Cannot import graph_tool

jq-ding commented 6 months ago

Solution to issue cannot be found in the documentation.

[X] I checked the documentation.

Issue

I installed graph_tool through conda enviroment, and then I installed to pytorch and PyG packages, the list is as beow. But when I import graph_tool, thr error is: ImportError: /USERS/usr/miniconda3/envs/gt2/lib/python3.12/site-packages/torch/lib/libgomp-a34b3233.so.1: versionGOMP_5.0' not found (required by /USERS/usr/miniconda3/envs/gt2/lib/python3.12/site-packages/graph_tool/libgraph_tool_core.so)`

Installed packages

package list

```shell conda list _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aiohttp 3.9.4 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.3 h0630a04_0 conda-forge atk-1.0 2.38.0 hd4edc92_1 conda-forge attrs 23.2.0 pypi_0 pypi brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.2.2 hbcca054_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge cairomm-1.16 1.16.2 h7e731d7_1 conda-forge certifi 2024.2.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py312hf06ca03_0 conda-forge charset-normalizer 3.3.2 pypi_0 pypi contourpy 1.2.1 py312h8572e83_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge epoxy 1.5.10 h166bdaf_1 conda-forge expat 2.6.2 h59595ed_0 conda-forge filelock 3.13.4 pypi_0 pypi font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_1 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.51.0 py312h98912ed_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozenlist 1.4.1 pypi_0 pypi fsspec 2024.3.1 pypi_0 pypi gdk-pixbuf 2.42.10 h829c605_5 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge glib-tools 2.80.0 hde27a5a_4 conda-forge gmp 6.3.0 h59595ed_1 conda-forge graph-tool 2.59 py312hf63df81_1 conda-forge graph-tool-base 2.59 py312h2c0dc93_1 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gtk3 3.24.41 h280cfa0_0 conda-forge harfbuzz 8.3.0 h3d44ed6_0 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pypi_0 pypi jinja2 3.1.3 pypi_0 pypi joblib 1.4.0 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py312h8572e83_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libboost 1.84.0 h8013b2b_2 conda-forge libboost-python 1.84.0 py312hfb10629_2 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 13.2.0 h69a702a_5 conda-forge libgfortran5 13.2.0 ha4646dd_5 conda-forge libgirepository 1.80.1 h003a4f0_0 conda-forge libglib 2.80.0 hf2295e7_4 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libpng 1.6.43 h2797004_0 conda-forge librsvg 2.58.0 hce6bd6c_0 conda-forge libsqlite 3.45.2 h2797004_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.2 hd590300_1 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h662e7e4_0 conda-forge libxml2 2.12.6 h232c23b_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge markupsafe 2.1.5 pypi_0 pypi matplotlib-base 3.8.4 py312he5832f3_0 conda-forge mpmath 1.3.0 pypi_0 pypi multidict 6.0.5 pypi_0 pypi munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4.20240210 h59595ed_0 conda-forge networkx 3.3 pypi_0 pypi numpy 1.26.4 py312heda63a1_0 conda-forge nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi nvidia-curand-cu12 10.3.2.106 pypi_0 pypi nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi nvidia-nccl-cu12 2.19.3 pypi_0 pypi nvidia-nvjitlink-cu12 12.4.127 pypi_0 pypi nvidia-nvtx-cu12 12.1.105 pypi_0 pypi openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.2.1 hd590300_1 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pango 1.52.2 ha41ecd1_0 conda-forge pcre2 10.43 hcad00b1_0 conda-forge pillow 10.3.0 py312hdcec9eb_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge psutil 5.9.8 pypi_0 pypi pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycairo 1.26.0 py312he48a392_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pyg-lib 0.4.0+pt22cu121 pypi_0 pypi pygobject 3.48.2 py312h15a1d3f_0 conda-forge pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge python 3.12.2 hab00c5b_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python_abi 3.12 4_cp312 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.31.0 pypi_0 pypi scikit-learn 1.4.2 pypi_0 pypi scipy 1.13.0 py312heda63a1_0 conda-forge setuptools 69.5.1 pyhd8ed1ab_0 conda-forge sigcpp-3.0 3.6.0 h59595ed_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sparsehash 2.0.4 hcb278e6_1 conda-forge sqlite 3.45.2 h2c6b66d_0 conda-forge sympy 1.12 pypi_0 pypi threadpoolctl 3.4.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge torch 2.2.2 pypi_0 pypi torch-cluster 1.6.3+pt22cu121 pypi_0 pypi torch-geometric 2.5.2 pypi_0 pypi torch-scatter 2.1.2+pt22cu121 pypi_0 pypi torch-sparse 0.6.18+pt22cu121 pypi_0 pypi torch-spline-conv 1.2.2+pt22cu121 pypi_0 pypi torchaudio 2.2.2 pypi_0 pypi torchvision 0.17.2 pypi_0 pypi tqdm 4.66.2 pypi_0 pypi typing-extensions 4.11.0 pypi_0 pypi tzdata 2024a h0c530f3_0 conda-forge urllib3 2.2.1 pypi_0 pypi wayland 1.22.0 h8c25dac_1 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge xkeyboard-config 2.41 hd590300_0 conda-forge xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxinerama 1.1.5 h27087fc_0 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yarl 1.9.4 pypi_0 pypi zlib 1.2.13 hd590300_5 conda-forge zstandard 0.22.0 py312hd58854c_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge torch_sparse 0.6.18+pt22cu121 torch_spline_conv 1.2.2+pt22cu121 torchaudio 2.2.2 torchvision 0.17.2 pip list aiohttp 3.9.4 aiosignal 1.3.1 attrs 23.2.0 certifi 2024.2.2 cffi 1.16.0 charset-normalizer 3.3.2 contourpy 1.2.1 cycler 0.12.1 filelock 3.13.4 fonttools 4.51.0 frozenlist 1.4.1 fsspec 2024.3.1 idna 3.7 Jinja2 3.1.3 joblib 1.4.0 kiwisolver 1.4.5 MarkupSafe 2.1.5 matplotlib 3.8.4 mpmath 1.3.0 multidict 6.0.5 munkres 1.1.4 networkx 3.3 numpy 1.26.4 nvidia-cublas-cu12 12.1.3.1 nvidia-cuda-cupti-cu12 12.1.105 nvidia-cuda-nvrtc-cu12 12.1.105 nvidia-cuda-runtime-cu12 12.1.105 nvidia-cudnn-cu12 8.9.2.26 nvidia-cufft-cu12 11.0.2.54 nvidia-curand-cu12 10.3.2.106 nvidia-cusolver-cu12 11.4.5.107 nvidia-cusparse-cu12 12.1.0.106 nvidia-nccl-cu12 2.19.3 nvidia-nvjitlink-cu12 12.4.127 nvidia-nvtx-cu12 12.1.105 packaging 24.0 pillow 10.3.0 pip 24.0 psutil 5.9.8 pycairo 1.26.0 pycparser 2.22 pyg_lib 0.4.0+pt22cu121 PyGObject 3.48.2 pyparsing 3.1.2 python-dateutil 2.9.0 requests 2.31.0 scikit-learn 1.4.2 scipy 1.13.0 setuptools 69.5.1 six 1.16.0 sympy 1.12 threadpoolctl 3.4.0 torch 2.2.2 torch_cluster 1.6.3+pt22cu121 torch_geometric 2.5.2 torch_scatter 2.1.2+pt22cu121 torch_sparse 0.6.18+pt22cu121 torch_spline_conv 1.2.2+pt22cu121 torchaudio 2.2.2 torchvision 0.17.2 tqdm 4.66.2 typing_extensions 4.11.0 urllib3 2.2.1 wheel 0.43.0 yarl 1.9.4 zstandard 0.22.0 ```

Environment info

active environment : gt2
    active env location : /USERS/usr/miniconda3/envs/gt2
            shell level : 2
       user config file : /export_home/usr/.condarc
 populated config files : /export_home/usr/.condarc
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __archspec=1=x86_64
                          __cuda=12.2=0
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /USERS/usr/miniconda3  (writable)
      conda av data dir : /USERS/usr/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /USERS/usr/miniconda3/pkgs
                          /export_home/usr/.conda/pkgs
       envs directories : /USERS/usr/miniconda3/envs/manifold2
                          /USERS/usr/miniconda3/envs
                          /export_home/usr/.conda/envs
               platform : linux-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.10.8 Linux/5.15.0-92-generic ubuntu/22.04.3 glibc/2.35
                UID:GID : 1028:1006
             netrc file : None
           offline mode : False

jq-ding commented 6 months ago

Thanks for any comments!

stuarteberg commented 4 months ago

From the error message, it appears that your version of pytorch is shipping its own copy of libgomp, and it's causing problems. The conda-forge package for pytorch does not ship libgomp in that manner. Did you install pytorch via pip? I recommend installing from conda-forge instead.

The following works for me:

conda create -n pyg-gt -c conda-forge --override-channels pytorch pytorch_geometric graph-tool
conda activate pyg-gt
conda list cuda
python -c 'import graph_tool.all as gt'

conda-forge / graph-tool-feedstock