Dockerfile

# syntax=docker/dockerfile:1
# =============================================================================
# Dockerfile for Amber MCP Server
#
# Builds AmberTools25 + PMEMD24 from source and sets up the FastMCP server
# for molecular dynamics simulations.
#
# The AmberTools25 build is CONDITIONAL:
#   - CI / base image builds succeed without the source (dependencies only).
#   - For a full local build, place the AmberTools25 source (with PMEMD24
#     merged in) at repo/ambertools25_src/ before running docker build.
#
# Build (CI / base image - no source required):
#   docker build -t amber_mcp .
#
# Build (local, full AmberTools install):
#   # 1. Download AmberTools25 + PMEMD24 and place merged source at:
#   #      repo/ambertools25_src/
#   docker build -t amber_mcp .
#
# Build (with CUDA - requires NVIDIA base image swap):
#   docker build --build-arg ENABLE_CUDA=true -t amber_mcp:cuda .
#
# Run:
#   docker run -i amber_mcp
# =============================================================================

FROM condaforge/miniforge3:latest AS builder

# Avoid interactive prompts
ENV DEBIAN_FRONTEND=noninteractive

# Install OS-level build dependencies
RUN apt-get update && apt-get install -y --no-install-recommends \
    build-essential \
    gfortran \
    flex \
    bison \
    patch \
    wget \
    ca-certificates \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /app

# ---- Dependency layer (cached across rebuilds) ----
# Install conda build dependencies with a persistent package cache
RUN --mount=type=cache,target=/opt/conda/pkgs \
    mamba install -y -n base \
        python=3.11 \
        cmake \
        gcc \
        gxx \
        gfortran \
        openmpi \
        openmpi-mpicc \
        openmpi-mpicxx \
        openmpi-mpifort \
        netcdf-fortran \
        netcdf4 \
        boost \
        fftw \
        arpack \
        flex \
        bison \
        patch \
        make

# Install Python MCP dependencies with a persistent pip cache
RUN --mount=type=cache,target=/root/.cache/pip \
    pip install fastmcp loguru 'numpy<2.0'

# ---- Build layer ----
# Copy the build script; create repo dir placeholder (source may not exist in CI)
COPY quick_setup.sh ./
RUN mkdir -p repo

# Conditionally copy and build AmberTools25 if source is present.
# In CI the source is not available (proprietary), so this is a no-op there.
# For local builds, place source at repo/ambertools25_src/ before running
# docker build, and it will be copied and compiled here.
COPY . /build_context_tmp/
RUN if [ -d /build_context_tmp/repo/ambertools25_src ]; then \
        echo "AmberTools25 source found - building full installation"; \
        cp -r /build_context_tmp/repo/ambertools25_src /app/repo/ambertools25_src; \
        chmod -R a+r /app/repo/; \
        bash quick_setup.sh \
            --source-dir /app/repo/ambertools25_src \
            --install-prefix /app/env \
            --no-cuda \
            --no-setup-env \
            --clean; \
    else \
        echo "AmberTools25 source not found - building base image without AmberTools"; \
        echo "For local builds with AmberTools, place source at repo/ambertools25_src/"; \
    fi

# Ensure /app/env exists even if AmberTools was not built (needed for runtime COPY)
RUN mkdir -p /app/env

# ---------------------------------------------------------------------------
# Runtime stage - keep only what's needed
# ---------------------------------------------------------------------------
FROM condaforge/miniforge3:latest AS runtime

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y --no-install-recommends \
    libgomp1 \
    libgfortran5 \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /app

# Copy the compiled Amber environment from builder (may be empty in CI builds)
COPY --from=builder /app/env /app/env

# Copy conda packages (runtime libraries: openmpi, netcdf, fftw, etc.)
COPY --from=builder /opt/conda /opt/conda

# Install Python MCP dependencies in runtime (uses builder's conda/python)
RUN --mount=type=cache,target=/root/.cache/pip \
    pip install fastmcp loguru 'numpy<2.0'

# Copy the MCP server source
COPY src/ ./src/
RUN chmod -R a+r /app/src/

# Create working directories
RUN mkdir -p results jobs tmp && chmod 777 /app /app/results /app/jobs /app/tmp

# Set environment variables for Amber
ENV AMBERHOME=/app/env
ENV PMEMDHOME=/app/env
ENV PATH="/app/env/bin:${PATH}"
ENV LD_LIBRARY_PATH="/app/env/lib:${LD_LIBRARY_PATH}"
ENV PYTHONPATH=/app
ENV OPAL_PREFIX=/opt/conda

# Source amber.sh environment on shell entry (only if present)
RUN echo 'test -f /app/env/amber.sh && source /app/env/amber.sh' >> /etc/bash.bashrc

CMD ["python", "src/server.py"]