[MacPorts] #68329: py311-scipy @1.10.1_0+gfortran+openblas not building on Sonoma apple silicon

[MacPorts]

#68329: py311-scipy @1.10.1_0+gfortran+openblas not building on Sonoma apple
silicon
--------------------------+-----------------------
  Reporter:  quintusdias  |      Owner:  michaelld
      Type:  defect       |     Status:  assigned
  Priority:  Normal       |  Milestone:
 Component:  ports        |    Version:  2.8.1
Resolution:               |   Keywords:
      Port:  py311-scipy  |
--------------------------+-----------------------

Comment (by markmentovai):

 @cjones051073 comment:13
 > I do not believe the `duplicate LC_RPATH` messages are the real issue
 here. They are just warnings, so whilst something we may need to clean up
 ourselves (assuming GCC upstream doesn't do something to prevent them) I
 think for now we ignore them.

 I’m not so sure. They’re not warnings, they’re the source of linker
 failures. Observe:

 {{{
 mark at arm-and-hammer zsh% cat main.c
 int main(int argc, char * argv[]) { return 0; }
 mark at arm-and-hammer zsh% otool -l /opt/local/lib/libopenblas.dylib| grep
 -B1 -A2 LC_RPATH
 Load command 15
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/libgcc (offset 12)
 Load command 16
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/libgcc (offset 12)
 Load command 17
           cmd LC_RPATH
       cmdsize 32
          path @loader_path (offset 12)
 Load command 18
           cmd LC_RPATH
       cmdsize 32
          path /opt/local/lib (offset 12)
 Load command 19
           cmd LC_RPATH
       cmdsize 72
          path /opt/local/lib/gcc13/gcc/arm64-apple-darwin23/13.2.0 (offset
 12)
 Load command 20
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/gcc13 (offset 12)
 mark at arm-and-hammer zsh% clang main.c -L/opt/local/lib -lopenblas && echo
 succeeded || echo failed
 ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in
 '/opt/local/lib/libopenblas-r1.dylib'
 clang: error: linker command failed with exit code 1 (use -v to see
 invocation)
 failed
 }}}

 But if the duplicate `LC_RPATH` is removed, the link succeeds:

 {{{
 mark at arm-and-hammer zsh% cp /opt/local/lib/libopenblas.dylib .
 mark at arm-and-hammer zsh% install_name_tool -delete_rpath
 /opt/local/lib/libgcc libopenblas.dylib
 mark at arm-and-hammer zsh% otool -l libopenblas.dylib | grep -B1 -A2
 LC_RPATH
 Load command 15
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/libgcc (offset 12)
 Load command 16
           cmd LC_RPATH
       cmdsize 32
          path @loader_path (offset 12)
 Load command 17
           cmd LC_RPATH
       cmdsize 32
          path /opt/local/lib (offset 12)
 Load command 18
           cmd LC_RPATH
       cmdsize 72
          path /opt/local/lib/gcc13/gcc/arm64-apple-darwin23/13.2.0 (offset
 12)
 Load command 19
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/gcc13 (offset 12)
 mark at arm-and-hammer zsh% clang main.c -L. -lopenblas && echo succeeded ||
 echo failed
 succeeded
 }}}

 You may think that this isn’t compelling enough, in case
 `install_name_tool` might be doing something else to the module. (It does,
 it makes changes in the `__LINKEDIT` segment.) So also consider:

 {{{
 mark at arm-and-hammer zsh% python3
 Python 3.11.6 (main, Oct  6 2023, 10:09:23) [Clang 15.0.0
 (clang-1500.0.40.1)] on darwin
 Type "help", "copyright", "credits" or "license" for more information.
 >>> b = bytearray(open('/opt/local/lib/libopenblas.dylib', 'rb').read())
 >>> path = b'/opt/local/lib/libgcc'
 >>> b[b.find(path, b.find(path) + 1) + len(path) - 1] += 1
 >>> open('libopenblas.dylib', 'wb').write(b)
 13067496
 >>> exit()
 mark at arm-and-hammer zsh% otool -l libopenblas.dylib | grep -B 1 -A 2
 LC_RPATH
 Load command 15
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/libgcc (offset 12)
 Load command 16
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/libgcd (offset 12)
 Load command 17
           cmd LC_RPATH
       cmdsize 32
          path @loader_path (offset 12)
 Load command 18
           cmd LC_RPATH
       cmdsize 32
          path /opt/local/lib (offset 12)
 Load command 19
           cmd LC_RPATH
       cmdsize 72
          path /opt/local/lib/gcc13/gcc/arm64-apple-darwin23/13.2.0 (offset
 12)
 Load command 20
           cmd LC_RPATH
       cmdsize 40
          path /opt/local/lib/gcc13 (offset 12)
 mark at arm-and-hammer zsh% clang main.c -L. -lopenblas && echo succeeded ||
 echo failed
 succeeded
 }}}

 An “easy” workaround for this would be to run `install_name_tool
 -delete_rpath` on `libopenblas.dylib`. But it would be better to find
 where the duplicate is coming from in the first place, and fix that.

-- 
Ticket URL: <https://trac.macports.org/ticket/68329#comment:14>
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