update to orca

.env

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+DOCKERFILE=Dockerfile.dev
+TAG=dev
+ENV=dev
+PORT=8081

.envprod

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+DOCKERFILE=Dockerfile.prod
+TAG=prod
+ENV=prod
+PORT=8080

docker-compose.yml

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+version: '3.9'
+
+# 定义通用的环境变量
+x-env: &common_env
+  O3_BABEL_PATH: "/usr/bin"
+  O3_GNUPLOT: "/usr/bin/gnuplot"
+  O3_PYMOL: "/usr/bin/pymol"
+  O3_TEMP_PATH: "/tmp"
+  O3_QM_ENGINE: "/opt/orca/orca"
+  O3_MD_GRID_PATH: "/usr/bin/mdgrid"
+  O3_CS3D: "/usr/bin/cs3d"
+
+services:
+  # 基础服务
+  open3dqsar:
+    build:
+      context: docker
+      dockerfile: ${DOCKERFILE}
+    image: hotwa/open3dqsar:${TAG}
+    container_name: open3dqsar_${ENV}
+    environment:
+      <<: *common_env  # 引用通用的环境变量
+      ENV: ${ENV}  # 动态设置 ENV 变量
+    volumes:
+      - ./data:/Open3DQSAR/data
+    ports:
+      - "${PORT}:8080"
+
+  # 开发环境服务
+  open3dqsar_dev:
+    profiles: ["dev"]  # 开发环境 profile
+    extends:
+      service: open3dqsar
+    environment:
+      <<: *common_env  # 引用通用的环境变量
+      ENV: dev  # 开发环境标识
+    volumes:
+      - ./src/Open3DQSAR:/Open3DQSAR  # 映射源代码目录，便于开发调试
+
+  # 生产环境服务
+  open3dqsar_prod:
+    profiles: ["prod"]  # 生产环境 profile
+    extends:
+      service: open3dqsar
+    environment:
+      <<: *common_env  # 引用通用的环境变量
+      ENV: prod  # 生产环境标识

docker/Dockerfile.dev

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+# 第一阶段：构建阶段
+FROM ubuntu:22.04 AS builder
+
+# 设置环境变量
+ENV DEBIAN_FRONTEND=noninteractive
+
+# 更新系统、安装依赖并清理缓存
+RUN apt update && apt upgrade -y && \
+    apt install -y \
+    build-essential \
+    gcc \
+    g++ \
+    gfortran \
+    cmake \
+    make \
+    wget \
+    tar \
+    libatlas-base-dev \
+    liblapacke-dev \
+    libblas-dev \
+    git \
+    libedit-dev \
+    zlib1g-dev \
+    openbabel \
+    libeigen3-dev \
+    automake \
+    autoconf \
+    libtool \
+    vim \
+    gnuplot \
+    pymol \
+    bzip2 \
+    && ln -s /usr/bin/obabel /usr/bin/babel \
+    && apt clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# 安装 OpenMPI
+COPY openmpi-4.1.6.tar.bz2 /
+RUN tar -xf openmpi-4.1.6.tar.bz2 && \
+    cd openmpi-4.1.6 && \
+    ./configure --prefix=/opt/openmpi --disable-builtin-atomics && \
+    make -j$(nproc) && \
+    make install && \
+    cd .. && \
+    rm -rf openmpi-4.1.6 openmpi-4.1.6.tar.bz2
+
+# 设置 OpenMPI 环境变量
+ENV PATH="/opt/openmpi/bin:$PATH" \
+    LD_LIBRARY_PATH="/opt/openmpi/lib:$LD_LIBRARY_PATH"
+
+# 克隆 Open3DQSAR 仓库
+RUN git clone https://github.com/UnixJunkie/Open3DQSAR
+
+# 安装 ORCA
+COPY orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz /
+RUN tar -xf orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz && \
+    mv orca_6_0_0_shared_openmpi416_avx2 /opt/orca && \
+    rm orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz
+
+# 进入 Open3DQSAR 目录并构建
+WORKDIR /Open3DQSAR/open3dqsar
+RUN ./bootstrap && \
+    ./configure --with-atlas && \
+    make -j$(nproc) && \
+    make install
+
+# 设置 ORCA 环境变量
+ENV PATH="/opt/orca:$PATH" \
+    LD_LIBRARY_PATH="/opt/orca:$LD_LIBRARY_PATH"
+
+# 第二阶段：运行阶段
+FROM ubuntu:22.04
+
+# 设置环境变量
+ENV DEBIAN_FRONTEND=noninteractive \
+    O3_BABEL_PATH=/usr/bin \
+    O3_GNUPLOT=/usr/bin/gnuplot \
+    O3_PYMOL=/usr/bin/pymol \
+    O3_TEMP_PATH=/tmp \
+    O3_QM_ENGINE=/opt/orca/orca \
+    O3_MD_GRID_PATH=/usr/bin/mdgrid \
+    O3_CS3D=/usr/bin/cs3d
+
+# 安装运行时依赖
+RUN apt update && apt install -y \
+    libatlas-base-dev \
+    liblapacke-dev \
+    libblas-dev \
+    openbabel \
+    gnuplot \
+    pymol \
+    bzip2 \
+    && ln -s /usr/bin/obabel /usr/bin/babel \
+    && apt clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# 从构建阶段复制构建结果
+COPY --from=builder /usr/local/bin /usr/local/bin
+COPY --from=builder /Open3DQSAR /Open3DQSAR
+COPY --from=builder /opt/openmpi /opt/openmpi
+COPY --from=builder /opt/orca /opt/orca
+
+# 设置 OpenMPI 和 ORCA 环境变量
+ENV PATH="/opt/openmpi/bin:/opt/orca:$PATH" \
+    LD_LIBRARY_PATH="/opt/openmpi/lib:/opt/orca:$LD_LIBRARY_PATH"
+
+# 进入测试目录并运行测试脚本
+WORKDIR /Open3DQSAR/open3dqsar/test
+RUN ./test.sh > test.log 2>&1 &
+
+# 设置容器启动时的默认命令（保持容器运行）
+ENTRYPOINT ["tail", "-f", "/dev/null"]