[petsc-dev] Kokkos build fail

Jacob Faibussowitsch jacob.fai at gmail.com
Wed Dec 8 08:13:56 CST 2021

So I had similar issues back when I originally wrote the clang linter — on Big Sur. The TL;DR for me was that Catalina originally shipped with broken cmath headers, something future updates wouldn’t necessarily fix. The only way to fix it was to:

1. Reinstall CLT
2. Reinstall/install Xcode
3. Repeat the above until it was fixed

Now you may have an unrelated issue, but my error messages (e.g. about missing “signbit”, “std::less_than”, etc in global namespace) were very very similar. See discussions here:

1. https://gitlab.com/petsc/petsc/-/merge_requests/3773 <https://gitlab.com/petsc/petsc/-/merge_requests/3773>
2. https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers-yield-error-no-member-named-signbit-in-th <https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers-yield-error-no-member-named-signbit-in-th>
3. https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with-c-code-after-updating-to-macos-catalina

If these help then you’re lucky I never clean out my “misc” bookmarks folder :)

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)

> On Dec 8, 2021, at 09:06, Mark Adams <mfadams at lbl.gov> wrote:
> Monterey.
> And my serial, optimized build works but it seems to use the same compiler.
> I am testing the parallel build again with debug turned off.
> On Wed, Dec 8, 2021 at 9:04 AM Jacob Faibussowitsch <jacob.fai at gmail.com <mailto:jacob.fai at gmail.com>> wrote:
> You aren’t by chance on Catalina are you?
> Best regards,
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
>> On Dec 8, 2021, at 08:49, Mark Adams <mfadams at lbl.gov <mailto:mfadams at lbl.gov>> wrote:
>> I am failing on OSX with openmpi. Kokkos is failing to build.
>> I seem to be using:
>> (conda_env) 08:46 1 adams/fix_mat_ex5k *= ~/Codes/petsc2$ /usr/local/Cellar/open-mpi/4.1.1_2/bin/mpicxx --version
>> Apple clang version 13.0.0 (clang-1300.0.29.3)
>> Target: x86_64-apple-darwin21.1.0
>> Thread model: posix
>> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>> Any ideas?
>> Thanks,
>> Mark
>> <configure.log>

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