Build failing on MacOS 15.2 (M1)

[sun51027]

Dear developers,

I am installing Hermes-3 (along with its automatic download of BOUT-dev) on my personal laptop (M1 Mac) running macOS 15.2. I have executed the cmake command: $ cmake . -B build -DBOUT_DOWNLOAD_SUNDIALS=ON -DBOUT_ENABLE_BACKTRACE=Off -DCMAKE_OSX_ARCHITECTURES=arm64 then built it by $ cmake --build build However, it is quite tricky for me to solve the issue below:

[ 13%] Built target pvode
[ 14%] Building CXX object external/BOUT-dev/externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o
[ 14%] Building CXX object external/BOUT-dev/externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/band.cpp.o
[ 14%] Linking CXX shared library ../../lib/libpvpre.dylib
Undefined symbols for architecture arm64:
  "pvode::N_VWrmsNorm(pvode::nvec_type*, pvode::nvec_type*)", referenced from:
      pvode::PVBBDPrecon(int, double, pvode::nvec_type*, pvode::nvec_type*, int, int*, double, pvode::nvec_type*, double, double, long*, void*, pvode::nvec_type*, pvode::nvec_type*, pvode::nvec_type*) in pvbbdpre.cpp.o
  "pvode::RSqrt(double)", referenced from:
      pvode::PVBBDPrecon(int, double, pvode::nvec_type*, pvode::nvec_type*, int, int*, double, pvode::nvec_type*, double, double, long*, void*, pvode::nvec_type*, pvode::nvec_type*, pvode::nvec_type*) in pvbbdpre.cpp.o
  "pvode::N_VScale(double, pvode::nvec_type*, pvode::nvec_type*)", referenced from:
      pvode::PVBBDPrecon(int, double, pvode::nvec_type*, pvode::nvec_type*, int, int*, double, pvode::nvec_type*, double, double, long*, void*, pvode::nvec_type*, pvode::nvec_type*, pvode::nvec_type*) in pvbbdpre.cpp.o
      pvode::PVBBDPSol(int, double, pvode::nvec_type*, pvode::nvec_type*, pvode::nvec_type*, double, pvode::nvec_type*, double, long*, pvode::nvec_type*, int, void*, pvode::nvec_type*) in pvbbdpre.cpp.o
ld: symbol(s) not found for architecture arm64
c++: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [external/BOUT-dev/lib/libpvpre.1.0.0.dylib] Error 1
make[1]: *** [external/BOUT-dev/externalpackages/PVODE/CMakeFiles/pvpre.dir/all] Error 2
make: *** [all] Error 2

I will appreciate if you could point me how to address this. Thank you!

[bendudson]

Welcome @sun51027 ! This is interesting; You may be the first person to try this on an M1 laptop :)

What happens if you don't specify the architecture? The system compiler should compile for the system architecture so this may work (?):

cmake . -B build -DBOUT_DOWNLOAD_SUNDIALS=ON -DBOUT_ENABLE_BACKTRACE=Off

I have an old Mac, and often have problems with shared libraries (like this .dylib). One thing you can try is disabling shared libraries (using -DBUILD_SHARED_LIBS=Off) and other things that can go wrong on MacOS:

cmake . -B build -DBOUT_DOWNLOAD_SUNDIALS=ON -DBOUT_ENABLE_BACKTRACE=Off -DBUILD_SHARED_LIBS=Off -DBOUT_USE_NLS=Off -DBOUT_USE_UUID_SYSTEM_GENERATOR=Off

[sun51027]

Hi @bendudson, thank you for your prompt response.

The second command you gave worked until the new error below:

[ 42%] Building CXX object external/BOUT-dev/CMakeFiles/bout++.dir/src/mesh/mesh.cxx.o
[ 44%] Building CXX object external/BOUT-dev/CMakeFiles/bout++.dir/src/mesh/parallel/fci.cxx.o
/Users/zero/workspace/phd_work/hermes-3/external/BOUT-dev/src/mesh/parallel/fci.cxx:295:13: error: no matching function for call to 'finite'
  295 |     ASSERT2(finite(result[inext]));
      |             ^~~~~~
/Users/zero/workspace/phd_work/hermes-3/external/BOUT-dev/include/bout/assert.hxx:50:9: note: expanded from macro 'ASSERT2'
   50 |   if (!(condition)) {                                                                    \
      |         ^~~~~~~~~
/Users/zero/workspace/phd_work/hermes-3/external/BOUT-dev/include/bout/field.hxx:632:13: note: candidate template ignored: requirement 'is_Field_v<double>' was not satisfied [with T = BoutReal]
  632 | inline bool finite(const T& f, const std::string& rgn = "RGN_ALL") {
      |             ^
1 error generated.
make[2]: *** [external/BOUT-dev/CMakeFiles/bout++.dir/src/mesh/parallel/fci.cxx.o] Error 1
make[1]: *** [external/BOUT-dev/CMakeFiles/bout++.dir/all] Error 2
make: *** [all] Error 2

On the other hand, I’m also curious about what will happen if we disable shared libraries, such as how it might affect execution (?) Thank you :)

[dschwoerer]

Ah, it seems we use are aware that finite is not-standard:

#ifdef _MSC_VER
// finite is not actually standard C++, it's a BSD extention for C
inline auto finite(BoutReal x) -> bool { return std::isfinite(x); }

So we just need to adjust the check above for whatever compiler you are using ...

Do you know how to check for that compiler?

[ZedThree]

Oh, we should probably just switch to the standard one anyway!

[bendudson]

Hi @sun51027 ! Could you please try updating Hermes-3 (git pull should do it), then try configuring again? On my old (x86) mac this works:

cmake . -B build -DBOUT_DOWNLOAD_SUNDIALS=ON -DBOUT_ENABLE_BACKTRACE=Off -DBOUT_USE_NLS=Off -DBOUT_USE_UUID_SYSTEM_GENERATOR=Off

The latest BOUT++ had problems building on mac, that I think are now fixed https://github.com/boutproject/BOUT-dev/pull/3063

I updated Hermes-3 to use the latest BOUT++ version, that includes the new fixes: https://github.com/bendudson/hermes-3/pull/284

[sun51027]

Hi @bendudson Thank you for the update and the new command. However, a new error pop up after I git pull Hermes-3.

[ 59%] Linking CXX shared library lib/libbout++.dylib
ld: library 'hdf5_hl-shared' not found
c++: error: linker command failed with exit code 1 (use -v to see invocation)

I’ve been trying to solve this for a while, but I still failed. Could you point out how to solve this? Thank you very much!