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‎vendor/ngc-autodock/Dockerfile.20.06-py3

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FROM nvcr.io/hpc/autodock:2020.06
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# NVIDIA Autodock-GPU
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ENV PYTHONUNBUFFERED=1 \
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_CUDA_COMPAT_PATH="/usr/local/cuda/compat" \
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LD_LIBRARY_PATH=/usr/local/cuda/lib:/usr/local/cuda/lib64: \
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LIBRARY_PATH=/usr/local/cuda/lib64/stubs: \
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NVIDIA_DRIVER_CAPABILITIES=all \
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NVIDIA_REQUIRE_CUDA=cuda>=11.0 \
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brand=tesla,driver>=440,driver<441 \
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brand=tesla,driver>=418,driver<419 \
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NVIDIA_VISIBLE_DEVICES=all \
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PATH=/opt/AutoDock-GPU/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
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LANG=C.UTF-8
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RUN apt-get update -y && \
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apt install -y --no-install-recommends \
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libgfortran3 libgomp1 \
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curl wget git \
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python3-dev \
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ncurses-term \
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unzip zlib1g-dev htop && \
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curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
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apt-get update -y && \
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apt install -y --no-install-recommends \
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nodejs && \
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rm -rf /var/lib/apt/lists/* && \
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ln -sf /usr/share/terminfo/x/xterm-color /usr/share/terminfo/x/xterm-256color
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# install git-lfs
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WORKDIR /tmp
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RUN curl -sLO https://github.com/git-lfs/git-lfs/releases/download/v2.12.1/git-lfs-linux-amd64-v2.12.1.tar.gz && \
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tar -zxf git-lfs-linux-amd64-v2.12.1.tar.gz && \
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bash install.sh && \
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rm -rf /tmp/*
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RUN curl -fL https://github.com/cdr/code-server/releases/download/v3.7.3/code-server-3.7.3-linux-amd64.tar.gz | tar -C /usr/local/lib -xz && \
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mv /usr/local/lib/code-server-3.7.3-linux-amd64 /usr/local/lib/code-server-3.7.3 && \
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ln -s /usr/local/lib/code-server-3.7.3/bin/code-server /usr/local/bin/code-server
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RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 2
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COPY ./service-defs /etc/backend.ai/service-defs
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WORKDIR /tmp
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RUN curl https://bootstrap.pypa.io/get-pip.py | python3 && \
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python3 -m pip install --no-cache-dir -U setuptools pip
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RUN python3 -m pip install --no-cache-dir pillow && \
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python3 -m pip install --no-cache-dir \
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jupyter==1.0.0 \
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jupyter-client==6.0.0 \
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jupyter-console==6.1.0 \
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jupyter-contrib-core==0.3.3 \
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jupyter-contrib-nbextensions==0.5.1 \
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jupyter-core==4.6.3 \
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jupyter-dash==0.4.0 \
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jupyter-highlight-selected-word==0.2.0 \
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jupyter-js-widgets-nbextension==0.0.2.dev0 \
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jupyter-lsp==0.8.0 \
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jupyter-latex-envs==1.4.6 \
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jupyter-nbextensions-configurator==0.4.1 \
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jupyter-server-proxy==1.2.0 \
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jupyterlab==2.1.4 \
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jupyterlabutils==0.9.0 \
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jupyterlab-git==0.20.0 \
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jupyterlab-github==2.0.0 \
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jupyterlab-server==1.1.5 \
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jupyterlab_hdf==0.3.0 \
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jupyterthemes==0.20.0
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RUN jupyter nbextensions_configurator enable && \
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jupyter contrib nbextension install && \
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jupyter nbextension enable --py --sys-prefix widgetsnbextension && \
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jupyter serverextension enable --py jupyterlab --sys-prefix && \
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jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager && \
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jupyter labextension install --no-build @krassowski/jupyterlab-lsp && \
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jupyter serverextension enable --py jupyter_lsp && \
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jupyter labextension install --no-build @jupyterlab/toc && \
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jupyter nbextension enable execute_time/ExecuteTime && \
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jupyter nbextension enable toc2/main && \
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jupyter labextension install @pyviz/jupyterlab_pyviz && \
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jupyter labextension install @bokeh/jupyter_bokeh && \
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jupyter labextension install --no-build jupyterlab-nvdashboard && \
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jupyter lab build
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RUN apt autoclean && \
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rm -rf /var/lib/apt/lists/* && \
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rm -rf /root/.cache && \
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rm -rf /tmp/*
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# Install ipython kernelspec
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RUN /usr/bin/python3 -m ipykernel install --display-name "NGC Autodock-GPU 20.06 on Backend.AI" && \
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cat /usr/local/share/jupyter/kernels/python3/kernel.json
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# Backend.AI specifics
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LABEL ai.backend.kernelspec="1" \
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ai.backend.envs.corecount="OPENBLAS_NUM_THREADS,OMP_NUM_THREADS,NPROC" \
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ai.backend.features="batch query uid-match user-input" \
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ai.backend.base-distro="ubuntu16.04" \
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ai.backend.accelerators="cuda" \
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ai.backend.resource.min.cpu="1" \
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ai.backend.resource.min.mem="1g" \
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ai.backend.resource.min.cuda.device=1 \
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ai.backend.resource.min.cuda.shares=0.1 \
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ai.backend.runtime-type="python" \
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ai.backend.runtime-path="/usr/bin/python" \
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ai.backend.service-ports="ipython:pty:3000,jupyter:http:8080,jupyterlab:http:8090"
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#/usr/bin/nventry
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WORKDIR /home/work
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# vim: ft=dockerfile

‎vendor/ngc-autodock/service-defs/ipython.json

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{
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"command": [
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"{runtime_path}", "-m", "IPython"
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]
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}

‎vendor/ngc-autodock/service-defs/jupyter.json

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{
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"prestart": [
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{
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"action": "write_tempfile",
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"args": {
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"body": [
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"c.NotebookApp.allow_root = True\n",
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"c.NotebookApp.ip = \"0.0.0.0\"\n",
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"c.NotebookApp.port = {ports[0]}\n",
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"c.NotebookApp.token = \"\"\n",
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"c.FileContentsManager.delete_to_trash = False\n"
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]
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},
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"ref": "jupyter_cfg"
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}
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],
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"command": [
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"{runtime_path}", "-m", "notebook", "--no-browser", "--config", "{jupyter_cfg}"
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]
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}

‎vendor/ngc-autodock/service-defs/jupyterlab.json

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{
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"prestart": [
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{
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"action": "write_tempfile",
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"args": {
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"body": [
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"c.NotebookApp.allow_root = True\n",
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"c.NotebookApp.ip = \"0.0.0.0\"\n",
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"c.NotebookApp.port = {ports[0]}\n",
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"c.NotebookApp.token = \"\"\n",
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"c.FileContentsManager.delete_to_trash = False\n"
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]
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},
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"ref": "jupyter_cfg"
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}
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],
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"command": [
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"{runtime_path}", "-m", "jupyterlab", "--no-browser", "--config", "{jupyter_cfg}"
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]
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}

‎vendor/ngc-autodock/service-defs/sftp.json

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{
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"command": [
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"{runtime_path}", "-m", "sftpserver", "--port", "{ports[0]}"
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]
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}

‎vendor/ngc-autodock/service-defs/vscode.json

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{
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"prestart": [],
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"command": [
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"/opt/kernel/code-server",
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"--port", "{ports[0]}",
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"--extensions-dir", "/etc/backend.ai/vscode-exts"
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],
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"allowed_arguments": [
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"--auth"
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],
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"allowed_envs": [
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"PASSWORD"
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],
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"default_arguments": {
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"--auth": "none"
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}
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}

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