search

kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
88 stars 31 forks source link

Broken Environment - RuntimeError: GET was unable to find an engine to execute this computation #228

Closed qin-yu closed 4 months ago

qin-yu commented 4 months ago

Installation with the following method results in cudatookit==11.1, which I guess is incompatible with pytorch-cuda==12.1 and causes error during prediction.

$ mamba env create -f ./environment-dev.yaml
name: plantseg-dev
channels:
  - pytorch
  - nvidia
  - conda-forge
dependencies:
  - python
  - pydantic>2
  - h5py
  - zarr
  - requests
  - pyyaml
  - scikit-image
  - tifffile
  - vigra
  - cudnn
  - pytorch
  - pytorch-cuda=12.1
  - python-elf
  - pyqt
  - napari
  - python-graphviz

Let's try both conda and cuda-version==12.3

qin-yu commented 4 months ago

Somehow cudatoolkit 11.1.74 from nvidia channel is installed.

cudatoolkit               11.1.74              h6bb024c_0    nvidia
qin-yu commented 4 months ago

With the same conda and mamba installation, specifying cuda-version==12.3 would avoid the installation for package cudatoolkit

$ mamba env create -f ./environment-dev.yaml
name: plantseg-dev-cuda-12.3
channels:
  - pytorch
  - nvidia
  - conda-forge
dependencies:
  - python
  - pydantic>2
  - h5py
  - zarr
  - requests
  - pyyaml
  - scikit-image
  - tifffile
  - vigra
  - cudnn
  - pytorch
  - pytorch-cuda=12.1
  - cuda-version==12.3
  - python-elf
  - pyqt
  - napari
  - python-graphviz
cuda-cudart               12.1.105                      0    nvidia
cuda-cupti                12.1.105                      0    nvidia
cuda-libraries            12.1.0                        0    nvidia
cuda-nvrtc                12.1.105                      0    nvidia
cuda-nvtx                 12.1.105                      0    nvidia
cuda-opencl               12.4.127                      0    nvidia
cuda-runtime              12.1.0                        0    nvidia
cuda-version              12.3                 h32bc705_3    conda-forge
cudnn                     8.9.7.29             h092f7fd_3    conda-forge
qin-yu commented 4 months ago

conda took more than 30 minutes to solve the environment, not done yet.

I'll update the dev env config.

qin-yu commented 4 months ago

It took 19 hours for conda to solve but it's not done yet. Let's stick with mamba