DedalusProject / dedalus

A flexible framework for solving PDEs with modern spectral methods.
http://dedalus-project.org/
GNU General Public License v3.0
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ERROR: Could not build wheels for dedalus, which is required to install pyproject.toml-based projects #234

Closed SomePersonSomeWhereInTheWorld closed 1 year ago

SomePersonSomeWhereInTheWorld commented 1 year ago

On RHEL 8, fftw 3.3.10 with threads and OpenMPI 4.1.5a1, and Python 3.9.12, when running pip3 install --no-cache http://github.com/dedalusproject/dedalus/zipball/master/ first errors:

Building wheels for collected packages: dedalus, docopt
  Building wheel for dedalus (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for dedalus (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [456 lines of output]
      Looking for mpi include path
        Found env var MPI_INCLUDE_PATH = /usr/mpi/gcc/openmpi-4.1.5a1/include
      Looking for fftw include path
        Found env var FFTW_INCLUDE_PATH = /cm/shared/apps/fftw/openmpi/gcc/64/3.3.10/include
      Looking for fftw library path
        Found env var FFTW_LIBRARY_PATH = /cm/shared/apps/fftw/openmpi/gcc/64/3.3.10/lib
      Looking for mpi library path
        Found env var MPI_LIBRARY_PATH = /path/to/mpi/gcc/openmpi-4.1.5a1/lib64
      /tmp/pip-build-env-o74lj2tx/overlay/lib/python3.9/site-packages/setuptools/dist.py:529: UserWarning: Normalizing '3.0.0a' to '3.0.0a0'
        warnings.warn(tmpl.format(**locals()))

many of these relocation errors such as: /path/to/anaconda3-2022.05/compiler_compat/ld: /cm/shared/apps/fftw/openmpi/gcc/64/3.3.10/lib/libfftw3.a(hc2hc-direct.o): relocation R_X86_64_32 against '.text' can not be used when making a shared object; recompile with -fPIC Then ends with:

direct.o): relocation R_X86_64_32 against `.text' can not be used when making a shared object; recompile with -fPIC
      /path/to/anaconda3-2022.05/compiler_compat/ld: /cm/shared/apps/fftw/openmpi/gcc/64/3.3.10/lib/libfftw3.a(codlist.o): warning: relocation in read-only section `.rodata'
      collect2: error: ld returned 1 exit status
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for dedalus
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=cba83f2b808093ac64014a8a8e608d1c16361c1be64b2843de35f0343b337aae
  Stored in directory: /tmp/pip-ephem-wheel-cache-r3nknbh0/wheels/4e/29/5e/e5f6f558e24e0d70f6808e3e8fdaf2c04ff597233098afc550
Successfully built docopt
Failed to build dedalus
ERROR: Could not build wheels for dedalus, which is required to install pyproject.toml-based projects

Is a package missing or incorrect path to something?

kburns commented 1 year ago

Discussing this stack installation on the mailing list.