changed the title Bump openblas 3.9.0 Bump OpenBLAS 0.3.9 Mar 15, 2020
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Overall looks good, but I know Keno was working on the win32 patch very recently, so let's see what he says. Once he weighs in, we can merge the Yggdrasil PR, get binaries uploaded, update the BB release and checksums, then merge this.

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haampie commented Mar 15, 2020

but I know Keno was working on the win32 patch very recently, so let's see what he says

On that note, from #34923 (comment)

If this works, I'll need to include the openblas patch in the julia

I think the Yggdrasil and Julia base patches are still not in sync at the moment.

@haampie haampie force-pushed the bump-openblas-3.9.0 branch from 109aaf7 to 0f30c45 Compare March 15, 2020 19:55
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haampie commented Mar 15, 2020

Seems like the tests still pass on Ubuntu 18.04 with this bumped version of OpenBLAS:

Step #1: Step 6/6 : RUN cd /julia && make test-LinearAlgebra
...
Step #1: Test Summary: |  Pass  Total
Step #1:   Overall     | 91305  91305
Step #1:     SUCCESS

so that looks promising. Can we trigger CI to not use binary builder btw?

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Keno commented Mar 17, 2020

  • Remove Keno's Windows patch since it has been incorporated into OpenBLAS already

Not the case. Part of it is definitely still needed.

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haampie commented Mar 23, 2020

Ok, so now the Windows patch is back and is identical to the one at JuliaPackaging/Yggdrasil#621

@staticfloat last difference between here and Yggdrasil is this change JuliaPackaging/Yggdrasil@b572419. Should the "Patch out -Ofast on power" patch also be included here?

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Yes, we still need to carry that patch both here and in Yggdrasil.

@haampie haampie force-pushed the bump-openblas-3.9.0 branch from 130c733 to 78fbde8 Compare March 23, 2020 20:57
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haampie commented Mar 23, 2020

Ok, so now everything is in sync with the Yggdrasil PR

@haampie haampie force-pushed the bump-openblas-3.9.0 branch from 81f9b71 to f5197a9 Compare March 29, 2020 14:00
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haampie commented Mar 29, 2020

Ok, so now that the BB OpenBLAS version is bumped we can finally see if it works with Julia 🤞

I've also bumped LAPACK to 3.9.0, but I don't really understand why it's still in the Makefile since it is almost always shipped with OpenBLAS?

Edit: files changed 166 🙄

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Thank you @haampie

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LAPACK is separately in the Makefile for the use case where you don't use it bundled with OpenBLAS. Increasingly a rare use case but useful for architectures where OpenBLAS may not be available.

It should usually be the version of LAPACK that ships with the OpenBLAS we are using.

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haampie commented Mar 29, 2020

tester_linuxaarch64 has linalg errors:

LinearAlgebra/special: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/special.jl:126
  Expression: op(A, B) ��� op(Matrix(A), Matrix(B)) ��� Matrix(op(A, B))
   Evaluated: [0.9601490412773276 0.07897628661563409 ��� 6.626530213604507 4.990367748161503; 0.0 0.021276677108488847 ��� 4.391867807764307 5.003436245324435; ��� ; 0.0 0.0 ��� 0.38028646737079386 0.14890935339477882; 0.0 0.0 ��� 0.0 0.208343087340652] ��� [0.9601490412773276 0.07897628661563409 ��� 6.626530213604507 4.990367748161503; 0.0 0.021276677108488847 ��� 4.391867807764307 5.003436245324435; ��� ; 0.0 0.0 ��� 0.38028646737079386 0.14890935339477882; 0.0 0.0 ��� 0.0 0.208343087340652] ��� [0.9601490412773276 0.07897628661563409 ��� 6.626530213604507 4.990367748161503; 0.0 0.021276677108488847 ��� 4.391867807764307 5.003436245324435; ��� ; 0.0 0.0 ��� 0.38028646737079386 0.14890935339477882; 0.0 0.0 ��� 0.0 0.208343087340652]
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490
LinearAlgebra/special: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/special.jl:126
  Expression: op(A, B) ��� op(Matrix(A), Matrix(B)) ��� Matrix(op(A, B))
   Evaluated: [0.5183657300754845 0.0 ��� 0.0 0.0; 0.0 0.6413577456911539 ��� 0.0 0.0; ��� ; 0.0 0.0 ��� 0.42311204165695826 0.0; 0.0 0.0 ��� 0.0 0.560892881044907] ��� [0.5183657300754845 0.0 ��� 0.0 0.0; 0.0 0.6413577456911539 ��� 0.0 0.0; ��� ; 0.0 0.0 ��� 0.42311204165695826 0.0; 0.0 0.0 ��� 0.0 0.560892881044907] ��� [0.5183657300754845 0.0 ��� 0.0 0.0; 0.0 0.6413577456911539 ��� 0.0 0.0; ��� ; 0.0 0.0 ��� 0.42311204165695826 0.0; 0.0 0.0 ��� 0.0 0.560892881044907]
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490
Worker 5 failed running test LinearAlgebra/matmul:
Some tests did not pass: 966 passed, 2 failed, 0 errored, 0 broken.
LinearAlgebra/matmul: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/matmul.jl:603
  Expression: D ��� C
   Evaluated: [-26.861334345553136 -23.65816474235872 ��� -23.010518420790522 -24.981235209458834; -26.081022396434065 -25.08768970170442 ��� -22.715362284007657 -28.380158209617118; ��� ; -24.431823779625308 -22.50450114181978 ��� -22.61410724022273 -23.746031013418346; -24.151580246169104 -23.944203004528433 ��� -24.214649928719943 -24.591809064286803] ��� [-26.861334345553143 -23.65816474235872 ��� -23.01051842079052 -24.981235209458845; -26.081022396434054 -25.087689701704416 ��� -22.715362284007657 -28.380158209617115; ��� ; -24.431823779625308 -22.504501141819784 ��� -22.614107240222722 -23.746031013418346; -24.151580246169104 -23.944203004528433 ��� -24.214649928719954 -24.5918090642868]
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490
LinearAlgebra/matmul: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/matmul.jl:609
  Expression: D ��� C
   Evaluated: [-26.861334345553136 -23.65816474235872 ��� -23.010518420790522 -24.981235209458834; -26.081022396434065 -25.08768970170442 ��� -22.715362284007657 -28.380158209617118; ��� ; -24.431823779625308 -22.50450114181978 ��� -22.61410724022273 -23.746031013418346; -24.151580246169104 -23.944203004528433 ��� -24.214649928719943 -24.591809064286803] ��� [-26.861334345553143 -23.65816474235872 ��� -23.01051842079052 -24.981235209458845; -26.081022396434054 -25.087689701704416 ��� -22.715362284007657 -28.380158209617115; ��� ; -24.431823779625308 -22.504501141819784 ��� -22.614107240222722 -23.746031013418346; -24.151580246169104 -23.944203004528433 ��� -24.214649928719954 -24.5918090642868]
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490
Worker 11 failed running test LinearAlgebra/pinv:
Some tests did not pass: 286 passed, 2 failed, 0 errored, 0 broken.
LinearAlgebra/pinv: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:92
  Expression: ���(norm(a * apinv * a - a) / norm(a), 0, atol = tol1)
   Evaluated: NaN32 ��� 0 (atol=1.0)
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490
LinearAlgebra/pinv: Test Failed at /buildworker/worker/tester_linuxaarch64/build/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:92
  Expression: ���(norm(a * apinv * a - a) / norm(a), 0, atol = tol1)
   Evaluated: NaN32 ��� 0 (atol=10000.0)
Stacktrace:
 [1] record(::Test.DefaultTestSet, ::Union{Test.Error, Test.Fail}) at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:775
 [2] (::var"#44#53")() at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:337
 [3] cd(::var"#44#53", ::String) at ./file.jl:104
 [4] top-level scope at /buildworker/worker/tester_linuxaarch64/build/share/julia/test/runtests.jl:75
 [5] include(::Function, ::Module, ::String) at ./Base.jl:380
 [6] include(::Module, ::String) at ./Base.jl:368
 [7] exec_options(::Base.JLOptions) at ./client.jl:288
 [8] _start() at ./client.jl:490

Seems like rounding errors mostly, but NaN32 \approx 0 seems worse than that

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ViralBShah commented Mar 29, 2020

Stating the obvious. If its only on aarch64, that suggests possible openblas bugs.

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haampie commented Mar 29, 2020

Is there any way to debug this easily? aarch64 docker image?

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I think @staticfloat may have something for you.

@staticfloat
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You.... can.... do an aarch64 docker image, but running everything inside of QEMU can be error-prone for things like this.

I suggest remoting into the aarch64 buildbot. PM me on Slack with your SSH public key and I'll give you temporary access to an environment where I have a julia session open with the failing test already loaded up. It's failing even in a build from source on the machine, so it's not a BB issue, it's most likely an issue with OpenBLAS itself.

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Any chance we can figure out what the issue is and get this in before code freeze?

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ViralBShah commented Apr 26, 2020

Of course, I have a bad feeling it is an openblas bug, and we'll need a new release or pull in some patches...

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OpenBLAS 0.3.9 is much faster than earlier versions on systems with AVX512 in my benchmarks, so I hope these issues can be solved.

Anyone have aarch64 to test?

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Anyone have aarch64 to test?

Best option is to send your ssh key to @staticfloat and he can give you access to the buildbot.

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ViralBShah commented Apr 29, 2020

Using the julia nightly on aarch64 from yesterday, and doing a few different runs, most of the errors seem to be related to tolerance and I am unable to reproduce all. The only one that seems worrisome as @haampie pointed out is:

LinearAlgebra/pinv: Test Failed at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:92
  Expression: ≈(norm(a * apinv * a - a) / norm(a), 0, atol = tol1)
   Evaluated: NaN32 ≈ 0 (atol=1.0)

The failure is clearly in the Float32 version of the hilbert matrix test case. However, it only gets triggered if you run the whole script. I am unable to reproduce it by itself.

julia> include("/home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl")
dense/ill-conditioned matrix: Test Failed at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:92
  Expression: ≈(norm(a * apinv * a - a) / norm(a), 0, atol = tol1)
   Evaluated: NaN32 ≈ 0 (atol=1.0)
Stacktrace:
 [1] test_pinv(::Array{Float32,2}, ::Int64, ::Int64, ::Float64, ::Float64, ::Float64) at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:92
 [2] macro expansion at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:116 [inlined]
 [3] macro expansion at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1114 [inlined]
 [4] macro expansion at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:115 [inlined]
 [5] macro expansion at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1188 [inlined]
 [6] macro expansion at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:103 [inlined]
 [7] top-level scope at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1188 [inlined]
 [8] top-level scope at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:0
Test Summary:                          | Pass  Fail  Total
eltya = Float32                        |   76     1     77
  (m, n) = (1000, 100)                 |   19     1     20
    dense/ill-conditioned matrix       |    3     1      4
    dense/diagonal matrix              |    4            4
    dense/tri-diagonal matrix          |    4            4
    Diagonal matrix                    |    4            4
    Vector                             |    2            2
    Adjoint/Transpose vector           |    2            2
  (m, n) = (100, 100)                  |   20           20
  (m, n) = (100, 1000)                 |   20           20
  zero valued numbers/vectors/matrices |    7            7
  sub-normal numbers/vectors/matrices  |   10           10
Test Summary:                          | Pass  Fail  Total
eltya = Float32                        |   76     1     77
  (m, n) = (1000, 100)                 |   19     1     20
    dense/ill-conditioned matrix       |    3     1      4
    dense/diagonal matrix              |    4            4
    dense/tri-diagonal matrix          |    4            4
    Diagonal matrix                    |    4            4
    Vector                             |    2            2
    Adjoint/Transpose vector           |    2            2
  (m, n) = (100, 100)                  |   20           20
  (m, n) = (100, 1000)                 |   20           20
  zero valued numbers/vectors/matrices |    7            7
  sub-normal numbers/vectors/matrices  |   10           10
ERROR: LoadError: Some tests did not pass: 76 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /home/sabae/julia-5cb3f3fbc1/share/julia/stdlib/v1.5/LinearAlgebra/test/pinv.jl:102
caused by [exception 1]
Some tests did not pass: 76 passed, 1 failed, 0 errored, 0 broken.

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@haampie Can you rebase this to master?

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ViralBShah commented Apr 29, 2020

It only fails the first time when run in tests. Can't reproduce it manually or in the debugger.

julia> test_pinv(a, m, n, tol1, tol2, tol3)
Test Failed at REPL[10]:4
  Expression: ≈(norm(a * apinv * a - a) / norm(a), 0, atol = tol1)
   Evaluated: NaN32 ≈ 0 (atol=1.0)
ERROR: There was an error during testing

julia> test_pinv(a, m, n, tol1, tol2, tol3)
Test Passed

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ViralBShah commented Apr 29, 2020

@chriselrod Would you be able to take a look? Maybe I am doing something wrong. Can you email/slack me your ssh public key if you have some time to look into this?

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Bumped to BB_REL 4. Let's see how this goes.

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giordano commented May 6, 2020

I think you also need to regenerate the checksum files?

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I think you also need to regenerate the checksum files?

Sigh. Yes.

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haampie commented May 6, 2020

I think you also need to regenerate the checksum files?

Sigh. Yes.

$ cat create_checksums.sh
#!/bin/bash

JULIA_ROOT="$1"
VERSION="$2"
BB="$3"
URL="https://github.com/JuliaBinaryWrappers/OpenBLAS_jll.jl/releases/tag/OpenBLAS-v$VERSION%2B$BB" 

# Download
curl -s "$URL" | grep -Eo "/JuliaBinaryWrappers/.*?/releases/.*?tar\.gz" | xargs -I{} wget https://github.com{}

# Create checksums
for f in *.tar.gz; do
    MD5=$(md5sum $f | awk '{ print $1 }')
    SHA512=$(sha512sum $f | awk '{ print $1 }')
    JULIA_NAME=$(basename "$f" | sed "s|v$VERSION|v$VERSION-$BB|g")
    DIR="$JULIA_ROOT/deps/checksums/$JULIA_NAME"

    mkdir -p "$DIR"
    echo "$MD5" > "$DIR/md5"
    echo "$SHA512" > "$DIR/sha512"
done

$ create_checksums.sh ~/project/julia 0.3.9 4

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haampie commented May 6, 2020

I think this is good news for linuxaarch64:

Test Summary:                       |     Pass  Error  Broken     Total
  Overall                           | 38658181      2  327766  38985949
...
    file                            |     1031      2              1033
...

So there's a test failing, but it is not openblas-related.

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giordano commented May 6, 2020

@haampie why not using contrib/refresh_bb_tarballs.sh? 😅

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haampie commented May 6, 2020

I will from now on 😆

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ViralBShah commented May 6, 2020

Let's try rebasing on master again to see if we get a green on CI.

@haampie haampie force-pushed the bump-openblas-3.9.0 branch from c4eb178 to bbd1c5b Compare May 6, 2020 16:35
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haampie commented May 6, 2020

Tests are green 🎉

@StefanKarpinski StefanKarpinski merged commit 52c9e3d into JuliaLang:master May 6, 2020
@haampie haampie deleted the bump-openblas-3.9.0 branch May 6, 2020 21:18
@chriscoey
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Hooray! Thank you everyone! This currently has the backport 1.5 label, does that mean it won't be in 1.5.0? Forgive my ignorance

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That means it will be in the 1.5 release (we also haven't branched yet).

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That was a lot of work for a version bump. Thanks @haampie! Taking off the label, since we have not yet branched.

Is an openblas version update something we can expect in a 1.4 backport?

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8 participants