Build Error on Mac (clang, linker, test_fire_energy_minimizer)

[Rob Campbell]

I'm getting a linker command error from clang 15 when trying to build version 4.2 from source on Mac. I saw that some clang 15 errors on Mac were fixed in 4.2.1, but both v4.2.0 and v4.2.1 gave me the same error. I had no issues installing on Linux, so I have access to a working version, just hoping to run from my Mac as well. Do you have any suggestions for how I can resolve this?

I encountered this error on a 2020 Macbook Pro (Intel Core i5), and had the same error on both macOS 13 (Venture) and macOS 14 (Sonoma). I am using Apple clang version 15.0.0 (clang-1500.0.40.1) and was building 4.2 using a virtual environment following the instructions on the docs (here). I tried both cloning from git and downloading specific versions from the tar files, but all the 4.2 versions I tried to install gave me the same error.

The error message I receive is at 42% when building test_fire_enery_minimizer.cc

[ 42%] Linking CXX executable test_fire_energy_minimizer
ld: Undefined symbols:
  _libintl_bind_textdomain_codeset, referenced from:
      _PyIntl_bind_textdomain_codeset in libpython3.9.a[135](_localemodule.o)
  _libintl_bindtextdomain, referenced from:
      _PyIntl_bindtextdomain in libpython3.9.a[135](_localemodule.o)
      _PyIntl_bindtextdomain in libpython3.9.a[135](_localemodule.o)
  _libintl_dcgettext, referenced from:
      _PyIntl_dcgettext in libpython3.9.a[135](_localemodule.o)
  _libintl_dgettext, referenced from:
      _PyIntl_dgettext in libpython3.9.a[135](_localemodule.o)
  _libintl_gettext, referenced from:
      _PyIntl_gettext in libpython3.9.a[135](_localemodule.o)
  _libintl_setlocale, referenced from:
      _PyLocale_setlocale in libpython3.9.a[135](_localemodule.o)
      _PyLocale_setlocale in libpython3.9.a[135](_localemodule.o)
      _PyLocale_localeconv in libpython3.9.a[135](_localemodule.o)
      _PyLocale_localeconv in libpython3.9.a[135](_localemodule.o)
      _PyLocale_localeconv in libpython3.9.a[135](_localemodule.o)
      _PyLocale_localeconv in libpython3.9.a[135](_localemodule.o)
  _libintl_textdomain, referenced from:
      _PyIntl_textdomain in libpython3.9.a[135](_localemodule.o)
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [hoomd/md/test/test_fire_energy_minimizer] Error 1
make[1]: *** [hoomd/md/test/CMakeFiles/test_fire_energy_minimizer.dir/all] Error 2
make: *** [all] Error 2


Thanks for the help!

Rob

[Joshua Anderson]

Rob,

This error is in building the C++ unit tests (ctest). You can set the CMake option BUILD_TESTING=off and see if the python module is functional with the Python unit tests (pytest).

What Python distribution do you use? HOOMD-blue should link C++ unit tests against the shared libpython3.9.dylib, not the static libpython3.9.a. It is possible that your Python distribution was built without shared libraries.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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[Rob Campbell]

That fixed it! I had installed Python 3.9.7 with pyenv, which apparently does not install shared libraries by default (or at least it didn't when I installed it). 
After reinstalling python with shared libraries enabled, I was able to install HOOMD-blue 4.2 without issue. Thanks for the help!


If anyone else comes across this issue, the pyenv command I used to install shared libraries is:

env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.7

and you can confirm that it worked by running python and checking if this returns 1 (True):

import sysconfig
sysconfig.get_config_var('Py_ENABLE_SHARED')