137 lines
4.7 KiB
Docker
137 lines
4.7 KiB
Docker
ARG CUDA_VERSION=12.1.0
|
|
FROM nvidia/cuda:${CUDA_VERSION}-cudnn8-devel-ubuntu20.04
|
|
ARG DEBIAN_FRONTEND="noninteractive"
|
|
ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
|
|
ENV MAMBA_ROOT_PREFIX=~/micromamba
|
|
ARG CONDA_ENV_NAME="deepspeed"
|
|
ENV CONDA_ENV_NAME=${CONDA_ENV_NAME}
|
|
ARG PYTHON_VERSION=3.10
|
|
ENV PYTHON_VERSION=${PYTHON_VERSION}
|
|
ARG ROOT_PASSWD="root"
|
|
ENV ROOT_PASSWD=${ROOT_PASSWD}
|
|
ENV PATH /opt/conda/bin:/opt/conda/envs/${CONDA_ENV_NAME}/bin:$PATH
|
|
WORKDIR /root
|
|
SHELL ["/bin/bash", "-c"]
|
|
# base tools
|
|
RUN <<EOT
|
|
#!/bin/bash
|
|
apt-get update
|
|
apt-get install -y wget curl htop jq vim bash libaio-dev build-essential openssh-server python3 python3-pip
|
|
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
|
|
# install latest cmake
|
|
wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc | sudo apt-key add -
|
|
sudo apt-add-repository "deb https://apt.kitware.com/ubuntu/ $(lsb_release -cs) main"
|
|
sudo apt-get update
|
|
sudo apt-get install -y cmake
|
|
# Configure SSH for password and public key authentication
|
|
sed -i 's/#PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config
|
|
sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
|
|
sed -i 's/PubkeyAuthentication no/PubkeyAuthentication yes/' /etc/ssh/sshd_config
|
|
sed -i 's/^#Port 22/Port 22/' /etc/ssh/sshd_config
|
|
sed -i 's/^Port [0-9]*/Port 22/' /etc/ssh/sshd_config
|
|
mkdir /var/run/sshd
|
|
echo 'root:${ROOT_PASSWD}' | chpasswd
|
|
mkdir -p ~/.pip
|
|
# 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
|
|
conda init bash
|
|
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
|
|
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
|
|
echo "conda activate ${CONDA_ENV_NAME}" >> ~/.bashrc
|
|
# 配置 .condarc 文件
|
|
cat <<EOF > ~/.condarc
|
|
channels:
|
|
- conda-forge
|
|
- bioconda
|
|
- pytorch
|
|
- pytorch-nightly
|
|
- nvidia
|
|
- defaults
|
|
show_channel_urls: true
|
|
EOF
|
|
# 安装 micromamba
|
|
echo 1 | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
|
|
micromamba shell init -s bash -p ~/micromamba
|
|
cat <<'EOF' >> ~/.bashrc
|
|
source ~/micromamba/etc/profile.d/micromamba.sh
|
|
alias mamba=micromamba
|
|
alias mba=mamba
|
|
EOF
|
|
# 配置 .mambarc 文件
|
|
cat <<EOF > ~/.mambarc
|
|
channels:
|
|
- conda-forge
|
|
- bioconda
|
|
- pytorch
|
|
- pytorch-nightly
|
|
- nvidia
|
|
- defaults
|
|
show_channel_urls: true
|
|
EOF
|
|
EOT
|
|
|
|
# reference: https://github.com/huggingface/transformers/blob/main/docker/transformers-pytorch-deepspeed-latest-gpu/Dockerfile
|
|
# PyTorch
|
|
ENV REF='main'
|
|
ENV STAGE_DIR=/tmp
|
|
ENV NV_PEER_MEM_VERSION=1.2
|
|
ENV NV_PEER_MEM_TAG=${NV_PEER_MEM_VERSION}-0
|
|
ENV OPENMPI_BASEVERSION=4.1
|
|
ENV OPENMPI_VERSION=${OPENMPI_BASEVERSION}.6
|
|
ARG CUDA='cu121'
|
|
ENV CUDA=${CUDA}
|
|
ARG PYTORCH_VERSION=2.3.0
|
|
ENV PYTORCH_VERSION=${PYTORCH_VERSION}
|
|
ARG TORCHVISION_VERSION=0.18.0
|
|
ENV TORCHVISION_VERSION=${TORCHVISION_VERSION}
|
|
ARG TORCHAUDIO_VERSION=2.3.0
|
|
ENV TORCHAUDIO_VERSION=${TORCHAUDIO_VERSION}
|
|
ARG PYTORCH_CUDA_VERSION=12.1
|
|
ENV PYTORCH_CUDA_VERSION=${PYTORCH_CUDA_VERSION}
|
|
ENV MLNX_OFED_VERSION=4.9-7.1.0.0
|
|
ARG SETUPTOOLS_VERSION=69.5.1
|
|
ENV SETUPTOOLS_VERSION=${SETUPTOOLS_VERSION}
|
|
RUN <<EOT
|
|
#!/bin/bash
|
|
source /opt/conda/etc/profile.d/conda.sh
|
|
conda activate ${CONDA_ENV_NAME}
|
|
# 克隆 ninja 源码并编译
|
|
git clone https://github.com/ninja-build/ninja.git
|
|
cd ninja
|
|
# 克隆 GoogleTest 源码
|
|
git clone https://github.com/google/googletest.git
|
|
conda run -n ${CONDA_ENV_NAME} python ./configure.py --bootstrap
|
|
# 配置并构建 Ninja 测试，添加 pthread 链接选项
|
|
# CXXFLAGS="-pthread" LDFLAGS="-pthread" ./configure.py --bootstrap --gtest-source-dir=$(pwd)/googletest
|
|
conda run -n ${CONDA_ENV_NAME} bash -c "CXXFLAGS='-pthread' LDFLAGS='-pthread' python ./configure.py --bootstrap --gtest-source-dir=$(pwd)/googletest"
|
|
./ninja all
|
|
# 运行 Ninja 单元测试
|
|
./ninja_test
|
|
conda create -n ${CONDA_ENV_NAME} python=${PYTHON_VERSION} pyyaml ipython -c conda-forge -y
|
|
python3 -m pip install --no-cache-dir --upgrade pip
|
|
conda clean -afy
|
|
EOT
|
|
|
|
RUN <<EOT
|
|
#!/bin/bash
|
|
source /opt/conda/etc/profile.d/conda.sh
|
|
conda activate ${CONDA_ENV_NAME}
|
|
git clone https://github.com/lingxusb/megaDNA.git ${STAGE_DIR}/megaDNA
|
|
cd ${STAGE_DIR}/megaDNA
|
|
pip install .
|
|
|
|
EOT
|
|
|
|
RUN <<EOT
|
|
#!/bin/bash
|
|
source /opt/conda/etc/profile.d/conda.sh
|
|
conda activate ${CONDA_ENV_NAME}
|
|
pip install ipykernel
|
|
python3 -m ipykernel install --user --name=${CONDA_ENV_NAME} --display-name=${CONDA_ENV_NAME}
|
|
EOT
|
|
|
|
CMD ["/usr/sbin/sshd", "-D"] |