December 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Kokkos build fail
by Mark Adams 09 Dec '21

09 Dec '21

OK, trying to use clang12. Installed it with brew and xcode clang (v13) and they both give this version error. Using C++ dialect c++14 as lower bound due to package(s): - kokkos But C++ compiler (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++) appears non-compliant with c++14 or didn't accept: - -std=gnu++17 - -std=c++17 - -std=gnu++14 - -std=c++14 ******************************************************************************* On Thu, Dec 9, 2021 at 8:57 AM Satish Balay <balay(a)mcs.anl.gov> wrote: > My build is with xcode clang - not brew clang > > Satish > > On Thu, 9 Dec 2021, Mark Adams wrote: > > > Mpich seems to give the same error. > > I use clang 13.0. I think I get that from homebrew. > > Should I try something like: > > brew install llvm@12 > > > > I see: > > > > (conda_env) 07:50 adams/fix_mat_ex5k= ~/Codes/petsc2$ brew info llvm > > llvm: stable 13.0.0 (bottled), HEAD [keg-only] > > Next-gen compiler infrastructure > > https://llvm.org/ > > Not installed > > From: > https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/llvm.rb > > License: Apache-2.0 with LLVM-exception > > ==> Dependencies > > Build: cmake ✔, swig ✘ > > Required: python(a)3.10 ✘ > > ==> Options > > --HEAD > > Install HEAD version > > ==> Caveats > > To use the bundled libc++ please add the following LDFLAGS: > > LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" > > > > llvm is keg-only, which means it was not symlinked into /usr/local, > > because macOS already provides this software and installing another > version > > in > > parallel can cause all kinds of trouble. > > > > ==> Analytics > > install: 32,204 (30 days), 98,525 (90 days), 299,560 (365 days) > > install-on-request: 17,978 (30 days), 62,171 (90 days), 212,999 (365 > days) > > build-error: 2,696 (30 days) > > > > > > On Wed, Dec 8, 2021 at 1:30 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > > This build goes through fine for me. [with petsc/main] > > > > > > xpro:petsc balay$ sw_vers > > > ProductName: Mac OS X > > > ProductVersion: 10.15.7 > > > BuildVersion: 19H1519 > > > xpro:petsc balay$ clang --version > > > Apple clang version 12.0.0 (clang-1200.0.32.2) > > > <snip> > > > xpro:petsc balay$ ./configure --download-mpich --with-fc=0 > COPTFLAGS="-g > > > -O" CXXOPTFLAGS="-g -O" --with-fortran-bindings=0 --download-kokkos=1 > > > --download-kokkos-kernels=1 --with-kokkos-kernels-tpl=0 --with-zlib=1 > > > --with-x=0 > > > > > > Satish > > > > > > > > > On Wed, 8 Dec 2021, Jacob Faibussowitsch wrote: > > > > > > > > And your algorithm looks idempotent to me.... > > > > > > > > Believe me, I was sufficiently shocked when everything magically > started > > > working the 3rd time around :) > > > > > > > > Best regards, > > > > > > > > Jacob Faibussowitsch > > > > (Jacob Fai - booss - oh - vitch) > > > > > > > > > On Dec 8, 2021, at 09:29, Mark Adams <mfadams(a)lbl.gov> wrote: > > > > > > > > > > Thanks, > > > > > And your algorithm looks idempotent to me.... > > > > > > > > > > > > > > > On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch < > > > jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > > > > > 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… > > > < > > > > https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers… > > > > > > > > > 3. > > > > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > > < > > > > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > > > > > > > > > > > > > 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(a)lbl.gov <mailto: > > > mfadams(a)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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto: > > > mfadams(a)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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perlmutter - nvhpc warnings
by Mark Adams 09 Dec '21

09 Dec '21

FYI, Perlmutter was upgraded to a new nvhpc and I get a lot of warning in make all: warning: incompatible redefinition of macro "CUDA_VERSION" and a lot of cupsarse deprecation warnings. Thanks, Mark

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Re: [petsc-dev] Kokkos build fail
by Satish Balay 09 Dec '21

09 Dec '21

My build is with xcode clang - not brew clang Satish On Thu, 9 Dec 2021, Mark Adams wrote: > Mpich seems to give the same error. > I use clang 13.0. I think I get that from homebrew. > Should I try something like: > brew install llvm@12 > > I see: > > (conda_env) 07:50 adams/fix_mat_ex5k= ~/Codes/petsc2$ brew info llvm > llvm: stable 13.0.0 (bottled), HEAD [keg-only] > Next-gen compiler infrastructure > https://llvm.org/ > Not installed > From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/llvm.rb > License: Apache-2.0 with LLVM-exception > ==> Dependencies > Build: cmake ✔, swig ✘ > Required: python(a)3.10 ✘ > ==> Options > --HEAD > Install HEAD version > ==> Caveats > To use the bundled libc++ please add the following LDFLAGS: > LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" > > llvm is keg-only, which means it was not symlinked into /usr/local, > because macOS already provides this software and installing another version > in > parallel can cause all kinds of trouble. > > ==> Analytics > install: 32,204 (30 days), 98,525 (90 days), 299,560 (365 days) > install-on-request: 17,978 (30 days), 62,171 (90 days), 212,999 (365 days) > build-error: 2,696 (30 days) > > > On Wed, Dec 8, 2021 at 1:30 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > > > This build goes through fine for me. [with petsc/main] > > > > xpro:petsc balay$ sw_vers > > ProductName: Mac OS X > > ProductVersion: 10.15.7 > > BuildVersion: 19H1519 > > xpro:petsc balay$ clang --version > > Apple clang version 12.0.0 (clang-1200.0.32.2) > > <snip> > > xpro:petsc balay$ ./configure --download-mpich --with-fc=0 COPTFLAGS="-g > > -O" CXXOPTFLAGS="-g -O" --with-fortran-bindings=0 --download-kokkos=1 > > --download-kokkos-kernels=1 --with-kokkos-kernels-tpl=0 --with-zlib=1 > > --with-x=0 > > > > Satish > > > > > > On Wed, 8 Dec 2021, Jacob Faibussowitsch wrote: > > > > > > And your algorithm looks idempotent to me.... > > > > > > Believe me, I was sufficiently shocked when everything magically started > > working the 3rd time around :) > > > > > > Best regards, > > > > > > Jacob Faibussowitsch > > > (Jacob Fai - booss - oh - vitch) > > > > > > > On Dec 8, 2021, at 09:29, Mark Adams <mfadams(a)lbl.gov> wrote: > > > > > > > > Thanks, > > > > And your algorithm looks idempotent to me.... > > > > > > > > > > > > On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch < > > jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > > > > 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… > > < > > https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers… > > > > > > > 3. > > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > < > > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > > > > > > > > > > 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(a)lbl.gov <mailto: > > mfadams(a)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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto: > > mfadams(a)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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Re: [petsc-dev] Kokkos build fail
by Mark Adams 09 Dec '21

09 Dec '21

Mpich seems to give the same error. I use clang 13.0. I think I get that from homebrew. Should I try something like: brew install llvm@12 I see: (conda_env) 07:50 adams/fix_mat_ex5k= ~/Codes/petsc2$ brew info llvm llvm: stable 13.0.0 (bottled), HEAD [keg-only] Next-gen compiler infrastructure https://llvm.org/ Not installed From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/llvm.rb License: Apache-2.0 with LLVM-exception ==> Dependencies Build: cmake ✔, swig ✘ Required: python(a)3.10 ✘ ==> Options --HEAD Install HEAD version ==> Caveats To use the bundled libc++ please add the following LDFLAGS: LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" llvm is keg-only, which means it was not symlinked into /usr/local, because macOS already provides this software and installing another version in parallel can cause all kinds of trouble. ==> Analytics install: 32,204 (30 days), 98,525 (90 days), 299,560 (365 days) install-on-request: 17,978 (30 days), 62,171 (90 days), 212,999 (365 days) build-error: 2,696 (30 days) On Wed, Dec 8, 2021 at 1:30 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > This build goes through fine for me. [with petsc/main] > > xpro:petsc balay$ sw_vers > ProductName: Mac OS X > ProductVersion: 10.15.7 > BuildVersion: 19H1519 > xpro:petsc balay$ clang --version > Apple clang version 12.0.0 (clang-1200.0.32.2) > <snip> > xpro:petsc balay$ ./configure --download-mpich --with-fc=0 COPTFLAGS="-g > -O" CXXOPTFLAGS="-g -O" --with-fortran-bindings=0 --download-kokkos=1 > --download-kokkos-kernels=1 --with-kokkos-kernels-tpl=0 --with-zlib=1 > --with-x=0 > > Satish > > > On Wed, 8 Dec 2021, Jacob Faibussowitsch wrote: > > > > And your algorithm looks idempotent to me.... > > > > Believe me, I was sufficiently shocked when everything magically started > working the 3rd time around :) > > > > Best regards, > > > > Jacob Faibussowitsch > > (Jacob Fai - booss - oh - vitch) > > > > > On Dec 8, 2021, at 09:29, Mark Adams <mfadams(a)lbl.gov> wrote: > > > > > > Thanks, > > > And your algorithm looks idempotent to me.... > > > > > > > > > On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch < > jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > > > 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… > < > https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers… > > > > > 3. > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > < > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > > > > > > > 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(a)lbl.gov <mailto: > mfadams(a)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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto: > mfadams(a)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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Re: [petsc-dev] Kokkos build fail
by Satish Balay 08 Dec '21

08 Dec '21

This build goes through fine for me. [with petsc/main] xpro:petsc balay$ sw_vers ProductName: Mac OS X ProductVersion: 10.15.7 BuildVersion: 19H1519 xpro:petsc balay$ clang --version Apple clang version 12.0.0 (clang-1200.0.32.2) <snip> xpro:petsc balay$ ./configure --download-mpich --with-fc=0 COPTFLAGS="-g -O" CXXOPTFLAGS="-g -O" --with-fortran-bindings=0 --download-kokkos=1 --download-kokkos-kernels=1 --with-kokkos-kernels-tpl=0 --with-zlib=1 --with-x=0 Satish On Wed, 8 Dec 2021, Jacob Faibussowitsch wrote: > > And your algorithm looks idempotent to me.... > > Believe me, I was sufficiently shocked when everything magically started working the 3rd time around :) > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > > > On Dec 8, 2021, at 09:29, Mark Adams <mfadams(a)lbl.gov> wrote: > > > > Thanks, > > And your algorithm looks idempotent to me.... > > > > > > On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > > 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… <https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers…> > > 3. https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… <https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with…> > > > > 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(a)lbl.gov <mailto:[email protected]>> 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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> 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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Re: [petsc-dev] Kokkos build fail
by Jacob Faibussowitsch 08 Dec '21

08 Dec '21

> And your algorithm looks idempotent to me.... Believe me, I was sufficiently shocked when everything magically started working the 3rd time around :) Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) > On Dec 8, 2021, at 09:29, Mark Adams <mfadams(a)lbl.gov> wrote: > > Thanks, > And your algorithm looks idempotent to me.... > > > On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: > 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… <https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers…> > 3. https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… <https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with…> > > 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(a)lbl.gov <mailto:[email protected]>> 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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> 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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Re: [petsc-dev] Kokkos build fail
by Mark Adams 08 Dec '21

08 Dec '21

Thanks, And your algorithm looks idempotent to me.... On Wed, Dec 8, 2021 at 9:13 AM Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > 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 > 2. > https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers… > 3. > https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… > > 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(a)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(a)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(a)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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Re: [petsc-dev] Kokkos build fail
by Jacob Faibussowitsch 08 Dec '21

08 Dec '21

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… <https://stackoverflow.com/questions/58628377/catalina-c-using-cmath-headers…> 3. https://stackoverflow.com/questions/58313047/cannot-compile-r-packages-with… 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(a)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(a)gmail.com <mailto:[email protected]>> 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(a)lbl.gov <mailto:[email protected]>> 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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Re: [petsc-dev] Kokkos build fail
by Mark Adams 08 Dec '21

08 Dec '21

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(a)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(a)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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Re: [petsc-dev] Kokkos build fail
by Jacob Faibussowitsch 08 Dec '21

08 Dec '21

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(a)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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