gcc: revision for new Xcode

[fxcoudert]

Now that Mojave has Xcode 11 and the 10.15 SDK, we need to update GCC there so that it fixes the system headers. Since High Sierra also now has a new Xcode version, it seems appropriate to refresh our bottles, so users avoid a mismatched GCC / Xcode / SDK combination.

[alebcay]

ld: warning: directory not found for option '-L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0'
ld: warning: directory not found for option '-L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../..'
ld: warning: directory not found for option '-L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0'
ld: warning: directory not found for option '-L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../..'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Error: ipopt: failed

It looks like ipopt is linking to #{lib} instead of #{opt_lib}.

[fxcoudert]

ipopt is making gcc dump its internal paths and records those. Nasty behaviour :(

[SMillerDev]

Anything we can do about that?

[fxcoudert]

On Mojave, and Mojave only:

ImportError: dlopen(/usr/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Symbol not found: _aligned_alloc
  Referenced from: /usr/local/opt/gcc/lib/gcc/9/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /usr/local/opt/gcc/lib/gcc/9/libgomp.1.dylib

It seems that libgomp (part of GCC) tries to use aligned_alloc, which is defined in the 10.15 SDK (part of Xcode 11 on Mojave) but apparement not available on Mojave system libraries.

One solution would be to force it off, configuring with ac_cv_func_aligned_alloc=no

[fxcoudert]

Trying to fix by forcing the use of the SDK version that corresponds to the macOS version currently running (instead of latest SDK).

[fxcoudert]

Compiling against the 10.14 SDK on Mojave is not enough. I need someone with access to a Mojave machine to tell me what the full output of brew install -s -v gcc is (in particular the libgomp configure).

[boris-kolpackov]

@fxcoudert Strange, I was able to manually change the XCode 11.0 SDK symlink to 10.14 on 10.14.5 and successfully rebuild GCC from source (as per #46393).

[Bo98]

@fxcoudert We've discovered that the 11.0 CLT (11.1 CLT does not exist), which the CI uses, shipped with the wrong system headers in the 10.14 SDK: #46466 (comment). The problem has been fixed in 11.2.

Apparently a lot of people don't have the 11.0 CLT because Apple also botched up the update process, henced why this fix worked locally for some - they weren't using the broken CLT.

[EricFromCanada]

@BrewTestBot Test this please

[Bo98]

This is building twice. Might want to kill the first one (I don't see how to).

[fxcoudert]

abyss test data is missing (temporarily?)
Other than that, all good!

[EricFromCanada]

Requested reupload of test data for abyss in bcgsc/abyss#305.