updated docker-related files

docker/Dockerfile

@@ -0,0 +1,53 @@
+FROM doduo1.umcn.nl/uokbaseimage/base:tf2.10-pt1.12
+
+USER root
+WORKDIR /home/user/
+
+# install pyvips
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
+
+# download & unpack vips
+RUN wget -q https://github.com/libvips/libvips/releases/download/v8.13.0/vips-8.13.0.tar.gz  && \
+    sudo -S apt-get update && \
+    sudo -S apt-get install -y libjpeg-turbo8-dev && \
+    sudo -S apt-get install -y libgtk2.0-dev && \
+    sudo -S apt-get install -y libgsf-1-dev && \
+    sudo -S apt-get install -y libtiff5-dev && \
+    sudo -S apt-get install -y libopenslide-dev && \
+    tar xf vips-8.13.0.tar.gz > /dev/null 2>&1
+
+# sepcify workdir
+WORKDIR /home/user/vips-8.13.0/
+
+# make and install vips
+RUN ./configure && \
+    make && \
+    sudo -S make install && \
+    cd .. && \
+    sudo -S ldconfig && \
+    sudo -S pip3.9 install pyvips
+
+WORKDIR /home/user/
+RUN rm vips-8.13.0.tar.gz
+
+# install ASAP
+COPY ASAP*.deb .
+RUN apt-get update && \
+    apt-get install --assume-yes /home/user/ASAP-2.1-Ubuntu2004.deb && \
+    ldconfig && \
+    SITE_PACKAGES=`python3 -c "import sysconfig; print(sysconfig.get_paths()['purelib'])"` && \
+    printf "/opt/ASAP/bin/\n" > "${SITE_PACKAGES}/asap.pth" && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN rm ASAP*.deb
+
+USER user
+
+# clone dino repo and install requirements
+RUN git clone https://github.com/computationalpathologygroup/dino.git
+RUN pip3 install -r dino/requirements.txt`
+
+#### Configure entrypoint
+COPY run.sh .
+ENTRYPOINT ["/bin/bash", "/home/user/run.sh"]

docker/run.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+#help
+display_help()
+{
+   echo "DINO by @clementgrisi"
+   echo
+   echo "Syntax: docker run dino [-p level] [-c filename] [-w wandb_api_key]"
+   echo "options:"
+   echo "-p     starts self-supervised pre-training at given level (can be either 'patch' or 'region')"
+   echo "-c     specify config filename"
+   echo "-w     specify wandb API key"
+   echo
+}
+
+#main
+while getopts ":t:p:c:h" opt; do
+  case $opt in
+    h)
+      display_help
+      exit 1
+      ;;
+    p)
+      level="$OPTARG"
+      ;;
+    c)
+      config="$OPTARG"
+      ;;
+    w)
+      key="$OPTARG"
+      ;;
+    \?)
+      echo "Invalid option: -$OPTARG" >&2
+      exit 1
+      ;;
+    :)
+      echo "Option -$OPTARG requires an argument." >&2
+      exit 1
+      ;;
+  esac
+done
+
+if [[ -n $key ]]; then
+  export WANDB_API_KEY=$key
+fi
+
+if [[ -n $level ]]; then
+  case $level in
+    patch)
+      python3 -m torch.distributed.run --standalone --nproc_per_node=gpu dino/patch.py --config-name "$config"
+      ;;
+    region)
+      python3 -m torch.distributed.run --standalone --nproc_per_node=gpu dino/region.py --config-name "$config"
+      ;;
+    *)
+      echo "Invalid level option. Please use 'patch' or 'region'"
+  esac
+else
+  echo "No flag specified. Please use -p flag."
+fi