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openblas 0.3.13 uses clock_gettime that is only available macOS 10.12 onwards #836

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jaakkor2 opened this issue Apr 6, 2021 · 13 comments · Fixed by JuliaPackaging/Yggdrasil#2842 or JuliaLang/julia#40499
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openblas 0.3.13 uses clock_gettime that is only available macOS 10.12 onwards #836

jaakkor2 opened this issue Apr 6, 2021 · 13 comments · Fixed by JuliaPackaging/Yggdrasil#2842 or JuliaLang/julia#40499
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system:mac Affects only macOS upstream The issue is with an upstream dependency, e.g. LLVM

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@jaakkor2
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jaakkor2 commented Apr 6, 2021

This version starts fine
https://julialangnightlies-s3.julialang.org/bin/mac/x64/1.7/julia-95a34a9020-mac64.dmg
JuliaLang/julia@95a34a9

julia> versioninfo()
Julia Version 1.7.0-DEV.609
Commit 95a34a9020 (2021-02-25 17:35 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.5.0)
  CPU: Intel(R) Core(TM)2 Duo CPU     P7350  @ 2.00GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, penryn)

This does not start
https://julialangnightlies-s3.julialang.org/bin/mac/x64/1.7/julia-dc81980e0b-mac64.dmg
JuliaLang/julia@dc81980

$ exec '/Applications/Julia-1.7.app/Contents/Resources/julia/bin/julia'
ERROR: Unable to load dependent library /Applications/Julia-1.7.app/Contents/Resources/julia/bin/../lib/julia/libopenblas64_.dylib
Message: dlopen(/Applications/Julia-1.7.app/Contents/Resources/julia/bin/../lib/julia/libopenblas64_.dylib, 6): Symbol not found: _clock_gettime
  Referenced from: /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia//libgfortran.5.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia//libgfortran.5.dylib
Unable to load "/Applications/Julia-1.7.app/Contents/Resources/julia/bin/../lib/julia/libopenblas64_.dylib"
┌ Error: No loaded BLAS libraries were built with ILP64 support
└ @ LinearAlgebra.BLAS /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/LinearAlgebra/src/blas.jl:154
Quitting.

[Process completed]

I believe this is a separate issue from #834 and I created a new issue.
@jaakkor2
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jaakkor2 commented Apr 6, 2021

Recent https://julialangnightlies-s3.julialang.org/bin/mac/x64/1.7/julia-89fff18d59-mac64.dmg JuliaLang/julia@89fff18 failed to start as well.

@ViralBShah ViralBShah added upstream The issue is with an upstream dependency, e.g. LLVM and removed upstream The issue is with an upstream dependency, e.g. LLVM labels Apr 6, 2021
@vtjnash
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vtjnash commented Apr 6, 2021

Seems to work for me, but I have an older kernel. What do you get with verbose=true?

julia> versioninfo(verbose=true)
Julia Version 1.7.0-DEV.847
Commit fedefe913a (2021-04-06 03:03 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin18.7.0)
  uname: Darwin 18.7.0 Darwin Kernel Version 18.7.0: Tue Jan 12 22:04:47 PST 2021; root:xnu-4903.278.56~1/RELEASE_X86_64 x86_64 i386
  CPU: Intel(R) Core(TM) i7-8559U CPU @ 2.70GHz: 
              speed         user         nice          sys         idle          irq
       JuliaLang/julia#1  2700 MHz     350469 s          0 s     196643 s    2802132 s          0 s
       JuliaLang/julia#2  2700 MHz      43470 s          0 s      22382 s    3283181 s          0 s
       JuliaLang/julia#3  2700 MHz     299995 s          0 s     137052 s    2911989 s          0 s
       JuliaLang/julia#4  2700 MHz      39964 s          0 s      16206 s    3292862 s          0 s
       JuliaLang/julia#5  2700 MHz     253623 s          0 s     106665 s    2988747 s          0 s
       JuliaLang/julia#6  2700 MHz      39651 s          0 s      14653 s    3294728 s          0 s
       JuliaLang/julia#7  2700 MHz     204878 s          0 s      74921 s    3069236 s          0 s
       JuliaLang/julia#8  2700 MHz      40513 s          0 s      13205 s    3295313 s          0 s
       
  Memory: 16.0 GB (438.875 MB free)
  Uptime: 651112.0 sec
  Load Avg:  1.5791015625  1.568359375  2.31005859375
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)
Environment:
  XPC_FLAGS = 0x0
  HOME = /Users/jameson
  TERM = xterm-256color
  PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMwareFusion.app/Contents/Public:/opt/X11/bin:/Users/jameson/.rvm/bin

@jaakkor2
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jaakkor2 commented Apr 6, 2021 

julia> versioninfo(verbose=true)
Julia Version 1.7.0-DEV.609
Commit 95a34a9020 (2021-02-25 17:35 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.5.0)
  uname: Darwin 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 i386
  CPU: Intel(R) Core(TM)2 Duo CPU     P7350  @ 2.00GHz: 
              speed         user         nice          sys         idle          irq
       #1  2000 MHz       4022 s          0 s       5172 s     176147 s          0 s
       #2  2000 MHz       4236 s          0 s       3494 s     176298 s          0 s
       
  Memory: 8.0 GB (2885.98046875 MB free)
  Uptime: 30591.0 sec
  Load Avg:  51.3974609375  17.18359375  7.8505859375
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, penryn)
Environment:
  MANPATH = /opt/local/share/man:/opt/local/share/man:
  TERM = xterm-256color
  PATH = /Users/jaakko/anaconda/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
  XPC_FLAGS = 0x0
  HOME = /Users/jaakko

This is on OS X 10.11.6. OS in platform info seems to be the version of kernel where the compilation was done.

@vtjnash
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vtjnash commented Apr 6, 2021

ah, right, I skimmed that too quickly (I was confused that penryn could run the latest version, so I should have double-checked).

We compile libjulia with -mmacosx-version-min=10.9, but looks here like gfortran might be missing that flag on https://github.com/JuliaPackaging/Yggdrasil / https://github.com/JuliaPackaging/BinaryBuilder.jl (@staticfloat)

@staticfloat
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staticfloat commented Apr 6, 2021 •
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We are setting -mmacosx-version-min=10.10 on Yggdrasil. Not great that it doesn't match Julia itself, but we had to bump for some software package at some point, I don't remember quite which one; perhaps something to do with GTK.

Right now that's kind of hardcoded, but we'll be able to control it in the future by building for x86_64-apple-darwin14 or x86_64-apple-darwin17, etc...

@giordano giordano mentioned this issue Apr 7, 2021
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@ViralBShah
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ViralBShah commented Apr 7, 2021 •
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We should probably bump it on Julia to 10.10 (which released in 2014), so hopefully that is still old enough to support users on older releases.

@staticfloat
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Can someone impacted by this try building with Julia set to 10.10 to verify that it fixes the issue?

@ViralBShah
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ViralBShah commented Apr 7, 2021 •
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According to https://stackoverflow.com/questions/5167269/clock-gettime-alternative-in-mac-os-x clock_gettime was only introduced in 10.12.

@ViralBShah ViralBShah added upstream The issue is with an upstream dependency, e.g. LLVM system:mac Affects only macOS labels Apr 7, 2021
@ViralBShah ViralBShah changed the title LIbtrampoline changes prevents 1.7 from starting on mac openblas 0.3.13 uses clock_gettime that is only available macOS 10.12 onwards Apr 7, 2021
@jaakkor2 jaakkor2 mentioned this issue Apr 8, 2021
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@jaakkor2
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jaakkor2 commented Apr 8, 2021

JuliaLang/julia#40396 did not fix this issue for me.

I created JuliaLang/julia#40400 to be able to download a binary with -mmacosx-version-min=10.10.

@jaakkor2
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jaakkor2 commented Apr 8, 2021

-mmacosx-version-min=10.10 on Julia side does not fix this, tested with JuliaLang/julia#40400.

OpenMathLib/OpenBLAS#2814 (comment) and the linked issue pocoproject/poco#1453 show many similar issues about _clock_gettime.

@Keno
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Keno commented Apr 8, 2021

The compiler can do OS x version detection. OpenBlas should not be using those symbols without checking that.

@vtjnash
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vtjnash commented Apr 8, 2021

Those issues are pretty closely related to this: it seems that the Apple headers are broken, so gcc/gfortran/openblas mis-detect the symbol as existing, when it should not (the ability to compile this header correctly is predicated on the existence of the clang extension #if __has_extension(enumerator_attributes))

@staticfloat
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I have identified the issue, and I have a fix making its way through the ecosystem: JuliaPackaging/BinaryBuilderBase.jl#134

staticfloat referenced this issue in JuliaPackaging/Yggdrasil Apr 15, 2021
@staticfloat
[CompilerSupportLibraries] rebuild to get new macOS build
372b340 
This should fix https://github.com/JuliaLang/julia/issues/40375 which is
due to the compiler shards containing `clock_gettime` symbol references
which are not allowed for macOS < 10.12.  The fix to the GCC shards was
made in #2836 and was
integrated into BinaryBuilderBase in JuliaPackaging/BinaryBuilderBase.jl#134
@staticfloat staticfloat mentioned this issue Apr 15, 2021
Merged
staticfloat referenced this issue in JuliaPackaging/Yggdrasil Apr 15, 2021
@staticfloat
[CompilerSupportLibraries] rebuild to get new macOS build
0961085 
This should fix https://github.com/JuliaLang/julia/issues/40375 which is
due to the compiler shards containing `clock_gettime` symbol references
which are not allowed for macOS < 10.12.  The fix to the GCC shards was
made in #2836 and was
integrated into BinaryBuilderBase in JuliaPackaging/BinaryBuilderBase.jl#134
@staticfloat staticfloat mentioned this issue Apr 15, 2021
Merged
@KristofferC KristofferC transferred this issue from JuliaLang/julia Nov 26, 2024
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@staticfloat @vtjnash @ViralBShah @Keno @jaakkor2