middle commit

.inputrc

@@ -97,3 +97,9 @@ set enable-bracketed-paste
 set enable-bracketed-paste
 set enable-bracketed-paste
 set enable-bracketed-paste
+set enable-bracketed-paste
+set enable-bracketed-paste
+set enable-bracketed-paste
+set enable-bracketed-paste
+set enable-bracketed-paste
+set enable-bracketed-paste

build-local-docker.sh

@@ -9,15 +9,13 @@ image="pharmbio-notebook"
 echo "tensorflow_version=$tensorflow_version"
 echo "tag=$tag"
 echo "image=$image"
-#switch to buildx build
+#switched to buildx build
 # Build docker image for this container.
 # docker buildx build --no-cache -t ghcr.io/pharmbio/$image:$tag \
 #              --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-jupyter \
-#              --build-arg FRAMEWORK=cpu \
-#              -f ./docker/env.Dockerfile . || exit 1
-docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag}-gpu \
+#              -f ./docker/env.cpu.Dockerfile . || exit 1
+DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag}-gpu \
              --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-gpu-jupyter \
-             --build-arg FRAMEWORK=cuda \
-             -f docker/env.Dockerfile . || exit 1
+             -f docker/env.cuda.Dockerfile . || exit 1
 
 #docker push "ghcr.io/pharmbio/$image:$tag-devel"

docker/env.Dockerfile → docker/env.cpu.Dockerfile

@@ -60,29 +60,13 @@ RUN python3 -m pip install --no-cache-dir --upgrade pip && \
     python3 -m pip install --no-cache-dir -r requirements.txt
 
 # Conditional install based on FRAMEWORK argument
-RUN <<EOF 
-        if [ "$FRAMEWORK" = "cuda" ]; then 
-                echo "Installing for CUDA framework" 
-                python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
-                        torch==2.2.1 \
-                        torchvision \
-                        torchaudio;
-                python3 -m pip install \
-                        --extra-index-url=https://pypi.nvidia.com \
-                        cudf-cu12==24.6.* dask-cudf-cu12==24.6.* cuml-cu12==24.6.* \
-                        cugraph-cu12==24.6.* cuspatial-cu12==24.6.* cuproj-cu12==24.6.* \
-                        cuxfilter-cu12==24.6.* cucim-cu12==24.6.* pylibraft-cu12==24.6.* \
-                        raft-dask-cu12==24.6.* cuvs-cu12==24.6.*; 
-        elif [ "$FRAMEWORK" = "cpu" ]; then 
-                echo "Installing for CPU framework" 
-                python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cpu \
-                        torch==2.2.1 \
-                        torchvision \
-                        torchaudio;
-        else 
-        echo "Error: unknown hardware" 
-        exit 1 
-        fi
+RUN <<EOF  
+        echo "Installing for CPU framework" 
+        python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cpu \
+                torch==2.4.1 \
+                torchvision \
+                torchaudio;
+
 EOF
 
 

docker/env.cuda.Dockerfile

@@ -0,0 +1,119 @@
+# Base image should be specified with --build-arg during build
+# syntax=docker/dockerfile:1.4
+ARG BASE_IMAGE="tensorflow/tensorflow:latest"  # Example default
+
+FROM $BASE_IMAGE
+# ARG FRAMEWORK need to be after the build stage FROM (since it is used in another build process)
+
+
+# Set shell
+ENV SHELL=/bin/bash
+
+# Set timezone
+ENV TZ=Europe/Stockholm
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# Install base dependencies
+ENV DEBIAN_FRONTEND=noninteractive
+# >apt_installs.txt to save instead of executing
+RUN <<EOF
+ apt-get update
+ apt-get install -y --no-install-recommends \
+    apt-transport-https \
+    ca-certificates \
+    software-properties-common \
+    libegl1-mesa-dev \
+    libgles2-mesa-dev \
+    python3-pip \
+    gnupg \
+    tmux \
+    sudo \
+    ssh \
+    nano \
+    mysql-client \
+    libpq-dev \
+    git \
+    vim \
+    wget \
+    curl \
+    ncdu \
+    less \
+    rsync \
+    zip \
+    unzip \
+    iputils-ping \
+    sqlite \
+    sqlite3 \
+    libgl1-mesa-glx \
+    python3-venv \
+    openjdk-17-jdk-headless \
+EOF
+
+# Install Rust (comment out if not needed)
+#RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
+#ENV PATH="/root/.cargo/bin:${PATH}"
+#RUN cargo --help
+
+# Upgrade pip and install base Python packages
+COPY requirements.txt .
+RUN python3 -m pip install --no-cache-dir --upgrade pip && \
+    python3 -m pip install --no-cache-dir -r requirements.txt
+
+
+# Breakpoint - temporary shell for debugging
+RUN --mount=type=cache,target=/tmp \
+    echo "Entering breakpoint shell"; \
+    sleep infinity
+
+RUN echo "Step 2: Continuing after breakpoint"
+
+RUN <<EOF 
+        echo "Installing for CUDA framework" 
+        python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
+                torch==2.4.1 \
+                torchvision \
+                torchaudio;
+EOF
+
+# RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
+#         torch==2.2.1 \
+#         torchvision \
+#         torchaudio;
+# RUN python3 -m pip install \
+#         --extra-index-url=https://pypi.nvidia.com \
+#         cudf-cu12==24.6.* dask-cudf-cu12==24.6.* cuml-cu12==24.6.* \
+#         cugraph-cu12==24.6.* cuspatial-cu12==24.6.* cuproj-cu12==24.6.* \
+#         cuxfilter-cu12==24.6.* cucim-cu12==24.6.* pylibraft-cu12==24.6.* \
+#         raft-dask-cu12==24.6.* cuvs-cu12==24.6.*; 
+
+
+
+
+# Add pharmbio templates, examples and misc
+#WORKDIR /pharmbio/
+#COPY README.md .
+#COPY notebooks/* ./notebooks/
+
+# Custom bashrc
+COPY bash.bashrc /etc/bash.bashrc
+
+# Set up user
+RUN useradd -m -s /bin/bash -N -u 1000 jovyan && \
+    echo "jovyan ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+# Set ownership for directories jovyan might need to modify
+RUN chown jovyan /opt/
+
+# Final user and work directory setup
+USER jovyan
+WORKDIR /home/jovyan
+
+#
+# The entrypoint will first copy /pharmbio/ files to user home
+# This is because /home/jovyan will be mountpoint for persistent volume
+# and all contents that is there already in this image will be masqued with
+# persistent volume contents
+# Then the entrypoint will start jupyter notebook server
+#
+COPY entrypoint.sh /
+CMD /entrypoint.sh