update

.gitignore

@@ -1 +1,3 @@
-/docker-stacks
+/docker-stacks
+jupyterhub-data
+*.tar

Dockerfile

@@ -1,3 +1,4 @@
+# syntax=docker/dockerfile:1
 FROM debian:bullseye
 ARG CREATE_USER="jovyan"
 ARG CREATE_USER_PASSWD="password"

Dockerfile.jupyterhub

@@ -8,6 +8,8 @@ ARG ROOT_PASSWD="password"
 ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG NODEJS_VERSION='18'
+ENV NODEJS_VERSION=${NODEJS_VERSION}
 
 USER root
 RUN <<EOT
@@ -19,6 +21,8 @@ apt-get install -y tzdata
 ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
 echo 'Asia/Shanghai' > /etc/timezone
 dpkg-reconfigure -f noninteractive tzdata
+sudo apt-get remove --purge libnode72:amd64 -y
+curl -fsSL https://deb.nodesource.com/setup_${NODEJS_VERSION}.x | sudo -E bash - 
 # 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
@@ -30,8 +34,25 @@ EOT
 RUN <<EOT
 #!/bin/bash
 # 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-unfold 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
+npm install -g configurable-http-proxy yarn --registry=https://registry.npmmirror.com
+python3 -m pip install ipython jupyter_packaging 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-unfold 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
+git clone https://ghproxy.dockless.eu.org/https://github.com/arose/nglview
+cd nglview
+python3 setup.py install
+cd js
+rm -rf node_modules package-lock.json
+npm install typescript@latest --registry=https://registry.npmmirror.com
+npm install --registry=https://registry.npmmirror.com
+cd ../..
+python -m ipykernel install --sys-prefix
+jupyter nbextension enable --py --sys-prefix widgetsnbextension
+jupyter nbextension enable --py --sys-prefix nglview
+jupyter-nbextension enable nglview --py --sys-prefix
 # 创建 JupyterHub 配置目录
 mkdir -p /root/.jupyterhub
 EOT
@@ -48,26 +69,13 @@ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sud
 sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
 apt-get update
 apt install --no-install-recommends r-base
-sudo wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-server-2023.06.1-524-amd64.deb" -O /tmp/rstudio-server.deb
+sudo wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-server-2024.09.1-394-amd64.deb" -O /tmp/rstudio-server.deb
 sudo chmod +x /tmp/rstudio-server.deb 
 sudo gdebi -n /tmp/rstudio-server.deb
 sudo rm -rf /tmp/rstudio-server.deb
-EOT
-
-RUN <<EOT
-#!/bin/bash
-# 安装micromamba
-echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
-mkdir -p /root/workspace/personal /root/workspace/project
-EOT
-
-RUN <<EOT
-#!/bin/bash
 # 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
 
-
-
 CMD ["jupyterhub", "-f", "/srv/jupyterhub/jupyterhub_config.py"]

README.md

@@ -53,6 +53,26 @@ cd docker-stacks/images/base-notebook
 docker buildx build -t hotwa/notebook:latest . -f Dockerfile
 ```
 
+## 修改jupyterhub启动notebook的路径映射
+
+修改jupyterhub_config.py文件，修改卷的路径：
+
+```python
+c.DockerSpawner.volumes = {
+    "jupyterhub-user-{username}": notebook_dir,
+    "/mnt/mydrive": "/home/jovyan/work/mydrive",
+    "/mnt/mydrive/project/docker-jupyterhub/id_rsa": "/home/jovyan/.ssh/id_rsa",
+}
+```
+
+## 启动notebook修改
+
+启动notebook修改docker-compose.yml文件，修改notebook的基础镜像：
+
+```yaml
+      DOCKER_NOTEBOOK_IMAGE: hotwa/notebook:latest
+```
+
 ## Alternatives
 
 - [rocker/binder](https://rocker-project.org/images/versioned/binder.html) -
@@ -77,6 +97,7 @@ curl -s -L https://nvidia.github.io/libnvidia-container/stable/deb/nvidia-contai
     | sudo tee /etc/apt/sources.list.d/nvidia-container-toolkit.list
 sudo apt-get update
 sudo apt-get install -y nvidia-container-toolkit
+sudo apt-get install nvidia-container-runtime -y
 ```
 
 Configure Docker to use Nvidia driver
@@ -86,6 +107,26 @@ sudo nvidia-ctk runtime configure --runtime=docker
 sudo systemctl restart docker
 ```
 
+实际上这个操作修改了/etc/docker/daemon.json文件：
+
+```shell
+{
+    "registry-mirrors": [
+        "https://0b27f0a81a00f3560fbdc00ddd2f99e0.mirror.swr.myhuaweicloud.com",
+        "https://ypzju6vq.mirror.aliyuncs.com",
+        "https://registry.docker-cn.com",
+        "http://hub-mirror.c.163.com",
+        "https://docker.mirrors.ustc.edu.cn"
+    ],
+    "runtimes": {
+        "nvidia": {
+            "args": [],
+            "path": "nvidia-container-runtime"
+        }
+    }
+}
+```
+
 配置完成之后：
 
 ```shell
@@ -118,6 +159,25 @@ docker volume rm docker-jupyterhub_jupyterhub-data
 docker volume rm jupyterhub-user-admin
 ```
 
+## 修改绑定到notebook的卷
+
+修改jupyterhub_config.py文件，修改卷的路径：
+
+```python
+c.DockerSpawner.volumes = {
+    "jupyterhub-user-{username}": notebook_dir,
+    "/mnt/mydrive": "/home/jovyan/work/mydrive",
+    "/mnt/mydrive/project/docker-jupyterhub/id_rsa": "/home/jovyan/.ssh/id_rsa",
+}
+```
+
+docker-compose.yml文件，修改notebook的基础镜像：
+
+```yaml
+DOCKER_NOTEBOOK_IMAGE: hotwa/notebook:latest
+```
+
+
 ## 构建
 
 构建基础notebook镜像

docker-compose.yml

@@ -12,7 +12,7 @@ services:
       args:
         JUPYTERHUB_VERSION: latest
     restart: always
-    image: hotwa/jupyterhub # registry.cn-hangzhou.aliyuncs.com/hotwa/jupyterhub
+    image: quay.io/hotwa/jupyterhub:latest
     container_name: jupyterhub
     networks:
       - jupyterhub-network
@@ -23,16 +23,17 @@ services:
       # within the container
       - "/var/run/docker.sock:/var/run/docker.sock:rw"
       # Bind Docker volume on host for JupyterHub database and cookie secrets
-      - "jupyterhub-data:/data"
+      - "./jupyterhub-data:/data"
     ports:
       - "8000:8000"
+      - "8080:8080"
     environment:
       # This username will be a JupyterHub admin
       JUPYTERHUB_ADMIN: admin
       # 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
 

jupyterhub_config.py

@@ -10,7 +10,21 @@ c = get_config()  # noqa: F821
 # avoid having to rebuild the JupyterHub container every time we change a
 # configuration parameter.
 
+# from dockerspawner import DockerSpawner
+
+# class MyDockerSpawner(DockerSpawner):
+#     def start(self):
+#         # 启动父类的start方法
+#         self.user_options['environment']['JUPYTER_ENABLE_NBEXTENSIONS'] = 'true'
+#         self.user_options['cmd'] = [
+#             'bash',
+#             '-c',
+#             'pip install nglview jupyter_packaging -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com && jupyter nbextension enable nglview --py --sys-prefix && jupyter labextension install nglview-js-widgets && jupyter labextension install @jupyter-widgets/jupyterlab-manager && start-singleuser.sh'
+#         ]
+#         return super().start()
+        
 # Spawn single-user servers as Docker containers
+c.Authenticator.allow_all = True
 c.JupyterHub.spawner_class = "dockerspawner.DockerSpawner"
 
 # Spawn containers from this image
@@ -30,7 +44,15 @@ c.DockerSpawner.notebook_dir = notebook_dir
 
 # Mount the real user's Docker volume on the host to the notebook user's
 # notebook directory in the container
-c.DockerSpawner.volumes = {"jupyterhub-user-{username}": notebook_dir}
+# c.DockerSpawner.volumes = {"jupyterhub-user-{username}": notebook_dir}
+# Mount the real user's Docker volume on the host to the notebook user's
+# notebook directory in the container
+c.DockerSpawner.volumes = {
+    "jupyterhub-user-{username}": notebook_dir,
+    "/mnt/mydrive": "/home/jovyan/work/mydrive",
+    "/mnt/mydrive/project/docker-jupyterhub/id_rsa": "/home/jovyan/.ssh/id_rsa",
+}
+
 
 # Remove containers once they are stopped
 c.DockerSpawner.remove = True
@@ -62,9 +84,10 @@ 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"}
 })
 
 
@@ -74,7 +97,6 @@ c.DockerSpawner.extra_create_kwargs.update({
 #     'JUPYTERHUB_CORS': '{"allow_origin_pat": "https?://.*\\.example\\.com"}'
 # }
 
-
 # GPU 和网络配置
 c.DockerSpawner.extra_host_config = {
     'runtime': 'nvidia'

nginx.conf

@@ -1,9 +1,12 @@
 events {}
 
 http {
+    # 增加上传文件大小限制
+    client_max_body_size 0; # 0表示无限制
+
     map $http_upgrade $connection_upgrade {
         default upgrade;
-        ''      close;
+        '' close;
     }
 
     server {
@@ -30,6 +33,7 @@ http {
             proxy_set_header Host $host;
             proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
             proxy_set_header X-Forwarded-Proto $scheme;
+            proxy_set_header X-Forwarded-Port $server_port; # 添加这一行,保持原有的端口号
 
             # WebSocket support
             proxy_http_version 1.1;
@@ -38,6 +42,8 @@ http {
             proxy_set_header X-Scheme $scheme;
 
             proxy_buffering off;
+            # 增加临时文件大小限制，0表示禁止使用临时文件
+            proxy_max_temp_file_size 0;
         }
 
         # Managing requests to verify letsencrypt host

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}"

spawnerdockerfile/Dockerfile.base-notebook

@@ -1,3 +1,4 @@
+# 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
@@ -77,7 +78,10 @@ ARG ROOT_PASSWD="password"
 ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG NODEJS_VERSION='18'
+ENV NODEJS_VERSION=${NODEJS_VERSION}
 
+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -88,18 +92,26 @@ 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
+sudo apt-get remove --purge libnode72:amd64 -y
+curl -fsSL https://deb.nodesource.com/setup_${NODEJS_VERSION}.x | sudo -E bash - 
+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
+npm install -g configurable-http-proxy yarn --registry=https://registry.npmmirror.com
 # 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://raw.githubusercontent.com/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
 EOT
 
+# 安装 Jupyter 和相关软件
+RUN <<EOT
+#!/bin/bash
+python3 -m pip install ipython jupyterhub jupyterlab notebook jupyter_packaging -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+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-2024.09.1-394-amd64.deb"
+ENV RSERVER_VERSION=${RSERVER_VERSION}
 RUN <<EOT
 #!/bin/bash
 # install rserver
@@ -110,7 +122,7 @@ 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
@@ -122,51 +134,63 @@ 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=5ca1ab1e
-ENV AUTH_KEY=$AUTH_KEY
-
-RUN curl https://get.modular.com | sh - && \
-    modular auth $AUTH_KEY 
-RUN 
-
 ARG MODULAR_HOME="/home/${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
 
+# 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
-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
-RUN <<EOT
-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
 EOT
 
-WORKDIR "${HOME}"
+RUN <<EOT
+#!/bin/bash
+sudo apt update
+sudo apt install -y texlive-full
+mamba create -n torch tensorboard jupyter_packaging pytorch biopython biopandas pymol-open-source mdtraj torchvision torchaudio python=3 ipython requests scienceplots autopep8 ipykernel\
+ pandas numpy matplotlib scipy seaborn orange3 -c pytorch -c nvidia -c conda-forge -y 
+git clone https://ghproxy.dockless.eu.org/https://github.com/arose/nglview
+cd nglview
+mamba run -n torch python3 setup.py install
+cd js
+rm -rf node_modules package-lock.json
+npm install typescript@latest --registry=https://registry.npmmirror.com
+npm install --registry=https://registry.npmmirror.com
+cd ../..
+mamba run -n torch python -m ipykernel install --user --name="torch" --display-name="torch_env"
+EOT
+
+WORKDIR "${HOME}"
+

spawnerdockerfile/Dockerfile.ngc

@@ -0,0 +1,156 @@
+ARG REGISTRY=quay.io
+ARG OWNER=jupyter
+ARG LABEL=notebook
+ARG VERSION
+ARG BASE_CONTAINER=$REGISTRY/$OWNER/$LABEL:$VERSION
+FROM $BASE_CONTAINER
+ARG HTTP_PROXY
+ARG HTTPS_PROXY
+ENV http_proxy=${HTTP_PROXY}
+ENV https_proxy=${HTTPS_PROXY}
+ARG DEBIAN_FRONTEND="noninteractive"
+ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG ROOT_PASSWD="root"
+ENV ROOT_PASSWD=${ROOT_PASSWD}
+WORKDIR /root
+SHELL ["/bin/bash", "-c"]
+
+# https://network.nvidia.com/products/infiniband-drivers/linux/mlnx_ofed/
+ENV MLNX_OFED_VERSION=23.10-3.2.2.0 
+ENV STAGE_DIR=/tmp
+RUN <<EOT
+#!/bin/bash
+# install Mellanox OFED prepare
+apt-get update
+apt install -y libnvidia-compute-535
+apt-get install -y pciutils tk kmod libusb-1.0-0 tcl chrpath libpci3 bison lsof graphviz ethtool swig udev libltdl-dev libelf1 libmnl0 debhelper flex libfuse2
+# install Mellanox OFED
+mkdir -p ${STAGE_DIR}
+wget http://www.mellanox.com/downloads/ofed/MLNX_OFED-${MLNX_OFED_VERSION}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu22.04-x86_64.tgz -O ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu22.04-x86_64.tgz
+tar xzf ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu22.04-x86_64.tgz -C ${STAGE_DIR}
+cd ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu22.04-x86_64
+./mlnxofedinstall --user-space-only --without-fw-update --all -q > ${STAGE_DIR}/mlnxofedinstall.log 2>&1
+cd ${STAGE_DIR} 
+rm -rf ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu22.04-x86_64*
+EOT
+
+ARG NV_PEER_MEM_VERSION="1.2"
+ENV NV_PEER_MEM_VERSION=${NV_PEER_MEM_VERSION}
+ENV NV_PEER_MEM_TAG=${NV_PEER_MEM_VERSION}-0
+RUN <<EOT
+#!/bin/bash
+# install nv_peer_mem
+mkdir -p ${STAGE_DIR}
+git clone https://github.com/Mellanox/nv_peer_memory.git --branch ${NV_PEER_MEM_TAG} ${STAGE_DIR}/nv_peer_memory
+cd ${STAGE_DIR}/nv_peer_memory
+./build_module.sh
+cd ${STAGE_DIR}
+tar xzf ${STAGE_DIR}/nvidia-peer-memory_${NV_PEER_MEM_VERSION}.orig.tar.gz
+cd ${STAGE_DIR}/nvidia-peer-memory-${NV_PEER_MEM_VERSION}
+apt-get update
+apt --fix-broken install -y
+apt-get install -y dkms
+dpkg-buildpackage -us -uc
+dpkg -i ${STAGE_DIR}/nvidia-peer-memory_${NV_PEER_MEM_TAG}_all.deb
+EOT
+
+# base tools
+RUN <<EOT
+#!/bin/bash
+apt-get update
+apt-get install -y bash-completion wget curl htop jq vim bash libaio-dev build-essential openssh-server python3 python3-pip bzip2 sudo 
+apt-get install -y --no-install-recommends software-properties-common build-essential autotools-dev nfs-common pdsh cmake g++ gcc curl wget vim tmux emacs less unzip htop iftop iotop ca-certificates openssh-client openssh-server rsync iputils-ping net-tools sudo llvm-dev re2c
+add-apt-repository ppa:git-core/ppa -y
+apt-get install -y git libnuma-dev wget
+# Configure SSH for password and public key authentication
+sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
+sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/PubkeyAuthentication no/PubkeyAuthentication yes/' /etc/ssh/sshd_config
+sed -i 's/^#Port 22/Port 22/' /etc/ssh/sshd_config
+sed -i 's/^Port [0-9]*/Port 22/' /etc/ssh/sshd_config
+mkdir /var/run/sshd
+echo "root:${ROOT_PASSWD}" | chpasswd
+mkdir -p ~/.pip
+eval "$(curl https://get.x-cmd.com)"
+# install pixi
+curl -fsSL https://pixi.sh/install.sh | bash
+EOT
+
+RUN <<EOT
+#!/bin/bash
+pip install -v -U git+https://github.com/facebookresearch/xformers.git@main#egg=xformers
+pip install git+https://github.com/huggingface/transformers
+EOT
+
+RUN <<EOT
+#!/bin/bash
+git clone https://github.com/microsoft/DeepSpeed-Kernels.git ${STAGE_DIR}/DeepSpeed-Kernels
+cd ${STAGE_DIR}/DeepSpeed-Kernels
+python -m pip install -v .
+EOT
+
+RUN <<EOT
+#!/bin/bash
+git clone https://github.com/oneapi-src/oneCCL.git ${STAGE_DIR}/oneCCL
+cd ${STAGE_DIR}/oneCCL
+git checkout . 
+git checkout master
+mkdir build
+cd build 
+cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local
+make -j"$(nproc)" install
+EOT
+
+ARG DEEPSPEED_VERSION="v0.14.3"
+ENV DEEPSPEED_VERSION=${DEEPSPEED_VERSION}
+ARG DEEPSPEED_INSTALL_FLAGS="--allow_sudo --pip_sudo --verbose"
+ENV DEEPSPEED_INSTALL_FLAGS=${DEEPSPEED_INSTALL_FLAGS}
+ARG DS_BUILD_SPARSE_ATTN=0
+ENV DS_BUILD_SPARSE_ATTN=${DS_BUILD_SPARSE_ATTN}
+ARG DS_BUILD_FUSED_ADAM=1
+ENV DS_BUILD_FUSED_ADAM=${DS_BUILD_FUSED_ADAM}
+ARG DS_BUILD_CPU_ADAM=1
+ENV DS_BUILD_CPU_ADAM=${DS_BUILD_CPU_ADAM}
+ARG DS_BUILD_OPS=1
+ENV DS_BUILD_OPS=${DS_BUILD_OPS}
+ARG HOSTFILE_CONTENT=""
+ENV HOSTFILE_CONTENT=${HOSTFILE_CONTENT}
+ENV CUTLASS_PATH="/opt/pytorch/pytorch/third_party/cutlass"
+ENV CUDA_HOME="/usr/local/cuda"
+ENV LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
+ENV PATH=${CUDA_HOME}/bin:${PATH}
+RUN <<EOT
+#!/bin/bash
+git clone https://github.com/microsoft/DeepSpeed.git ${STAGE_DIR}/DeepSpeed
+cd ${STAGE_DIR}/DeepSpeed
+git checkout ${DEEPSPEED_VERSION}
+./install.sh ${DEEPSPEED_INSTALL_FLAGS}
+ds_report
+EOT
+
+RUN <<EOT
+#!/bin/bash
+python -m pip install --upgrade pip
+python -m pip install peft tiktoken seaborn blobfile open_clip_torch zstandard mpi4py
+# optimum 手动解决依赖
+python -m pip install black~=23.1 ruff==0.1.5 diffusers>=0.17.0
+python -m pip install --no-deps git+https://github.com/huggingface/optimum.git#egg=optimum[diffusers,quality]
+EOT
+
+RUN <<EOT
+#!/bin/bash
+# 项目目录中的定义通常会覆盖用户家目录中的定义
+# 配置 .deepspeed_env 文件
+cat <<EOF > ~/.deepspeed_env
+TORCH_USE_CUDA_DSA=1
+DEEPSPEED_VERBOSE=1
+DEEPSPEED_LOG_LEVEL=DEBUG
+CUTLASS_PATH=${CUTLASS_PATH}
+TORCH_CUDA_ARCH_LIST=${TORCH_CUDA_ARCH_LIST}
+CUDA_HOME=${CUDA_HOME}
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
+EOF
+unset https_proxy http_proxy
+EOT
+
+CMD ["/usr/sbin/sshd", "-D"]

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}"

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/${CREATE_USER}/micromamba
+# 安装 Jupyter 和相关软件
+npm install -g configurable-http-proxy
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+EOT
+
+ARG RSERVER_VERSION="rstudio-server-2024.09.1-394-amd64.deb"
+ENV RSERVER_VERSION=${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}"

spawnerdockerfile/README.md

@@ -1,5 +1,54 @@
 # Base Jupyter Notebook Stack
 
+## ds_report
+
+```shell
+[2024-07-17 02:25:56,956] [INFO] [real_accelerator.py:203:get_accelerator] Setting ds_accelerator to cuda (auto detect)
+ [WARNING]  async_io requires the dev libaio .so object and headers but these were not found.
+ [WARNING]  async_io: please install the libaio-dev package with apt
+ [WARNING]  If libaio is already installed (perhaps from source), try setting the CFLAGS and LDFLAGS environment variables to where it can be found.
+ [WARNING]  Please specify the CUTLASS repo directory as environment variable $CUTLASS_PATH
+ [WARNING]  sparse_attn requires a torch version >= 1.5 and < 2.0 but detected 2.4
+ [WARNING]  using untested triton version (3.0.0), only 1.0.0 is known to be compatible
+
+(deepspeed) root@ubuntu-finetune:~/binbbt/train/pretrain# cat .deepspeed_env 
+CUDA_HOME=/usr/local/cuda/
+TORCH_USE_CUDA_DSA=1
+CUTLASS_PATH=/opt/cutlass
+TORCH_CUDA_ARCH_LIST="80;89;90;90a"
+LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/lib:/usr/local/mpi/lib:/usr/local/mpi/lib64:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
+NCCL_DEBUG=WARN
+NCCL_SOCKET_IFNAME=bond0
+NCCL_IB_HCA=mlx5_0:1,mlx5_2:1,mlx5_4:1,mlx5_6:1
+NCCL_IB_GID_INDEX=3
+NCCL_NET_GDR_LEVEL=2
+NCCL_P2P_DISABLE=0
+NCCL_IB_DISABLE=0
+```
+
+## test command
+
+docker run -it --rm --network=host --privileged --ipc=host --ulimit memlock=-1 --gpus all hotwa/notebook:ngc
+docker run --rm -it --network=host --privileged --ipc=host --gpus all --ulimit memlock=-1 stack=67108864 hotwa/notebook:ngc /bin/bash
+docker run --rm -it --privileged --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 hotwa/notebook:ngc /bin/bash
+
+```shell
+nvidia-smi
+nvcc -V
+ninja --version
+ds_report
+python -c "import torch; print('torch:', torch.__version__, torch)"
+python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
+python -c "import deepspeed; deepspeed.ops.op_builder.CPUAdamBuilder().load()"
+python -c "from flash_attn import flash_attn_func, flash_attn_varlen_func"
+python -c "import apex.amp; print('Apex is installed and the amp module is available.')"
+python -c "from xformers import ops as xops"
+ibstat
+ofed_info  -s # 如果输出显示了 OFED 版本号，则说明 OFED 驱动已安装。
+mst version
+mpirun --version
+```
+
 > **Images hosted on Docker Hub are no longer updated. Please, use [quay.io image](https://quay.io/repository/jupyter/base-notebook)**
 
 [![docker pulls](https://img.shields.io/docker/pulls/jupyter/base-notebook.svg)](https://hub.docker.com/r/jupyter/base-notebook/)
@@ -52,3 +101,49 @@ 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 spawnerdockerfile/docker-stacks/images/docker-stacks-foundation
+nerdctl --namespace buildkit build --no-cache --build-arg ROOT_IMAGE=nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04 -t quay.io/hotwa/docker-stacks-foundation:latest .
+nerdctl --namespace buildkit build --build-arg ROOT_IMAGE=nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04 -t quay.io/hotwa/docker-stacks-foundation:latest .
+nerdctl --namespace buildkit push quay.io/hotwa/docker-stacks-foundation:latest
+docker buildx build --build-arg ROOT_IMAGE=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
+nerdctl build --build-arg OWNER=hotwa -t quay.io/hotwa/base-notebook:latest .
+cd ../minimal-notebook/
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/minimal-notebook:latest . --load
+nerdctl build --build-arg OWNER=hotwa -t quay.io/hotwa/minimal-notebook:latest .
+cd ../scipy-notebook
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/scipy-notebook:latest . --load
+nerdctl build --build-arg OWNER=hotwa -t quay.io/hotwa/scipy-notebook:latest .
+cd ../pytorch-notebook
+docker buildx build --build-arg OWNER=hotwa -t quay.io/hotwa/pytorch-notebook:latest . --load
+nerdctl build --build-arg OWNER=hotwa -t quay.io/hotwa/pytorch-notebook:latest .
+```
+
+# 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
+
+```

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
+

spawnerdockerfile/docker-compose_ngc.yml

@@ -0,0 +1,72 @@
+version: '3.9'
+
+# DeepSpeed支持多种C++/CUDA扩展（ops），这些ops旨在优化深度学习的训练和推理过程。以下是一些主要的DeepSpeed ops及其功能：
+
+# FusedAdam - 提供融合优化的Adam优化器，适用于GPU。
+# FusedLamb - 类似FusedAdam，针对LAMB优化器，适用于大规模分布式训练。
+# SparseAttention - 用于高效计算稀疏注意力机制。
+# Transformer - 提供Transformer模型的高效实现。
+# TransformerInference - 专门用于Transformer模型的推理优化。
+# CPUAdam - 针对CPU优化的Adam优化器。
+# CPULion - 针对CPU的Lion优化器。
+# Quantizer - 提供量化支持，以减少模型大小和提高推理速度。
+# RandomLTD - 用于随机层裁剪的优化器。
+# StochasticTransformer - 支持随机Transformer模型的训练和推理。
+
+# 检测系统总内存（以GB为单位）
+# TOTAL_MEM=$(awk '/MemTotal/ {printf "%.0f\n", $2/1024/1024}' /proc/meminfo)
+# echo "Docker Compose 文件已生成，shm_size 设置为 ${TOTAL_MEM}GB。"
+
+services:
+  ubuntu-finetune:
+    build: 
+      context: .
+      dockerfile: Dockerfile.ngc
+      args: # PyTorch版本、Python版本与pytorch_lightning版本的对应关系表 https://blog.csdn.net/qq_41813454/article/details/137421822
+        REGISTRY: "nvcr.io"
+        OWNER: "nvidia" # nvcr.io/nvidia/pytorch:24.06-py3
+        LABEL: "pytorch"
+        VERSION: "24.06-py3"
+        DS_BUILD_OPS: 1
+        DEEPSPEED_VERSION: "master"
+        DEEPSPEED_INSTALL_FLAGS: "--allow_sudo"
+        HTTP_PROXY: "http://127.0.0.1:15777"
+        HTTPS_PROXY: "http://127.0.0.1:15777"
+        CACHEBUST: 1
+    # volumes:
+    #   - ./workspace:/workspace
+      # - /tmp:/tmp
+    container_name: ubuntu-ngc
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    # tty: true
+    # stdin_open: true
+    restart: unless-stopped
+    image: quay.io/hotwa/ngc:latest
+    privileged: true
+    ipc: host
+    network_mode: host
+    shm_size: '128gb'
+    # ports:
+    #   - 3228:2222
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    # networks:
+    #   - network_finetune
+    # command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]
+
+# networks:
+#   network_finetune:
+#     name: network_finetune

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

spawnerdockerfile/install_conda.sh

@@ -0,0 +1,20 @@
+# install miniconda
+wget -qO- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
+bash /tmp/miniconda.sh -b -p /opt/conda 
+rm /tmp/miniconda.sh 
+ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
+echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc 
+. /opt/conda/etc/profile.d/conda.sh 
+conda init bash
+conda config --set show_channel_urls true
+# 配置 .condarc 文件
+cat <<EOF > ~/.condarc
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - pytorch-nightly
+  - nvidia
+  - defaults
+show_channel_urls: true
+EOF