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I've been using this toolkit for a long time, and it has been incredibly helpful for testing deep learning brain tumor segmentation models! Thanks for your hard work 🙏!
Recently, I changed the platform from Ubuntu 20.04 to Windows and set up all the requirements (running all commands in the Anaconda Prompt terminal). Here are the steps I've taken:
Verified Docker and GPU setup:
docker run --rm --gpus all nvidia/cuda:11.6.2-base-ubuntu20.04 nvidia-smi
Checked WSL version:
wsl -l -v
Successfully ran the BraTs Preprocessor in CPU mode and finished preprocessing the example data.
Problem Description
When I attempted to run the segmentation, I encountered issues related to cuDNN:
Using mic-dkfz:
Encountered CUDNN_STATUS_MAPPING_ERROR.
Using scan-20:
Encountered an error stating that a valid cuDNN algorithm could not be found.
To verify the cuDNN installation in the container, I ran the container in interactive mode and printed the package information:
Running nvidia-smi inside the interactive terminal:
Request for Assistance
I am seeking guidance on whether the segmentation steps are correct for running under the Windows platform. The same process worked fine under Ubuntu, so I suspect there may be different considerations for running the segmentation model with GPU on Windows.
Any insights or suggestions for running the segmentation model with GPU support on Windows would be greatly appreciated.
I also tried to run the segmentation model under wsl2 Ubuntu terminal, the preprocessing using cpu can be run successfully. And the cuDNN algorithm still can't be captured with the scan-20 model.
I thought would it be possible for this GPU to be too new to run the inference under the docker container environment? Referring to this packages' versions:
Hello!
I've been using this toolkit for a long time, and it has been incredibly helpful for testing deep learning brain tumor segmentation models! Thanks for your hard work 🙏!
Recently, I changed the platform from Ubuntu 20.04 to Windows and set up all the requirements (running all commands in the Anaconda Prompt terminal). Here are the steps I've taken:
Verified Docker and GPU setup:
Checked WSL version:
Successfully ran the BraTs Preprocessor in CPU mode and finished preprocessing the example data.
Problem Description
When I attempted to run the segmentation, I encountered issues related to cuDNN:
Using
mic-dkfz
:CUDNN_STATUS_MAPPING_ERROR
.Using
scan-20
:To verify the cuDNN installation in the container, I ran the container in interactive mode and printed the package information:
Output:
![Package Information](https://private-user-images.githubusercontent.com/56018137/336586620-049c586b-8697-499e-9cae-79344389bf27.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.DskpJucbvSFjnH7EZLFi5PXrPQlkz5UYPvAzoGizTP0)
Running
![nvidia-smi Output](https://private-user-images.githubusercontent.com/56018137/336586863-5f6da6dd-efcb-4c59-8975-672cbf3ce023.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.0mBzZ1G7twFxPYP7hfMCjmgC3zb5YExv3hMVa6TeYqg)
nvidia-smi
inside the interactive terminal:Request for Assistance
I am seeking guidance on whether the segmentation steps are correct for running under the Windows platform. The same process worked fine under Ubuntu, so I suspect there may be different considerations for running the segmentation model with GPU on Windows.
Any insights or suggestions for running the segmentation model with GPU support on Windows would be greatly appreciated.
Thank you!
P.S. Here is my script to run Segmentation
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