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HuangDDU avatar HuangDDU commented on August 17, 2024 3

Appreciate your help, thank you @qinqian.. I have run the docs/source/notebook/pancreas.ipynb on Windows platform with GPU GTX1050Ti. My environment.yml below may help others.

name: pyrovelocity
channels:
  - pytorch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
  - conda-forge
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
  - defaults
dependencies:
  - asttokens=2.0.8=pyhd8ed1ab_0
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=py_2
  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
  - blas=1.0=mkl
  - bzip2=1.0.8=h8ffe710_4
  - ca-certificates=2022.9.24=h5b45459_0
  - cudatoolkit=10.2.89=hb195166_10
  - debugpy=1.6.3=py38h885f38d_0
  - decorator=5.1.1=pyhd8ed1ab_0
  - entrypoints=0.4=pyhd8ed1ab_0
  - executing=1.1.1=pyhd8ed1ab_0
  - freetype=2.4.10=0
  - intel-openmp=2022.1.0=h57928b3_3787
  - ipykernel=6.16.1=pyh025b116_0
  - ipython=8.5.0=pyh08f2357_1
  - jedi=0.18.1=pyhd8ed1ab_2
  - jpeg=8d=0
  - jupyter_client=7.4.3=pyhd8ed1ab_0
  - jupyter_core=4.11.1=py38haa244fe_0
  - libblas=3.9.0=16_win64_mkl
  - libcblas=3.9.0=16_win64_mkl
  - libffi=3.4.2=h8ffe710_5
  - liblapack=3.9.0=16_win64_mkl
  - libpng=1.6.17=0
  - libsodium=1.0.18=h8d14728_1
  - libsqlite=3.39.4=hcfcfb64_0
  - libtiff=4.0.2=1
  - libuv=1.44.2=h8ffe710_0
  - libwebp=1.2.4=h8ffe710_0
  - libwebp-base=1.2.4=h8ffe710_0
  - libzlib=1.2.13=hcfcfb64_4
  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
  - mkl=2022.1.0=h6a75c08_874
  - msys2-conda-epoch=20160418=1
  - nest-asyncio=1.5.6=pyhd8ed1ab_0
  - ninja=1.7.2=0
  - numpy=1.23.4=py38h90ce339_1
  - openssl=3.0.5=hcfcfb64_2
  - packaging=21.3=pyhd8ed1ab_0
  - parso=0.8.3=pyhd8ed1ab_0
  - pickleshare=0.7.5=py_1003
  - pip=22.3=pyhd8ed1ab_0
  - prompt-toolkit=3.0.31=pyha770c72_0
  - psutil=5.9.3=py38h91455d4_0
  - pure_eval=0.2.2=pyhd8ed1ab_0
  - pygments=2.13.0=pyhd8ed1ab_0
  - pyparsing=3.0.9=pyhd8ed1ab_0
  - python=3.8.13=hcf16a7b_0_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python_abi=3.8=2_cp38
  - pytorch=1.8.1=py3.8_cuda10.2_cudnn7_0
  - pywin32=303=py38h294d835_0
  - pyzmq=24.0.1=py38ha85f68a_0
  - six=1.16.0=pyh6c4a22f_0
  - sqlite=3.39.4=hcfcfb64_0
  - stack_data=0.5.1=pyhd8ed1ab_0
  - tbb=2021.6.0=h91493d7_0
  - tk=8.6.12=h8ffe710_0
  - torchaudio=0.8.1=py38
  - torchvision=0.9.1=py38_cu102
  - tornado=6.2=py38h294d835_0
  - traitlets=5.5.0=pyhd8ed1ab_0
  - typing_extensions=4.4.0=pyha770c72_0
  - ucrt=10.0.20348.0=h57928b3_0
  - vc=14.2=hac3ee0b_8
  - vs2015_runtime=14.29.30139=h890b9b1_8
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - wheel=0.37.1=pyhd8ed1ab_0
  - xz=5.2.6=h8d14728_0
  - zeromq=4.3.4=h0e60522_1
  - zlib=1.2.13=hcfcfb64_4
  - pip:
    - absl-py==1.3.0
    - adjusttext==0.7.3
    - aiohttp==3.8.3
    - aiosignal==1.2.0
    - anndata==0.8.0
    - astropy==5.1.1
    - async-timeout==4.0.2
    - attrs==22.1.0
    - cachetools==5.2.0
    - certifi==2022.9.24
    - charset-normalizer==2.1.1
    - click==8.1.3
    - colorama==0.4.6
    - commonmark==0.9.1
    - contourpy==1.0.5
    - cycler==0.11.0
    - docrep==0.3.2
    - et-xmlfile==1.1.0
    - fonttools==4.38.0
    - frozenlist==1.3.1
    - fsspec==2022.10.0
    - future==0.18.2
    - google-auth==2.13.0
    - google-auth-oauthlib==0.4.6
    - grpcio==1.50.0
    - h5py==3.7.0
    - idna==3.4
    - importlib-metadata==5.0.0
    - ipywidgets==8.0.2
    - joblib==1.2.0
    - jupyterlab-widgets==3.0.3
    - kiwisolver==1.4.4
    - llvmlite==0.39.1
    - loompy==3.0.7
    - markdown==3.4.1
    - markupsafe==2.1.1
    - matplotlib==3.6.0
    - multidict==6.0.2
    - natsort==8.2.0
    - networkx==2.8.7
    - numba==0.56.3
    - numpy-groupies==0.9.20
    - oauthlib==3.2.2
    - openpyxl==3.0.10
    - opt-einsum==3.3.0
    - pandas==1.5.1
    - patsy==0.5.3
    - pillow==9.2.0
    - protobuf==3.19.6
    - pyasn1==0.4.8
    - pyasn1-modules==0.2.8
    - pydeprecate==0.3.0
    - pyerfa==2.0.0.1
    - pynndescent==0.5.7
    - pyro-api==0.1.2
    - pyro-ppl==1.6.0
    - pyrovelocity==0.1.0
    - pytorch-lightning==1.3.8
    - pytz==2022.5
    - pyyaml==5.4.1
    - requests==2.28.1
    - requests-oauthlib==1.3.1
    - rich==12.6.0
    - rsa==4.9
    - scanpy==1.9.1
    - scikit-learn==1.1.3
    - scipy==1.9.3
    - scvelo==0.2.4
    - scvi-tools==0.13.0
    - seaborn==0.12.1
    - session-info==1.0.0
    - setuptools==59.5.0
    - statsmodels==0.13.2
    - stdlib-list==0.8.0
    - tensorboard==2.10.1
    - tensorboard-data-server==0.6.1
    - tensorboard-plugin-wit==1.8.1
    - threadpoolctl==3.1.0
    - torchmetrics==0.5.0
    - tqdm==4.64.1
    - umap-learn==0.5.3
    - urllib3==1.26.12
    - werkzeug==2.2.2
    - widgetsnbextension==4.0.3
    - yarl==1.8.1
    - zipp==3.10.0
prefix: F:\ProgrammingEnvironment\Anaconda\Anaconda\envs\pyrovelocity

from pyrovelocity.

HuangDDU avatar HuangDDU commented on August 17, 2024

I think that scvi-tools is installed by uncorrected version or other packages. Can you share your conda evironment by .yaml file, which help me install all dependencies correctly.

from pyrovelocity.

HuangDDU avatar HuangDDU commented on August 17, 2024

@qinqian

from pyrovelocity.

qinqian avatar qinqian commented on August 17, 2024

Sure, please see environment.yml below. My guess might be that the latest scvi-tools are not compatible with our package, please consider downgrading to 0.13.0. I cannot find a windows GPU machine to test the package yet, thank you for your help!

name: pyrovelocity
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python==3.8.8
  - pyro-ppl==1.6.0
  - seaborn==0.11.2
  - scvelo
  - scvi-tools==0.13.0
  - pytorch-lightning==1.3.0
  - pytorch-gpu=1.8.*=*cuda*
  - torchmetrics==0.5.1
  - h5py==3.2.1
  - anndata==0.7.5
  - adjusttext
  - astropy
  - jupyterlab

from pyrovelocity.

qinqian avatar qinqian commented on August 17, 2024

Thank you for sharing the solution @HuangDDU. I'll pin this issue.

from pyrovelocity.

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