Merge pull request #4 from ohsu-comp-bio/ai-readi

AI-READi

ai-readi/Dockerfile

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+# use base image
+FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:restricted-gpu-root
+
+# return to non-root user
+USER $NB_UID
+WORKDIR /home/$NB_USER
+
+# create image from requirements.txt
+RUN conda create --name ai-readi
+SHELL ["conda", "run", "-n", "ai-readi", "/bin/bash", "-c"]
+COPY --chown=$NB_USER:$NB_GID requirements.txt .
+RUN pip install -r requirements.txt && \
+    rm requirements.txt
+
+# setup retfound
+RUN conda create -n retfound python=3.7.5 -y
+SHELL ["conda", "run", "-n", "retfound", "/bin/bash", "-c"]
+RUN git clone https://github.com/rmaphoh/RETFound_MAE/ && \
+    cd RETFound_MAE && \
+    pip install -r requirement.txt && \
+    cd $HOME
+
+# setup automorph
+RUN conda create -n automorph python=3.6 -y
+SHELL ["conda", "run", "-n", "automorph", "/bin/bash", "-c"]
+RUN git clone https://github.com/rmaphoh/AutoMorph.git && \
+    cd AutoMorph && \
+    conda install pytorch==1.7.0 torchvision==0.8.0 torchaudio==0.7.0 cudatoolkit=11.1 -c pytorch -y && \
+    pip install --ignore-installed certifi && \
+    pip install -r requirement.txt && \
+    pip install efficientnet_pytorch
+
+# allow use of conda envs
+RUN conda init bash && exec bash
+
+# USER root

ai-readi/README.md

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+# AI-READi
+
+Docker file for AI-READi. Builds off `restricted-gpu-root` image, reverting use back to  non-root privileges. Creates environment with requirements.txt, a retfound environment, and a Automorph envrionment. 

ai-readi/requirements.txt

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+appnope==0.1.4
+asttokens==2.4.1
+comm==0.2.2
+contourpy==1.2.1
+cycler==0.12.1
+debugpy==1.8.1
+decorator==5.1.1
+executing==2.0.1
+fonttools==4.50.0
+ipykernel==6.29.4
+ipython==8.23.0
+jedi==0.19.1
+jupyter_client==8.6.1
+jupyter_core==5.7.2
+kiwisolver==1.4.5
+matplotlib==3.8.3
+matplotlib-inline==0.1.6
+nest-asyncio==1.6.0
+numpy==1.26.4
+packaging==24.0
+parso==0.8.3
+pexpect==4.9.0
+pillow==10.3.0
+platformdirs==4.2.0
+prompt-toolkit==3.0.43
+psutil==5.9.8
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pydicom==2.4.4
+Pygments==2.17.2
+pyparsing==3.1.2
+python-dateutil==2.9.0.post0
+pyzmq==25.1.2
+six==1.16.0
+stack-data==0.6.3
+tornado==6.4
+traitlets==5.14.2
+wcwidth==0.2.13

restricted-cpu-root/README.md

@@ -1,3 +1,3 @@
 # Restricted CPU Root
 
-Dockerfile containing the Jupyter Notebooks for the Bridge2AI project, adapted from the [restricted-gpu-slim/Dockerfile](https://github.com/uc-cdis/containers/blob/master/jupyter-slim/Dockerfile) from Center for Translational Data Science at University of Chicago. No GPU features are enabled in this Dockerfile but root access is provided, making this a suitable image for building off of.
+Dockerfile containing the Jupyter Notebooks for the Bridge2AI project, adapted from the [restricted-gpu-slim/Dockerfile](https://github.com/uc-cdis/containers/blob/master/jupyter-slim/Dockerfile) from Center for Translational Data Science at University of Chicago. Briefly, it provides a VM with a Jupyter Notebooks server and restrictions on downloads (disabled access to download buttons). No GPU features are enabled in this Dockerfile but root access is provided, making this a suitable image for building off of. 

restricted-gpu-root/Dockerfile

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+# use base image
+FROM quay.io/ohsu-comp-bio/bridge2ai-jupyter:cpu-root
+
+RUN sudo apt update
+
+# setup CUDA
+RUN sudo apt-get install -y kmod \
+    && wget https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_520.61.05_linux.run \
+    && sudo bash cuda_11.8.0_520.61.05_linux.run --silent --toolkit
+
+# setup cuDNN
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb \
+    && sudo dpkg -i cuda-keyring_1.1-1_all.deb \
+    && sudo apt-get update \
+    && sudo apt-get -y install cudnn \
+    && echo 'export PATH=$PATH:/usr/local/cuda-11.8/bin' > ~/.bashrc \
+    && echo 'export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib6:$LD_LIBRARY_PATH' >> ~/.bashrc \
+    && source ~/.bashrc
+
+RUN rm cuda_11.8.0_520.61.05_linux.run cuda-keyring_1.1-1_all.deb

restricted-gpu-root/README.md

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+# Restricted GPU
+
+Builds on top of the `restricted-cpu-root` image. Provides GPU setup with CUDA and CuDNN. Tested on AWS GPU P3 instance (Tesla V100 GPUs). See Dockerfile for more details.