Merge branch 'github'

2024-05-26 20:21:54 +08:00
parent 6f78c463be 98265022aa
commit bf55bf8e5b
22 changed files with 717 additions and 45 deletions
--- a/.gitignore
+++ b/.gitignore
--- a/0
+++ b/0
--- a/Dockerfile.jupyterhub
+++ b/Dockerfile.jupyterhub
--- a/Dockerfile.jupyterhub.bak
+++ b/Dockerfile.jupyterhub.bak
--- a/README.md
+++ b/README.md
--- a/dhparam.pem
+++ b/dhparam.pem
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -32,7 +32,7 @@ services:
      # All containers will join this network
      DOCKER_NETWORK_NAME: jupyterhub-network
      # JupyterHub will spawn this Notebook image for users
-      DOCKER_NOTEBOOK_IMAGE: hotwa/notebook:latest
+      DOCKER_NOTEBOOK_IMAGE: quay.io/hotwa/notebook:latest
      # Notebook directory inside user image
      DOCKER_NOTEBOOK_DIR: /home/jovyan/work

--- a/jupyterhub_config.py
+++ b/jupyterhub_config.py
@@ -70,9 +70,10 @@ if admin:
 #    "environment": {"JUPYTER_ENABLE_LAB": "yes"}
 # })

-# 启动jupyter时候增加跨域支持
+# 启动jupyter时候增加跨域支持, 否则反向代理的时候出现问题
+# --NotebookApp.iopub_data_rate_limit=10000000 给nglview使用
 c.DockerSpawner.extra_create_kwargs.update({
-    "environment": {"NOTEBOOK_ARGS": "--NotebookApp.allow_origin='*'"}
+    "environment": {"NOTEBOOK_ARGS": "--NotebookApp.allow_origin='*' --NotebookApp.iopub_data_rate_limit=10000000"}
 })


--- a/jupyterhub_config.py.bak
+++ b/jupyterhub_config.py.bak
--- a/micromamba_install.sh
+++ b/micromamba_install.sh
--- a/nginx-selfsigned.crt
+++ b/nginx-selfsigned.crt
--- a/nginx-selfsigned.key
+++ b/nginx-selfsigned.key
--- a/nginx.conf
+++ b/nginx.conf
--- a/spawnerdockerfile/Dockerfile
+++ b/spawnerdockerfile/Dockerfile
--- a/spawnerdockerfile/Dockerfile.base
+++ b/spawnerdockerfile/Dockerfile.base
@@ -0,0 +1,127 @@
+# syntax=docker/dockerfile:1
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+# https://github.com/jupyter/docker-stacks/blob/main/images/base-notebook/Dockerfile
+ARG REGISTRY=quay.io
+ARG OWNER=jupyter
+ARG BASE_CONTAINER=$REGISTRY/$OWNER/docker-stacks-foundation
+FROM $BASE_CONTAINER
+
+LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Install all OS dependencies for the Server that starts but lacks all
+# features (e.g., download as all possible file formats)
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    fonts-liberation \
+    # - pandoc is used to convert notebooks to html files
+    #   it's not present in the aarch64 Ubuntu image, so we install it here
+    pandoc \
+    # - run-one - a wrapper script that runs no more
+    #   than one unique  instance  of  some  command with a unique set of arguments,
+    #   we use `run-one-constantly` to support the `RESTARTABLE` option
+    run-one && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+USER ${NB_UID}
+
+# Install JupyterLab, Jupyter Notebook, JupyterHub and NBClassic
+# Generate a Jupyter Server config
+# Cleanup temporary files
+# Correct permissions
+# Do all this in a single RUN command to avoid duplicating all of the
+# files across image layers when the permissions change
+WORKDIR /tmp
+RUN mamba install --yes \
+    'jupyterlab' \
+    'notebook' \
+    'jupyterhub' \
+    'nbclassic' && \
+    jupyter server --generate-config && \
+    mamba clean --all -f -y && \
+    npm cache clean --force && \
+    jupyter lab clean && \
+    rm -rf "/home/${NB_USER}/.cache/yarn" && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+ENV JUPYTER_PORT=8888
+EXPOSE $JUPYTER_PORT
+
+# Configure container startup
+CMD ["start-notebook.py"]
+
+# Copy local files as late as possible to avoid cache busting
+COPY start-notebook.py start-notebook.sh start-singleuser.py start-singleuser.sh /usr/local/bin/
+COPY jupyter_server_config.py docker_healthcheck.py /etc/jupyter/
+
+# Fix permissions on /etc/jupyter as root
+USER root
+RUN fix-permissions /etc/jupyter/
+
+# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
+# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server`, and `retro` jupyter commands
+# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
+HEALTHCHECK --interval=5s --timeout=3s --start-period=5s --retries=3 \
+    CMD /etc/jupyter/docker_healthcheck.py || exit 1
+
+# here add
+ARG CREATE_USER="jovyan"
+ARG CREATE_USER_PASSWD="password"
+ARG ROOT_PASSWD="password"
+ARG HOME="/home/${CREATE_USER}"
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+
+RUN <<EOT
+#!/bin/bash
+# 更新软件源
+apt-get update
+# 安装时区数据包并设置时区
+apt-get install -y tzdata 
+ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
+echo 'Asia/Shanghai' > /etc/timezone
+dpkg-reconfigure -f noninteractive tzdata
+# 安装所需的软件包
+apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
+# 创建新用户
+useradd -m -s /bin/bash ${CREATE_USER}
+echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
+echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
+# 安装 Jupyter 和相关软件
+npm install -g configurable-http-proxy
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+EOT
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER ${NB_UID}
+
+# install mojo
+ARG MODULAR_HOME="/home/${CREATE_USER}/.modular"
+ENV MODULAR_HOME=$MODULAR_HOME
+ENV PATH="$MODULAR_HOME/pkg/packages.modular.com_mojo/bin:/home/${CREATE_USER}/.local/bin:$PATH"
+RUN <<EOT
+#!/bin/bash
+curl https://get.modular.com | sh - 
+mamba create -n mojo python=3.10 -c conda-forge -y 
+mamba activate mojo
+modular install mojo
+EOT
+
+# Install Rust
+ENV PATH="/home/${CREATE_USER}/.cargo/bin:$PATH"
+RUN <<EOT
+#!/bin/bash
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+source $HOME/.cargo/env
+cargo install evcxr_jupyter
+evcxr_jupyter --install
+EOT
+
+WORKDIR "${HOME}"
--- a/spawnerdockerfile/Dockerfile.base-notebook
+++ b/spawnerdockerfile/Dockerfile.base-notebook
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}

+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -89,18 +90,27 @@ ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
 echo 'Asia/Shanghai' > /etc/timezone
 dpkg-reconfigure -f noninteractive tzdata
 # 安装所需的软件包
-apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
+apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git nodejs
 # 创建新用户
 useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
-# 安装micromamba
-echo 1 | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
-# 安装 Jupyter 和相关软件
-npm install -g configurable-http-proxy
-python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
 EOT

+# 安装 Jupyter 和相关软件
+RUN <<EOT
+#!/bin/bash
+npm install -g configurable-http-proxy
+git clone https://github.com/arose/nglview
+cd nglview
+python setup.py install
+cd ..
+python3 -m pip install aiohttp -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl aiohttp jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+EOT
+
+ARG RSERVER_VERSION="rstudio-server-2024.04.1-748-amd64.deb"
+ENV RSERVER_VERSION=${RSERVER_VERSION}
 RUN <<EOT
 #!/bin/bash
 # install rserver
@@ -111,7 +121,7 @@ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee
 echo | add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
 apt-get update
 apt install -y --no-install-recommends r-base
-wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-server-2023.06.1-524-amd64.deb" -O /tmp/rstudio-server.deb
+wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/${RSERVER_VERSION}" -O /tmp/rstudio-server.deb
 chmod +x /tmp/rstudio-server.deb 
 gdebi -n /tmp/rstudio-server.deb
 rm -rf /tmp/rstudio-server.deb
@@ -123,49 +133,42 @@ EOT

 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
-ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
-RUN <<EOT
-#!/bin/bash
-sudo apt update
-sudo apt install -y texlive-full
-micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
-micromamba run -n plot python -m pip install bamboolib
-micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
-EOT

 # install mojo
-ENV PATH="/home/${CREATE_USER}/.local/bin:$PATH"
-# A random default token
-ARG AUTH_KEY="mut_efe460b898e3482bb6208bfcd4a51d7e"
-ENV AUTH_KEY=$AUTH_KEY
-
-RUN curl https://get.modular.com | sh - && \
-    modular auth $AUTH_KEY 
-
 ARG MODULAR_HOME="/home/${CREATE_USER}/.modular"
 ENV MODULAR_HOME=$MODULAR_HOME
-ENV PATH="$PATH:$MODULAR_HOME/pkg/packages.modular.com_mojo/bin"
+ENV PATH="$MODULAR_HOME/pkg/packages.modular.com_mojo/bin:/home/${CREATE_USER}/.local/bin:$PATH"
+ARG HTTP_PROXY=""
+ARG HTTPS_PROXY=""
+ARG NO_PROXY="localhost,127.0.0.1"
+ENV HTTP_PROXY=$HTTP_PROXY
+ENV HTTPS_PROXY=$HTTPS_PROXY
 RUN <<EOT
 #!/bin/bash
-curl https://get.modular.com | sh - && \
-modular auth $AUTH_KEY 
-modular install mojo
+curl --retry 5 https://get.modular.com | sh - 
+mamba create -n mojo python=3.10 ipykernel ipython nglview -c conda-forge -y 
+mamba activate mojo && modular install mojo
+mamba run -n mojo python -m ipykernel install --user --name="mojo" --display-name="mojo_env"
 EOT

-RUN <<EOT
-#!/bin/bash
-micromamba create -n mixtral_env -c conda-forge ipykernel -y
-git clone https://github.com/Lightning-AI/lit-gpt.git
-cd lit-gpt
-micromamba run -n mixtral_env python -m pip install -r requirements.txt
-micromamba run -n mixtral_env python -m ipykernel install --user --name="mixtral" --display-name="mixtral Environment"
-EOT
-
-# Install Rust
+# Install Rust https://rsproxy.cn/#getStarted
+ENV RUSTUP_DIST_SERVER="https://rsproxy.cn"
+ENV RUSTUP_UPDATE_ROOT="https://rsproxy.cn/rustup"
 ENV PATH="/home/${CREATE_USER}/.cargo/bin:$PATH"
+ENV CARGO_UNSTABLE_SPARSE_REGISTRY="true"
 RUN <<EOT
 #!/bin/bash
-curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+curl --proto '=https' --tlsv1.2 -sSf https://rsproxy.cn/rustup-init.sh | sh -s -- -y
+echo '[source.crates-io]
+replace-with = "rsproxy-sparse"
+[source.rsproxy]
+registry = "https://rsproxy.cn/crates.io-index"
+[source.rsproxy-sparse]
+registry = "sparse+https://rsproxy.cn/index/"
+[registries.rsproxy]
+index = "https://rsproxy.cn/crates.io-index"
+[net]
+git-fetch-with-cli = true' >> ~/.cargo/config.toml
 source $HOME/.cargo/env
 cargo install evcxr_jupyter
 evcxr_jupyter --install
@@ -173,9 +176,12 @@ EOT

 RUN <<EOT
 #!/bin/bash
-micromamba create -n mdgnn -c pytorch -c conda-forge python=3.9 pytorch=1.10.2 torchvision torchaudio cudatoolkit=11.3 pandas matplotlib seaborn scipy numpy=1.24.4 mdanalysis biopandas pymol-open-source ipykernel ipywidgets jupyter einops python-calamine scikit-learn  -y
-micromamba run -n mdgnn python -m ipykernel install --user --name="mdgnn" --display-name="mdgnn Environment"
+sudo apt update
+sudo apt install -y texlive-full
+mamba create -n torch pytorch torchvision torchaudio python=3 ipython nglview requests scienceplots autopep8 ipykernel\
+ pandas numpy matplotlib scipy seaborn orange3 -c pytorch -c nvidia -c conda-forge -y 
+mamba run -n torch python -m ipykernel install --user --name="torch" --display-name="torch_env"
 EOT

-
 WORKDIR "${HOME}"
+
--- a/spawnerdockerfile/Dockerfile.plot
+++ b/spawnerdockerfile/Dockerfile.plot
@@ -0,0 +1,120 @@
+# syntax=docker/dockerfile:1
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+# https://github.com/jupyter/docker-stacks/blob/main/images/base-notebook/Dockerfile
+ARG REGISTRY=quay.io
+ARG OWNER=jupyter
+ARG BASE_CONTAINER=$REGISTRY/$OWNER/docker-stacks-foundation
+FROM $BASE_CONTAINER
+
+LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Install all OS dependencies for the Server that starts but lacks all
+# features (e.g., download as all possible file formats)
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    fonts-liberation \
+    # - pandoc is used to convert notebooks to html files
+    #   it's not present in the aarch64 Ubuntu image, so we install it here
+    pandoc \
+    # - run-one - a wrapper script that runs no more
+    #   than one unique  instance  of  some  command with a unique set of arguments,
+    #   we use `run-one-constantly` to support the `RESTARTABLE` option
+    run-one && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+USER ${NB_UID}
+
+# Install JupyterLab, Jupyter Notebook, JupyterHub and NBClassic
+# Generate a Jupyter Server config
+# Cleanup temporary files
+# Correct permissions
+# Do all this in a single RUN command to avoid duplicating all of the
+# files across image layers when the permissions change
+WORKDIR /tmp
+RUN mamba install --yes \
+    'jupyterlab' \
+    'notebook' \
+    'jupyterhub' \
+    'nbclassic' && \
+    jupyter server --generate-config && \
+    mamba clean --all -f -y && \
+    npm cache clean --force && \
+    jupyter lab clean && \
+    rm -rf "/home/${NB_USER}/.cache/yarn" && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+ENV JUPYTER_PORT=8888
+EXPOSE $JUPYTER_PORT
+
+# Configure container startup
+CMD ["start-notebook.py"]
+
+# Copy local files as late as possible to avoid cache busting
+COPY start-notebook.py start-notebook.sh start-singleuser.py start-singleuser.sh /usr/local/bin/
+COPY jupyter_server_config.py docker_healthcheck.py /etc/jupyter/
+
+# Fix permissions on /etc/jupyter as root
+USER root
+RUN fix-permissions /etc/jupyter/
+
+# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
+# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server`, and `retro` jupyter commands
+# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
+HEALTHCHECK --interval=5s --timeout=3s --start-period=5s --retries=3 \
+    CMD /etc/jupyter/docker_healthcheck.py || exit 1
+
+# here add
+ARG CREATE_USER="jovyan"
+ARG CREATE_USER_PASSWD="password"
+ARG ROOT_PASSWD="password"
+ARG HOME="/home/${CREATE_USER}"
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+
+COPY install.sh /tmp
+RUN <<EOT
+#!/bin/bash
+# 更新软件源
+apt-get update
+# 安装时区数据包并设置时区
+apt-get install -y tzdata 
+ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
+echo 'Asia/Shanghai' > /etc/timezone
+dpkg-reconfigure -f noninteractive tzdata
+# 安装所需的软件包
+apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
+# 创建新用户
+useradd -m -s /bin/bash ${CREATE_USER}
+echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
+echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
+# 安装micromamba
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
+# 安装 Jupyter 和相关软件
+npm install -g configurable-http-proxy
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+EOT
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER ${NB_UID}
+ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
+RUN <<EOT
+#!/bin/bash
+sudo apt update
+sudo apt install -y texlive-full
+micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
+micromamba run -n plot python -m pip install bamboolib
+micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
+EOT
+
+
+WORKDIR "${HOME}"
--- a/spawnerdockerfile/Dockerfile.rserver
+++ b/spawnerdockerfile/Dockerfile.rserver
@@ -0,0 +1,133 @@
+# syntax=docker/dockerfile:1
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+# https://github.com/jupyter/docker-stacks/blob/main/images/base-notebook/Dockerfile
+ARG REGISTRY=quay.io
+ARG OWNER=jupyter
+ARG BASE_CONTAINER=$REGISTRY/$OWNER/docker-stacks-foundation
+FROM $BASE_CONTAINER
+
+LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Install all OS dependencies for the Server that starts but lacks all
+# features (e.g., download as all possible file formats)
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    fonts-liberation \
+    # - pandoc is used to convert notebooks to html files
+    #   it's not present in the aarch64 Ubuntu image, so we install it here
+    pandoc \
+    # - run-one - a wrapper script that runs no more
+    #   than one unique  instance  of  some  command with a unique set of arguments,
+    #   we use `run-one-constantly` to support the `RESTARTABLE` option
+    run-one && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+USER ${NB_UID}
+
+# Install JupyterLab, Jupyter Notebook, JupyterHub and NBClassic
+# Generate a Jupyter Server config
+# Cleanup temporary files
+# Correct permissions
+# Do all this in a single RUN command to avoid duplicating all of the
+# files across image layers when the permissions change
+WORKDIR /tmp
+RUN mamba install --yes \
+    'jupyterlab' \
+    'notebook' \
+    'jupyterhub' \
+    'nbclassic' && \
+    jupyter server --generate-config && \
+    mamba clean --all -f -y && \
+    npm cache clean --force && \
+    jupyter lab clean && \
+    rm -rf "/home/${NB_USER}/.cache/yarn" && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+ENV JUPYTER_PORT=8888
+EXPOSE $JUPYTER_PORT
+
+# Configure container startup
+CMD ["start-notebook.py"]
+
+# Copy local files as late as possible to avoid cache busting
+COPY start-notebook.py start-notebook.sh start-singleuser.py start-singleuser.sh /usr/local/bin/
+COPY jupyter_server_config.py docker_healthcheck.py /etc/jupyter/
+
+# Fix permissions on /etc/jupyter as root
+USER root
+RUN fix-permissions /etc/jupyter/
+
+# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
+# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server`, and `retro` jupyter commands
+# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
+HEALTHCHECK --interval=5s --timeout=3s --start-period=5s --retries=3 \
+    CMD /etc/jupyter/docker_healthcheck.py || exit 1
+
+# here add
+ARG CREATE_USER="jovyan"
+ARG CREATE_USER_PASSWD="password"
+ARG ROOT_PASSWD="password"
+ARG HOME="/home/${CREATE_USER}"
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+
+COPY install.sh /tmp
+RUN <<EOT
+#!/bin/bash
+# 更新软件源
+apt-get update
+# 安装时区数据包并设置时区
+apt-get install -y tzdata 
+ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
+echo 'Asia/Shanghai' > /etc/timezone
+dpkg-reconfigure -f noninteractive tzdata
+# 安装所需的软件包
+apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
+# 创建新用户
+useradd -m -s /bin/bash ${CREATE_USER}
+echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
+echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
+# 安装micromamba
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
+# 安装 Jupyter 和相关软件
+npm install -g configurable-http-proxy
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+EOT
+
+ARG RSERVER_VERSION="rstudio-server-2024.04.1-748-amd64.deb"
+ENV RSERVER_VERSION=${RSERVER_VERSION}
+RUN <<EOT
+#!/bin/bash
+# install rserver
+apt update 
+apt update -qq
+apt install -y --no-install-recommends software-properties-common dirmngr
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+echo | add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+apt-get update
+apt install -y --no-install-recommends r-base
+wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/${RSERVER_VERSION}" -O /tmp/rstudio-server.deb
+chmod +x /tmp/rstudio-server.deb 
+gdebi -n /tmp/rstudio-server.deb
+rm -rf /tmp/rstudio-server.deb
+chown -R ${CREATE_USER}:users /home/${CREATE_USER}
+# 清理和减小镜像大小
+apt-get clean 
+rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/man/?? /usr/share/man/??_*
+EOT
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER ${NB_UID}
+ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
+
+WORKDIR "${HOME}"
--- a/spawnerdockerfile/README.md
+++ b/spawnerdockerfile/README.md
@@ -52,3 +52,42 @@ source ~/.bashrc

 这个操作会激活micromamba(mamba, conda)的安装目录`etc/profile.d/micromamba.sh`激活添加到bash初始化文件`.bashrc`里面

+# docker镜像
+
+关于这个jupyterlab的spawner的notebook启动的镜像来源于：quay.io/jupyterdocker-stacks-foundation
+
+这个镜像的构建仓库是：https://github.com/jupyter/docker-stacks/blob/main/images/docker-stacks-foundation/Dockerfile
+
+可以把这个Dockerfile的ARG参数ROOT_CONTAINER修改为docker pull nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04
+
+pytorch-notebook构建顺序是：
+
+docker-stacks-foundation
+base-notebook
+minimal-notebook
+scipy-notebook
+pytorch-notebook
+
+第一步
+
+```shell
+git clone https://github.com/jupyter/docker-stacks.git
+cd docker-stacks/images/docker-stacks-foundation
+docker buildx build --build-arg ROOT_CONTAINER=nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04 -t quay.io/hotwa/docker-stacks-foundation:latest . --load # docker pull nvidia/cuda:12.4.1-devel-ubuntu22.04
+cd ../base-notebook
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/base-notebook:latest . --load
+cd ../minimal-notebook/
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/minimal-notebook:latest . --load
+cd ../scipy-notebook
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/scipy-notebook:latest . --load
+cd ../pytorch-notebook
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/pytorch-notebook:latest . --load
+```
+
+# 然后构建自己的基础镜像
+
+```shell
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/notebook:latest -f Dockerfile.base-notebook . --load
+# 导出保存
+
+```
--- a/spawnerdockerfile/docker-compose.yml
+++ b/spawnerdockerfile/docker-compose.yml
@@ -0,0 +1,17 @@
+version: '3.8'
+services:
+  molscribe:
+    build: 
+      context: .
+      dockerfile: Dockerfile.base-notebook
+    image: hotwa/notebook:latest
+    container_name: notebook
+    deploy:
+      resources:
+        reservations:
+          devices:
+          - driver: nvidia
+            count: 1
+            capabilities: [gpu]
+    # command: micromamba run -n molscribe jupyter notebook --ip=0.0.0.0 --NotebookApp.allow_origin='*' --debug --no-browser --NotebookApp.disable_check_xsrf=True --port=8888 --allow-root --NotebookApp.token='' --NotebookApp.password='' --log-level=DEBUG
+
--- a/spawnerdockerfile/install.sh
+++ b/spawnerdockerfile/install.sh
@@ -0,0 +1,229 @@
+#!/bin/bash
+
+# 安装所需依赖
+install_dependencies() {
+    # 检查并安装 jq, curl, tar, bzip2
+    for dep in jq curl tar bzip2; do
+        if ! command -v $dep >/dev/null 2>&1; then
+            sudo apt-get update && sudo apt-get install -y $dep
+        fi
+    done
+}
+
+# 在脚本开始时调用依赖安装函数
+install_dependencies
+
+# 默认的MAMBA_ROOT_PREFIX路径
+DEFAULT_MAMBA_ROOT_PREFIX="/usr/local/bin"
+
+# 显示用法信息
+usage() {
+    echo "用法: sudo $0 [--silent-install [custom_root_prefix]] [--silent-uninstall] [--silent-update]"
+    echo "  --silent-install      静默模式安装，不进行任何交互"
+    echo "  custom_root_prefix    (可选) 在静默模式下设置 MAMBA_ROOT_PREFIX 的路径"
+    echo "  --silent-uninstall    静默模式卸载，不进行任何交互"
+    echo "  --silent-update       静默模式更新，不进行任何交互"
+    exit 1
+}
+
+# 安装micromamba
+install_micromamba() {
+    local mamba_prefix="$1"
+
+    # 自动检测操作系统和处理器架构
+    OS="$(uname)"
+    ARCH="$(uname -m)"
+
+    # 根据操作系统和架构设置下载链接
+    case "$OS" in
+        "Linux")
+            case "$ARCH" in
+                "x86_64") URL="https://micro.mamba.pm/api/micromamba/linux-64/latest" ;;
+                "aarch64") URL="https://micro.mamba.pm/api/micromamba/linux-aarch64/latest" ;;
+                "ppc64le") URL="https://micro.mamba.pm/api/micromamba/linux-ppc64le/latest" ;;
+                *) echo "不支持的架构: $ARCH"; exit 1 ;;
+            esac
+            ;;
+        "Darwin")
+            case "$ARCH" in
+                "x86_64") URL="https://micro.mamba.pm/api/micromamba/osx-64/latest" ;;
+                "arm64") URL="https://micro.mamba.pm/api/micromamba/osx-arm64/latest" ;;
+                *) echo "不支持的架构: $ARCH"; exit 1 ;;
+            esac
+            ;;
+        *)
+            echo "不支持的操作系统: $OS"; exit 1 ;;
+    esac
+
+    # 下载并解压 micromamba 到指定的路径
+    echo "正在下载 micromamba..."
+    if curl -Ls "$URL" | tar -xvj -C "$mamba_prefix"; then
+        echo "micromamba 下载并解压完成。"
+        ls -l /usr/local/bin/bin/micromamba
+        echo "micromamba 赋予执行权限"
+        chmod +x /usr/local/bin/bin/micromamba
+        echo "micromamba 安装完成"
+        echo "MAMBA_ROOT_PREFIX 路径：$mamba_prefix"
+        # 初始化 shell 环境
+        echo "正在为root初始化 micromamba shell 环境..."
+        "$mamba_prefix/bin/micromamba" shell init -s bash -p "~/micromamba"
+        ln -s /usr/local/bin/bin/micromamba /usr/local/bin/micromamba 
+    else
+        echo "micromamba 下载失败"
+    fi
+}
+
+# 清理 .bashrc 文件
+cleanup_bashrc() {
+    local mamba_bin_path="$1"
+    
+    # 删除 .bashrc 中相关的行
+    sed -i '/MICROMAMBA_BIN_PATH/d' ~/.bashrc
+    sed -i '/MAMBA_ROOT_PREFIX/d' ~/.bashrc
+    sed -i '/alias mba=/d' ~/.bashrc
+}
+
+# 删除micromamba
+uninstall_micromamba() {
+
+    echo "正在卸载 micromamba..."
+    rm -rf /usr/local/bin/micromamba /usr/local/bin/bin /usr/local/bin/info /usr/local/bin/etc
+
+    # 清理 .bashrc 文件
+    cleanup_bashrc "$mamba_prefix"
+
+    echo "micromamba 已卸载。"
+}
+
+
+# 获取当前 micromamba 版本
+get_current_version() {
+    local mamba_path="$1/micromamba"
+    if [ -f "$mamba_path" ]; then
+        local current_version
+        current_version=$("$mamba_path" --version | grep -o 'version [^ ]*' | cut -d ' ' -f2 | cut -d '-' -f1)
+        echo "$current_version"
+    else
+        echo "未安装"
+    fi
+}
+
+# 获取最新的 micromamba 版本
+get_latest_version() {
+    local latest_version
+    latest_version=$(curl -s https://api.github.com/repos/mamba-org/micromamba-releases/releases/latest | jq -r '.tag_name' | cut -d '-' -f1)
+    echo "$latest_version"
+}
+
+# 检查是否有更新并提示用户
+check_for_updates() {
+    local current_version latest_version
+    current_version=$(get_current_version "$1")
+    latest_version=$(get_latest_version)
+
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
+        read -p "是否更新到最新版本? (y/N): " confirm
+        if [[ "$confirm" =~ ^[Yy]$ ]]; then
+            update_micromamba "$1"
+        else
+            echo "更新已取消"
+        fi
+    else
+        echo "当前已是最新版本 ($current_version)"
+    fi
+}
+
+# 更新micromamba
+update_micromamba() {
+    local mamba_prefix="$1"
+    local current_version latest_version
+    current_version=$(get_current_version "$mamba_prefix")
+    latest_version=$(get_latest_version)
+
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
+        read -p "是否更新到最新版本? (y/N): " confirm
+        if [[ "$confirm" =~ ^[Yy]$ ]]; then
+            echo "正在卸载旧版本 micromamba..."
+            uninstall_micromamba "$mamba_prefix"
+            echo "正在安装最新版本 micromamba..."
+            install_micromamba "$mamba_prefix"
+        else
+            echo "更新已取消"
+        fi
+    else
+        echo "当前已是最新版本 ($current_version)"
+    fi
+}
+
+
+# 交互式安装、卸载和更新菜单
+interactive_menu() {
+    local current_version latest_version
+    current_version=$(get_current_version "$DEFAULT_MAMBA_ROOT_PREFIX")
+    latest_version=$(get_latest_version)
+
+    # 检测并显示当前和最新版本
+    echo "当前 micromamba 版本: $current_version"
+    echo "最新 micromamba 版本: $latest_version"
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新。"
+    fi
+
+    echo "选择操作："
+    echo "1) 安装 micromamba"
+    echo "2) 删除 micromamba"
+    echo "3) 更新 micromamba"
+    echo "q) 退出"
+    read -p "请输入选项（1、2、3或q）: " main_choice
+
+    case "$main_choice" in
+        1)
+            echo "MAMBA_ROOT_PREFIX 的路径: $DEFAULT_MAMBA_ROOT_PREFIX: " 
+            install_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        2)
+            uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        3)
+            update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        q)
+            echo "退出。"
+            exit 0
+            ;;
+        *)
+            echo "无效的选项。退出。"
+            exit 1
+            ;;
+    esac
+}
+
+# 静默卸载
+silent_uninstall() {
+    # 在卸载之前保留虚拟环境目录
+    local envs_dir="$DEFAULT_MAMBA_ROOT_PREFIX/envs"
+    mkdir -p "$envs_dir"
+    mv "$DEFAULT_MAMBA_ROOT_PREFIX/envs" "$(mktemp -d)"
+    uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+    mv "$(mktemp -d)/envs" "$envs_dir"
+}
+
+# 静默更新
+silent_update() {
+    update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+}
+
+# 解析命令行参数
+if [ "$1" = "--silent-install" ]; then
+    silent_install "$2"
+elif [ "$1" = "--silent-uninstall" ]; then
+    silent_uninstall
+elif [ "$1" = "--silent-update" ]; then
+    silent_update
+elif [ "$1" = "--help" ]; then
+    usage
+else
+    interactive_menu
+fi
--- a/spawnerdockerfile/jupyter_server_config.py
+++ b/spawnerdockerfile/jupyter_server_config.py