Failure using homebrew-provided llvm

[WardF]

brew gist-logs <formula> link OR brew config AND brew doctor output

wfisher@icelandic:~$ brew config
HOMEBREW_VERSION: 4.4.20
ORIGIN: https://github.com/Homebrew/brew
HEAD: 47ef1a3b0b742a78be35c016df6a0279d6035ebb
Last commit: 7 days ago
Branch: stable
Core tap JSON: 10 Feb 17:22 UTC
Core cask tap JSON: 10 Feb 17:22 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.rwKysaPwGx/org.xquartz:0
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 3.3.7 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.3.7/bin/ruby
CPU: deca-core 64-bit arm_donan
Clang: 16.0.0 build 1600
Git: 2.39.5 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.3-arm64
CLT: 16.2.0.0.1.1733547573
Xcode: 16.2
Rosetta 2: false

wfisher@icelandic:~$ brew doctor
Your system is ready to brew.
wfisher@icelandic:~$

Verification

• My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue.
• I ran brew update and am still able to reproduce my issue.
• I have resolved all warnings from brew doctor and that did not fix my problem.
• I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.

What were you trying to do (and why)?

(This issue originally reported by @czender at Unidata/netcdf-c#3083)

Original goal is to use the homebrew-installed llvm suite of tools (clang, etc) to compile netCDF-C (https://github.com/Unidata/netcdf-c).

What happened (include all command output)?

(from @czender)

A few months ago my default build environment on MacOS stopped working due to a Clang compiler error on the file ocdump.c. I usually do not report compiler errors because they have nothing to do with netCDF per se, and the compiler authors usually resolved these things eventually. So consider this a heads-up and feel free to resolve without taking action. However, note that this particular compiler error on this particular file has been there for ~3-4 months, and survived many patch releases of Clang. So it may be something that prevents other users from building/testing netCDF 4.9.3. Everything here (Clang, MacOS, and the netCDF-main branch are the latest available as of today.

zender@spectral:~/netcdf-c$ clang --version
Homebrew clang version 19.1.7
Target: arm64-apple-darwin24.3.0
Thread model: posix
InstalledDir: /opt/homebrew/Cellar/llvm/19.1.7/bin
Configuration file: /opt/homebrew/etc/clang/arm64-apple-darwin24.cfg
zender@spectral:~/netcdf-c$ 
zender@spectral:~/netcdf-c$ make
...
Normal output ...
...
/bin/sh ../libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I. -I..  -I.. -I.. -I../include -I/opt/homebrew/include  -fno-strict-aliasing -MT liboc_la-ocdump.lo -MD -MP -MF .deps/liboc_la-ocdump.Tpo -c -o liboc_la-ocdump.lo `test -f 'ocdump.c' || echo './'`ocdump.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -I.. -I.. -I.. -I../include -I/opt/homebrew/include -fno-strict-aliasing -MT liboc_la-ocdump.lo -MD -MP -MF .deps/liboc_la-ocdump.Tpo -c ocdump.c  -fno-common -DPIC -o .libs/liboc_la-ocdump.o
PLEASE submit a bug report to https://github.com/Homebrew/homebrew-core/issues and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0.      Program arguments: clang -DHAVE_CONFIG_H -I. -I.. -I.. -I.. -I../include -I/opt/homebrew/include -fno-strict-aliasing -MT liboc_la-ocdump.lo -MD -MP -MF .deps/liboc_la-ocdump.Tpo -c ocdump.c -fno-common -DPIC -o .libs/liboc_la-ocdump.o
1.      <eof> parser at end of file
2.      Code generation
3.      Running pass 'Function Pass Manager' on module 'ocdump.c'.
4.      Running pass 'InstructionSelect' on function '@dumpfield'
 #0 0x00000001186da9dc llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x4a129dc)
 #1 0x0000000113e27808 llvm::sys::CleanupOnSignal(unsigned long) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x15f808)
 #2 0x00000001186caa00 (anonymous namespace)::CrashRecoveryContextImpl::HandleCrash(int, unsigned long) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x4a02a00)
 #3 0x00000001186caadc CrashRecoverySignalHandler(int) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x4a02adc)
 #4 0x000000019aa3ede4 (/usr/lib/system/libsystem_platform.dylib+0x180482de4)
 #5 0x0000000114b644fc llvm::InstructionSelect::runOnMachineFunction(llvm::MachineFunction&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0xe9c4fc)
 #6 0x0000000114b644fc llvm::InstructionSelect::runOnMachineFunction(llvm::MachineFunction&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0xe9c4fc)
 #7 0x0000000114344c18 llvm::MachineFunctionPass::runOnFunction(llvm::Function&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x67cc18)
 #8 0x000000011400aa9c llvm::FPPassManager::runOnModule(llvm::Module&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x342a9c)
 #9 0x0000000113ffe70c llvm::legacy::PassManagerImpl::run(llvm::Module&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x33670c)
#10 0x00000001071d2f68 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::StringRef, llvm::Module*, clang::BackendAction, llvm::IntrusiveRefCntPtr<llvm::vfs::FileSystem>, std::__1::unique_ptr<llvm::raw_pwrite_stream, std::__1::default_delete<llvm::raw_pwrite_stream>>, clang::BackendConsumer*) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x17def68)
#11 0x000000010759f700 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x1bab700)
#12 0x0000000105c2af60 clang::ParseAST(clang::Sema&, bool, bool) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x236f60)
#13 0x0000000107d692f0 clang::FrontendAction::Execute() (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x23752f0)
#14 0x0000000107cdfda8 clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x22ebda8)
#15 0x0000000107dc2e04 clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x23cee04)
#16 0x00000001006e6b3c cc1_main(llvm::ArrayRef<char const*>, char const*, void*) (/opt/homebrew/Cellar/llvm/19.1.7/bin/clang-19+0x100006b3c)
#17 0x00000001006e478c ExecuteCC1Tool(llvm::SmallVectorImpl<char const*>&, llvm::ToolContext const&) (/opt/homebrew/Cellar/llvm/19.1.7/bin/clang-19+0x10000478c)
#18 0x000000010791a9b4 void llvm::function_ref<void ()>::callback_fn<clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const::$_0>(long) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x1f269b4)
#19 0x0000000113d5822c llvm::CrashRecoveryContext::RunSafely(llvm::function_ref<void ()>) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libLLVM.dylib+0x9022c)
#20 0x000000010791a1e4 clang::driver::CC1Command::Execute(llvm::ArrayRef<std::__1::optional<llvm::StringRef>>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>*, bool*) const (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x1f261e4)
#21 0x00000001078d06bc clang::driver::Compilation::ExecuteCommand(clang::driver::Command const&, clang::driver::Command const*&, bool) const (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x1edc6bc)
#22 0x00000001078f8140 clang::driver::Driver::ExecuteCompilation(clang::driver::Compilation&, llvm::SmallVectorImpl<std::__1::pair<int, clang::driver::Command const*>>&) (/opt/homebrew/Cellar/llvm/19.1.7/lib/libclang-cpp.dylib+0x1f04140)
#23 0x00000001006e3500 clang_main(int, char**, llvm::ToolContext const&) (/opt/homebrew/Cellar/llvm/19.1.7/bin/clang-19+0x100003500)
#24 0x00000001006f104c main (/opt/homebrew/Cellar/llvm/19.1.7/bin/clang-19+0x10001104c)
#25 0x000000019a688274 
clang: error: clang frontend command failed with exit code 139 (use -v to see invocation)
Homebrew clang version 19.1.7
Target: arm64-apple-darwin24.3.0
Thread model: posix
InstalledDir: /opt/homebrew/Cellar/llvm/19.1.7/bin
Configuration file: /opt/homebrew/etc/clang/arm64-apple-darwin24.cfg
clang: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ocdump-2069b1.c
clang: note: diagnostic msg: /var/folders/ct/rzzvxlqn4_3f9cr8wgn2pm480000gn/T/ocdump-2069b1.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: /Users/zender/Library/Logs/DiagnosticReports/clang-19_<YYYY-MM-DD-HHMMSS>_<hostname>.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your crash)
clang: note: diagnostic msg: 

********************
gmake[2]: *** [Makefile:643: liboc_la-ocdump.lo] Error 1
gmake[2]: Leaving directory '/Users/zender/netcdf-c/oc2'
gmake[1]: *** [Makefile:816: all-recursive] Error 1
gmake[1]: Leaving directory '/Users/zender/netcdf-c'
gmake: *** [Makefile:658: all] Error 2
zender@spectral:~/netcdf-c$ 

What did you expect to happen?

Expectation was that netcdf-c would compile properly instead of throwing the compiler-specific error above.

Step-by-step reproduction instructions (by running brew commands)

$ brew install llvm hdf5 cmake
    $ git clone https://github.com/Unidata/netcdf-c
    $ cd netcdf-c && mkdir build && cd build
    $ cmake .. -DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang
    $ make

[cho-m]

Could be an upstream LLVM issue but would need to try narrowing down to a minimal reproducer.

Seems to be happening in GlobalIsel which is only used in -O0. So a workaround could be a higher optimization or just disabling GlobalIsel (-mllvm --aarch64-enable-global-isel-at-O=-1).

Doesn't seem to happen if using older LLVM (brew install llvm@18) though hard to compare as main llvm is built with higher optimization (PGO + LTO) and more features enabled.

[carlocab]

I think this is an upstream issue -- I get a similar failure with upstream's build too. See https://github.com/carlocab/netcdf-llvm/actions/runs/13278624843/job/37072645813

[WardF]

Thank you! @czender, since this appears to be upstream, do you want to open an LLVM issue or shall I? Also, does the workaround in #207161 (comment) work on your end? I'll give it a test here when I get the chance, but I can only test whether it works functionally, not whether it works for your workflow. Thank you @cho-m and @carlocab!

[czender]

Thanks everyone for verifying the issue and supplying a potential workaround. I just tested to suggested compiler flag and ... it works for me! Yippee! @WardF I would appreciate it if you opened the LLVM issue since it will affect a lot of netCDF users unless/until it's fixed upstream.

[carlocab]

Closing as this is not a Homebrew-specific issue. Please report this at https://github.com/llvm/llvm-project/issues/new?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen&template=Blank+issue to ensure this is fixed.

Thanks!