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PLUMED doesn't recognise Cython during install #1185

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a-ws-m opened this issue Jan 24, 2025 · 1 comment
Open

PLUMED doesn't recognise Cython during install #1185

a-ws-m opened this issue Jan 24, 2025 · 1 comment

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@a-ws-m
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a-ws-m commented Jan 24, 2025 •
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I'm trying to install PLUMED from the current master branch.
I would like PLUMED to use a python environment created by micromamba, in which I have installed cython and some other packages (see below).

During ./configure --disable-mpi, PLUMED recognises that Cython is installed:

checking for python3... python3
configure: Python executable is python3
checking pycv: support for required python modules (python3, pybind11, numpy)... yes
checking python wrapper: support for required python modules (python3, setuptools, cython)... yes

Running make -j 4 also has no issues. However, during sudo make install, I get the following:

cd install/python && rm -fr *.so plumed.cpp build && \
          unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
          plumed_program_name=plumed \
          plumed_force_cython=yes \
          plumed_version=2.11.0-dev \
          plumed_include_dir=../../../wrapper \
          plumed_default_kernel="/usr/local/lib/libplumedKernel.so" \
          python3 setup.py build_ext -i
Module name plumed
Version number 2.11.0-dev
Hardcoded PLUMED_KERNEL /usr/local/lib/libplumedKernel.so
plumed_force_cython=yes
importing cython
Error: building plumed requires cython. Please install it first with pip install cython

The packages in my environment are as follows:

List of packages in environment: "/home/awsm/micromamba/envs/pycv"

  Name                         Version     Build                     Channel
──────────────────────────────────────────────────────────────────────────────────
  _libgcc_mutex                0.1         conda_forge               conda-forge
  _openmp_mutex                4.5         2_gnu                     conda-forge
  bzip2                        1.0.8       h4bc722e_7                conda-forge
  c-ares                       1.34.4      hb9d3cd8_0                conda-forge
  ca-certificates              2024.12.14  hbcca054_0                conda-forge
  cuda-cccl_linux-64           12.6.77     ha770c72_0                conda-forge
  cuda-crt-dev_linux-64        12.6.85     ha770c72_0                conda-forge
  cuda-crt-tools               12.6.85     ha770c72_0                conda-forge
  cuda-cudart                  12.6.77     h5888daf_0                conda-forge
  cuda-cudart-dev_linux-64     12.6.77     h3f2d84a_0                conda-forge
  cuda-cudart-static_linux-64  12.6.77     h3f2d84a_0                conda-forge
  cuda-cudart_linux-64         12.6.77     h3f2d84a_0                conda-forge
  cuda-cupti                   12.6.80     hbd13f7d_0                conda-forge
  cuda-cupti-dev               12.6.80     h5888daf_0                conda-forge
  cuda-nvcc-tools              12.6.85     he02047a_0                conda-forge
  cuda-nvrtc                   12.6.85     hbd13f7d_0                conda-forge
  cuda-nvtx                    12.6.77     hbd13f7d_0                conda-forge
  cuda-nvvm-tools              12.6.85     he02047a_0                conda-forge
  cuda-version                 12.6        h7480c83_3                conda-forge
  cudnn                        9.3.0.75    h62a6f1c_2                conda-forge
  cython                       3.0.11      py312h8fd2918_3           conda-forge
  importlib-metadata           8.6.1       pyha770c72_0              conda-forge
  jax                          0.4.35      pyhd8ed1ab_1              conda-forge
  jaxlib                       0.4.35      cuda126py312hd27b167_200  conda-forge
  ld_impl_linux-64             2.43        h712a8e2_2                conda-forge
  libabseil                    20240722.0  cxx17_hbbce691_4          conda-forge
  libblas                      3.9.0       26_linux64_openblas       conda-forge
  libcblas                     3.9.0       26_linux64_openblas       conda-forge
  libcublas                    12.6.4.1    hbd13f7d_0                conda-forge
  libcublas-dev                12.6.4.1    h5888daf_0                conda-forge
  libcufft                     11.3.0.4    hbd13f7d_0                conda-forge
  libcufft-dev                 11.3.0.4    h5888daf_0                conda-forge
  libcurand                    10.3.7.77   hbd13f7d_0                conda-forge
  libcurand-dev                10.3.7.77   h5888daf_0                conda-forge
  libcusolver                  11.7.1.2    hbd13f7d_0                conda-forge
  libcusolver-dev              11.7.1.2    h5888daf_0                conda-forge
  libcusparse                  12.5.4.2    hbd13f7d_0                conda-forge
  libcusparse-dev              12.5.4.2    h5888daf_0                conda-forge
  libexpat                     2.6.4       h5888daf_0                conda-forge
  libffi                       3.4.2       h7f98852_5                conda-forge
  libgcc                       14.2.0      h77fa898_1                conda-forge
  libgcc-ng                    14.2.0      h69a702a_1                conda-forge
  libgfortran                  14.2.0      h69a702a_1                conda-forge
  libgfortran5                 14.2.0      hd5240d6_1                conda-forge
  libgomp                      14.2.0      h77fa898_1                conda-forge
  libgrpc                      1.67.1      h25350d4_1                conda-forge
  liblapack                    3.9.0       26_linux64_openblas       conda-forge
  liblzma                      5.6.3       hb9d3cd8_1                conda-forge
  libnsl                       2.0.1       hd590300_0                conda-forge
  libnvjitlink                 12.6.85     hbd13f7d_0                conda-forge
  libopenblas                  0.3.28      pthreads_h94d23a6_1       conda-forge
  libprotobuf                  5.28.3      h6128344_1                conda-forge
  libre2-11                    2024.07.02  hbbce691_2                conda-forge
  libsqlite                    3.48.0      hee588c1_1                conda-forge
  libstdcxx                    14.2.0      hc0a3c3a_1                conda-forge
  libstdcxx-ng                 14.2.0      h4852527_1                conda-forge
  libuuid                      2.38.1      h0b41bf4_0                conda-forge
  libxcrypt                    4.4.36      hd590300_1                conda-forge
  libzlib                      1.3.1       hb9d3cd8_2                conda-forge
  ml_dtypes                    0.5.1       py312hf9745cd_0           conda-forge
  nccl                         2.24.3.1    hb92ee24_0                conda-forge
  ncurses                      6.5         h2d0b736_2                conda-forge
  numpy                        2.2.2       py312h72c5963_0           conda-forge
  openssl                      3.4.0       h7b32b05_1                conda-forge
  opt-einsum                   3.4.0       hd8ed1ab_1                conda-forge
  opt_einsum                   3.4.0       pyhd8ed1ab_1              conda-forge
  pip                          24.3.1      pyh8b19718_2              conda-forge
  pybind11                     2.11.1      py312h8572e83_2           conda-forge
  pybind11-global              2.11.1      py312h8572e83_2           conda-forge
  python                       3.12.8      h9e4cc4f_1_cpython        conda-forge
  python_abi                   3.12        5_cp312                   conda-forge
  re2                          2024.07.02  h9925aae_2                conda-forge
  readline                     8.2         h8228510_1                conda-forge
  scipy                        1.15.1      py312h180e4f1_0           conda-forge
  setuptools                   75.8.0      pyhff2d567_0              conda-forge
  tk                           8.6.13      noxft_h4845f30_101        conda-forge
  tzdata                       2025a       h78e105d_0                conda-forge
  wheel                        0.45.1      pyhd8ed1ab_1              conda-forge
  zipp                         3.21.0      pyhd8ed1ab_1              conda-forge
@a-ws-m
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a-ws-m commented Jan 24, 2025

I have also confirmed that using the v2.10 branch produces similar results:

cp -pr ../../python install
cd install/python && rm -fr *.so plumed.cpp build && \
          unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
          plumed_program_name=plumed \
          plumed_force_cython=yes \
          plumed_version=2.10b \
          plumed_include_dir=../../../wrapper \
          plumed_default_kernel="/usr/local/lib/libplumedKernel.so" \
          python3 setup.py build_ext -i
Module name plumed
Version number 2.10b
Hardcoded PLUMED_KERNEL /usr/local/lib/libplumedKernel.so
plumed_force_cython=yes
importing cython
Error: building plumed requires cython. Please install it first with pip install cython

Note that this isn't an issue during make:

make -C python
make[1]: Entering directory '/home/awsm/plumed2/python'
Building python interface for PLUMED
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
          plumed_program_name=plumed \
          plumed_force_cython=yes \
          plumed_version=2.10b \
          plumed_include_dir=../src/wrapper \
          plumed_default_kernel="$PWD/../src/lib/libplumedKernel.so" \
          python3 setup.py build_ext -i
Module name plumed
Version number 2.10b
Hardcoded PLUMED_KERNEL /home/awsm/plumed2/src/lib/libplumedKernel.so
plumed_force_cython=yes
importing cython
/home/awsm/micromamba/envs/pycv/lib/python3.12/site-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/home/awsm/micromamba/envs/pycv/lib/python3.12/site-packages/setuptools/dist.py:330: InformationOnly: Normalizing '2.10b' to '2.10b0'
  self.metadata.version = self._normalize_version(self.metadata.version)

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