change to mojo

2024-05-25 11:10:45 +08:00
parent d6e33de031
commit 3b3ee98f2d
2 changed files with 20 additions and 140 deletions
--- a/spawnerdockerfile/Dockerfile.base-notebook
+++ b/spawnerdockerfile/Dockerfile.base-notebook
@@ -90,20 +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 /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

+# 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
@@ -114,7 +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
@@ -126,24 +133,16 @@ EOT

 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
-ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba

 # 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"
 RUN <<EOT
 #!/bin/bash
-curl https://get.modular.com | sh - && \
-modular auth $AUTH_KEY 
+curl https://get.modular.com | sh - 
+mamba create -n mojo python=3.10 -c conda-forge -y 
+mamba activate mojo
 modular install mojo
 EOT

--- a/spawnerdockerfile/Dockerfile.mdgnn
+++ b/spawnerdockerfile/Dockerfile.mdgnn
@@ -1,119 +0,0 @@
-# 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
-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 -y
-micromamba run -n mdgnn python -m pip install einops python-calamine -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
-micromamba run -n mdgnn python -m pip install -U scikit-learn -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
-micromamba run -n mdgnn python -m ipykernel install --user --name="mdgnn" --display-name="mdgnn Environment"
-EOT
-
-
-WORKDIR "${HOME}"