Struggling to install qmllib with MACOS #19

rafaelbicudo · 2025-01-01T19:20:09Z

rafaelbicudo
Jan 1, 2025

Hi, happy new year!

I've been trying to install qmllib in my MacBook Air with M2, but I have been encountering the following error:

$ pip install qmllib
Collecting qmllib
  Using cached qmllib-1.1.5.tar.gz (99 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [123 lines of output]
      Using numpy 2.2.1
      export FFLAGS='-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
      export LDFLAGS='-lgomp -lpthread -lm -ldl -L/usr/lib/ -lblas -llapack'
      export FCC='gfortran'
      src/qmllib/representations /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12 -m numpy.f2py -c frepresentations.f90 -m frepresentations --backend meson
      Traceback (most recent call last):
        File "<frozen runpy>", line 198, in _run_module_as_main
        File "<frozen runpy>", line 88, in _run_code
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/__main__.py", line 5, in <module>
          main()
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/f2py2e.py", line 781, in main
          run_compile()
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/f2py2e.py", line 753, in run_compile
          builder.compile()
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/_backends/_meson.py", line 192, in compile
          self.run_meson(self.build_dir)
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/_backends/_meson.py", line 185, in run_meson
          self._run_subprocess_command(setup_command, build_dir)
        File "/private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/pip-build-env-91j343s2/overlay/lib/python3.12/site-packages/numpy/f2py/_backends/_meson.py", line 181, in _run_subprocess_command
          subprocess.run(command, cwd=cwd, check=True)
        File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/subprocess.py", line 571, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command '['meson', 'setup', 'bbdir']' returned non-zero exit status 1.


      The Meson build system
      Version: 1.6.1
      Source dir: /private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/tmpt0hdr3ec
      Build dir: /private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/tmpt0hdr3ec/bbdir
      Build type: native build
      Project name: frepresentations
      Project version: 0.1
      Fortran compiler for the host machine: gfortran (gcc 14.2.0 "GNU Fortran (Homebrew GCC 14.2.0_1) 14.2.0")
      Fortran linker for the host machine: gfortran ld64 1115.7.3

      meson.build:1:0: ERROR: Compiler cc cannot compile programs.

      A full log can be found at /private/var/folders/cn/gkwl43dx66b_sg1bzsht0_p40000gn/T/tmpt0hdr3ec/bbdir/meson-logs/meson-log.txt
      Using meson backend
      Will pass --lower to f2py
      See https://numpy.org/doc/stable/f2py/buildtools/meson.html
      Reading fortran codes...
          Reading file 'frepresentations.f90' (format:free)
      Post-processing...
          Block: frepresentations
                          Block: representations
                                  Block: get_indices
                          Block: fgenerate_coulomb_matrix
      In: :frepresentations:frepresentations.f90:fgenerate_coulomb_matrix
      analyzevars: could not parse dimension for variable '((nmax + 1)*nmax)/2'
                          Block: fgenerate_unsorted_coulomb_matrix
      In: :frepresentations:frepresentations.f90:fgenerate_unsorted_coulomb_matrix
      analyzevars: could not parse dimension for variable '((nmax + 1)*nmax)/2'
                          Block: fgenerate_local_coulomb_matrix
      In: :frepresentations:frepresentations.f90:fgenerate_local_coulomb_matrix
      param_eval: got "eval() arg 1 must be a string, bytes or code object" on 8
      In: :frepresentations:frepresentations.f90:fgenerate_local_coulomb_matrix
      analyzevars: could not parse dimension for variable '((nmax + 1)*nmax)/2'
                          Block: fgenerate_atomic_coulomb_matrix
      In: :frepresentations:frepresentations.f90:fgenerate_atomic_coulomb_matrix
      param_eval: got "eval() arg 1 must be a string, bytes or code object" on 8
      In: :frepresentations:frepresentations.f90:fgenerate_atomic_coulomb_matrix
      analyzevars: could not parse dimension for variable '((nmax + 1)*nmax)/2'
                          Block: fgenerate_eigenvalue_coulomb_matrix
                          Block: fgenerate_bob
      Applying post-processing hooks...
        character_backward_compatibility_hook
      Post-processing (stage 2)...
          Block: frepresentations
                  Block: unknown_interface
                          Block: representations
                                  Block: get_indices
                          Block: fgenerate_coulomb_matrix
                          Block: fgenerate_unsorted_coulomb_matrix
                          Block: fgenerate_local_coulomb_matrix
                          Block: fgenerate_atomic_coulomb_matrix
                          Block: fgenerate_eigenvalue_coulomb_matrix
                          Block: fgenerate_bob
      Building modules...
          Building module "frepresentations"...
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_coulomb_matrix"("fgenerate_coulomb_matrix")...
              Constructing wrapper function "fgenerate_coulomb_matrix"...
                cm = fgenerate_coulomb_matrix(atomic_charges,coordinates,nmax)
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_unsorted_coulomb_matrix"("fgenerate_unsorted_coulomb_matrix")...
              Constructing wrapper function "fgenerate_unsorted_coulomb_matrix"...
                cm = fgenerate_unsorted_coulomb_matrix(atomic_charges,coordinates,nmax)
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_local_coulomb_matrix"("fgenerate_local_coulomb_matrix")...
              Constructing wrapper function "fgenerate_local_coulomb_matrix"...
                cm = fgenerate_local_coulomb_matrix(central_atom_indices,central_natoms,atomic_charges,coordinates,natoms,nmax,cent_cutoff,cent_decay,int_cutoff,int_decay)
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_atomic_coulomb_matrix"("fgenerate_atomic_coulomb_matrix")...
              Constructing wrapper function "fgenerate_atomic_coulomb_matrix"...
                cm = fgenerate_atomic_coulomb_matrix(central_atom_indices,central_natoms,atomic_charges,coordinates,natoms,nmax,cent_cutoff,cent_decay,int_cutoff,int_decay)
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_eigenvalue_coulomb_matrix"("fgenerate_eigenvalue_coulomb_matrix")...
              Constructing wrapper function "fgenerate_eigenvalue_coulomb_matrix"...
                sorted_eigenvalues = fgenerate_eigenvalue_coulomb_matrix(atomic_charges,coordinates,nmax)
          Generating possibly empty wrappers"
          Maybe empty "frepresentations-f2pywrappers2.f90"
          Maybe empty "frepresentations-f2pywrappers.f"
                  Creating wrapper for Fortran subroutine "fgenerate_bob"("fgenerate_bob")...
              Constructing wrapper function "fgenerate_bob"...
                cm = fgenerate_bob(atomic_charges,coordinates,nuclear_charges,id,nmax,ncm)
                  Constructing F90 module support for "representations"...
                  Creating wrapper for Fortran subroutine "get_indices"("get_indices")...
                  Constructing wrapper function "representations.get_indices"...
                    type1_indices = get_indices(natoms,nuclear_charges,type1,n)
          Wrote C/API module "frepresentations" to file "./frepresentationsmodule.c"
          Fortran 90 wrappers are saved to "./frepresentations-f2pywrappers2.f90"

      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

I reinstalled gcc using brew and also followed the recommendations on the QML website to install it on MacOS, but I still get this same error. Do you have any idea how to fix it?

Thanks,
Rafael.

Answered by rafaelbicudo

Jan 8, 2025

Hi @charnley,

Thanks for the reply. Removing the -lgomp flag fixed it and I managed to compile it successfully. However, I had some issues when trying to use the rmsd package combined with qmllib in parallel. Specifically, it failed to import the generate_fchl19() function inside the calculate_rmsd.py script.

To make it work, I installed libomp via brew and changed the _compile.py file to add a few flags and paths. I'm sending the file attached (as a .txt) in case you want to check it.

Thanks for the support!

Best,
Rafael.

_compile.py.txt

View full answer

charnley · 2025-01-07T09:34:31Z

charnley
Jan 7, 2025
Maintainer

Hi @rafaelbicudo ,

There are some issues with OpenMP on Mac. For now, you can clone down the repository and remove -lgomp from the compiler flags in _compile.py. Then you should be able to install it.

Will find a general fix and push a new version to pip, ASAP.

4 replies

rafaelbicudo Jan 8, 2025
Author

Hi @charnley,

Thanks for the reply. Removing the -lgomp flag fixed it and I managed to compile it successfully. However, I had some issues when trying to use the rmsd package combined with qmllib in parallel. Specifically, it failed to import the generate_fchl19() function inside the calculate_rmsd.py script.

To make it work, I installed libomp via brew and changed the _compile.py file to add a few flags and paths. I'm sending the file attached (as a .txt) in case you want to check it.

Thanks for the support!

Best,
Rafael.

_compile.py.txt

Answer selected by charnley

charnley Jan 9, 2025
Maintainer

Interesting. I tried the same arguments on my Mac, but it didn't work. I will try again later today.

rafaelbicudo Jan 9, 2025
Author

I tried many different things before making it work, so maybe I set some additional environment variables I don't remember. If you want, I can try to recompile it to be sure about the details.

charnley Jan 10, 2025
Maintainer

It worked for me as well. I've added the changes to PR [#21]. I will merge them soon and make a new pip version.

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