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Environment setup file broken #1

Closed kyduff closed 3 years ago

kyduff commented 3 years ago

I tried creating a conda environment from your env.yml file but get a failure:

> conda env create -f env.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - markupsafe==1.1.1=py38h7b6447c_0
  - python-igraph==0.7.1.post7=py38h516909a_0
  - cairo==1.14.12=h8948797_3
  - libiconv==1.16=h516909a_0
  - mkl-service==2.3.0=py38he904b0f_0
  - cryptography==2.9.2=py38h1ba5d50_0
  - cffi==1.14.0=py38he30daa8_1
  - numpy==1.18.1=py38h4f9e942_0
  - intel-openmp==2020.1=217
  - libpng==1.6.37=hbc83047_0
  - scikit-learn==0.22.1=py38hd81dba3_0
  - scipy==1.4.1=py38h0b6359f_0
  - matplotlib-base==3.1.3=py38hef1b27d_0
  - libxml2==2.9.10=he19cac6_1
  - icu==58.2=he6710b0_3
  - sip==4.19.13=py38he6710b0_0
  - tornado==6.0.4=py38h7b6447c_1
  - ncurses==6.2=he6710b0_1
  - pcre==8.43=he6710b0_0
  - zeromq==4.3.1=he6710b0_3
  - qt==5.9.7=h5867ecd_1
  - glib==2.63.1=h3eb4bd4_1
  - cudatoolkit==10.1.243=h6bb024c_0
  - numpy-base==1.18.1=py38hde5b4d6_1
  - dgl-cuda10.1==0.4.3post2=py38_0
  - readline==8.0=h7b6447c_0
  - libprotobuf==3.13.0.1=h8b12597_0
  - openssl==1.1.1h=h7b6447c_0
  - zlib==1.2.11=h7b6447c_3
  - protobuf==3.13.0.1=py38h950e882_1
  - xz==5.2.5=h7b6447c_0
  - libsodium==1.0.16=h1bed415_0
  - gmp==6.1.2=h6c8ec71_1
  - brotlipy==0.7.0=py38h7b6447c_1000
  - libtiff==4.1.0=h2733197_1
  - gstreamer==1.14.0=hb31296c_0
  - jpeg==9b=h024ee3a_2
  - libuuid==1.0.3=h1bed415_2
  - sqlite==3.31.1=h62c20be_1
  - libffi==3.3=he6710b0_1
  - pytorch==1.5.0=py3.8_cuda10.1.243_cudnn7.6.3_0
  - ld_impl_linux-64==2.33.1=h53a641e_7
  - libxcb==1.13=h1bed415_1
  - python==3.8.3=hcff3b4d_0
  - libedit==3.1.20181209=hc058e9b_0
  - pixman==0.38.0=h516909a_1003
  - pillow==7.1.2=py38hb39fc2d_0
  - libstdcxx-ng==9.1.0=hdf63c60_0
  - expat==2.2.6=he6710b0_0
  - igraph==0.7.1=h2166141_1005
  - dbus==1.13.14=hb2f20db_0
  - torchvision==0.6.0=py38_cu101
  - zstd==1.4.4=h0b5b093_3
  - pycairo==1.19.1=py38h2a1e443_0
  - pyrsistent==0.16.0=py38h7b6447c_0
  - ninja==1.9.0=py38hfd86e86_0
  - libgcc-ng==9.1.0=hdf63c60_0
  - gst-plugins-base==1.14.0=hbbd80ab_1
  - mkl_fft==1.0.15=py38ha843d7b_0
  - pyqt==5.9.2=py38h05f1152_4
  - kiwisolver==1.2.0=py38hfd86e86_0
  - fontconfig==2.13.0=h9420a91_0
  - pyzmq==18.1.1=py38he6710b0_0
  - mistune==0.8.4=py38h7b6447c_1000
  - tk==8.6.8=hbc83047_0
  - mkl_random==1.1.1=py38h0573a6f_0
  - libgfortran-ng==7.3.0=hdf63c60_0
  - mkl==2020.1=217
  - freetype==2.9.1=h8a8886c_1
  - lz4-c==1.9.2=he6710b0_0

I have conda version 4.9.2 if that helps. You may want to consider regenerating the environment file including only top-level packages.

isaac-ward commented 3 years ago

Hi there. Thanks for bringing this to our attention. I'll attempt to recreate this bug and resolve it by updating the environment file shortly.

isaac-ward commented 3 years ago

Hi there. This has confirmed to be working on a fresh Ubuntu 20.04 install with the latest conda version (4.10.3). Can you try upgrading and recreating the environment?

kyduff commented 3 years ago

Just retried with conda 4.10.3 and the reproduced the same error. Perhaps this is an OS error? I'm running macOS 11.0.1. If there are build specs in there that are Linux-specific, it may cause problems on another OS

isaac-ward commented 3 years ago

Thanks kyduff. Provided below is an environment configuration with no build information. Could you please try pasting this content into env.yml and creating an environment as per the readme, and then let me know if that solves your problem?

name: gnn-tutorial-fix-0
channels:
  - pytorch
  - dglteam
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1
  - attrs=19.3.0
  - backcall=0.1.0
  - blas=1.0
  - bleach=3.1.4
  - brotlipy=0.7.0
  - ca-certificates=2020.10.14
  - cairo=1.14.12
  - certifi=2020.6.20
  - cffi=1.14.0
  - chardet=3.0.4
  - cryptography=2.9.2
  - cudatoolkit=10.1.243
  - cycler=0.10.0
  - dbus=1.13.14
  - decorator=4.4.2
  - defusedxml=0.6.0
  - dgl-cuda10.1=0.4.3post2
  - entrypoints=0.3
  - expat=2.2.6
  - fontconfig=2.13.0
  - freetype=2.9.1
  - glib=2.63.1
  - gmp=6.1.2
  - gst-plugins-base=1.14.0
  - gstreamer=1.14.0
  - icu=58.2
  - idna=2.9
  - igraph=0.7.1
  - importlib-metadata=1.6.0
  - importlib_metadata=1.6.0
  - intel-openmp=2020.1
  - ipykernel=5.1.4
  - ipython=7.13.0
  - ipython_genutils=0.2.0
  - ipywidgets=7.5.1
  - jedi=0.17.0
  - jinja2=2.11.2
  - joblib=0.15.1
  - jpeg=9b
  - jsonschema=3.2.0
  - jupyter=1.0.0
  - jupyter_client=6.1.3
  - jupyter_console=6.1.0
  - jupyter_core=4.6.3
  - kiwisolver=1.2.0
  - ld_impl_linux-64=2.33.1
  - libedit=3.1.20181209
  - libffi=3.3
  - libgcc-ng=9.1.0
  - libgfortran-ng=7.3.0
  - libiconv=1.16
  - libpng=1.6.37
  - libprotobuf=3.13.0.1
  - libsodium=1.0.16
  - libstdcxx-ng=9.1.0
  - libtiff=4.1.0
  - libuuid=1.0.3
  - libxcb=1.13
  - libxml2=2.9.10
  - lz4-c=1.9.2
  - markupsafe=1.1.1
  - matplotlib=3.1.3
  - matplotlib-base=3.1.3
  - mistune=0.8.4
  - mkl=2020.1
  - mkl-service=2.3.0
  - mkl_fft=1.0.15
  - mkl_random=1.1.1
  - nbconvert=5.6.1
  - nbformat=5.0.6
  - ncurses=6.2
  - networkx=2.4
  - ninja=1.9.0
  - notebook=6.0.3
  - numpy=1.18.1
  - numpy-base=1.18.1
  - olefile=0.46
  - openssl=1.1.1h
  - pandoc=2.2.3.2
  - pandocfilters=1.4.2
  - parso=0.7.0
  - pcre=8.43
  - pexpect=4.8.0
  - pickleshare=0.7.5
  - pillow=7.1.2
  - pip=20.0.2
  - pixman=0.38.0
  - prometheus_client=0.7.1
  - prompt-toolkit=3.0.5
  - prompt_toolkit=3.0.5
  - protobuf=3.13.0.1
  - ptyprocess=0.6.0
  - pycairo=1.19.1
  - pycparser=2.20
  - pygments=2.6.1
  - pyopenssl=19.1.0
  - pyparsing=2.4.7
  - pyqt=5.9.2
  - pyrsistent=0.16.0
  - pysocks=1.7.1
  - python=3.8.3
  - python-dateutil=2.8.1
  - python-igraph=0.7.1.post7
  - python_abi=3.8
  - pytorch=1.5.0
  - pyzmq=18.1.1
  - qt=5.9.7
  - qtconsole=4.7.4
  - qtpy=1.9.0
  - readline=8.0
  - requests=2.24.0
  - scikit-learn=0.22.1
  - scipy=1.4.1
  - send2trash=1.5.0
  - setuptools=47.1.1
  - sip=4.19.13
  - six=1.15.0
  - sqlite=3.31.1
  - tensorboardx=2.1
  - terminado=0.8.3
  - testpath=0.4.4
  - tk=8.6.8
  - torchvision=0.6.0
  - tornado=6.0.4
  - traitlets=4.3.3
  - urllib3=1.25.9
  - wcwidth=0.1.9
  - webencodings=0.5.1
  - wheel=0.34.2
  - widgetsnbextension=3.5.1
  - xz=5.2.5
  - zeromq=4.3.1
  - zipp=3.1.0
  - zlib=1.2.11
  - zstd=1.4.4
  - pip:
    - ase==3.20.1
    - cached-property==1.5.2
    - future==0.18.2
    - googledrivedownloader==0.4
    - h5py==3.0.0
    - isodate==0.6.0
    - llvmlite==0.34.0
    - numba==0.51.2
    - pandas==1.1.4
    - pytz==2020.1
    - rdflib==5.0.0
    - torch-cluster==1.5.7
    - torch-geometric==1.6.1
    - torch-scatter==2.0.5
    - torch-sparse==0.6.7
    - torch-spline-conv==1.2.0
    - tqdm==4.51.0
isaac-ward commented 3 years ago

Closing due to inactivity.

kyduff commented 3 years ago

I just ran it again with the new env.yml and arrived at a similar error:

> conda env create -f env.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - ld_impl_linux-64=2.33.1
  - libstdcxx-ng=9.1.0
  - cudatoolkit=10.1.243
  - dgl-cuda10.1=0.4.3post2
  - libgfortran-ng=7.3.0
  - libgcc-ng=9.1.0

I think this is still an OS issue, as ld_impl_linux-64 is a linux-specific linker.

PS: My apologies for the late response, I've been away on vacation.