Molecular dynamics simulation for new force calculations - Proteogram v2

Dockerfile

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+# syntax=docker/dockerfile:1.6
+
+############################
+# Builder: install deps with uv
+############################
+FROM python:3.11-slim AS builder
+
+# System deps (add more if you need: git, build-essential, etc.)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    git \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+
+WORKDIR /app
+
+# Install uv
+# (uv is a single binary; pip install also works, but this is usually faster/cleaner)
+RUN pip install --no-cache-dir uv
+
+# Copy only dependency metadata first for better layer caching
+COPY pyproject.toml ./
+# If you have a lockfile, copy it too:
+COPY uv.lock ./
+
+# Create a virtualenv and sync deps from lockfile
+# --frozen: fail if lockfile doesn't match pyproject
+RUN uv venv /opt/venv && \
+    . /opt/venv/bin/activate && \
+    uv sync --active --frozen --no-dev
+
+############################
+# Runtime: copy venv + code
+############################
+FROM python:3.11-slim AS runtime
+
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+ENV PYTHONUNBUFFERED=1
+WORKDIR /app
+
+# Copy venv from builder
+COPY --from=builder /opt/venv /opt/venv
+
+# Copy repo contents
+COPY . /app
+
+# Make sure imports work from repo root
+ENV PYTHONPATH=/app
+
+# Default help
+CMD ["python", "-c", "print('Container ready. Try: python scripts/measure_similarity.py')"]

Dockerfile.gpu

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+# syntax=docker/dockerfile:1.6
+
+############################
+# Builder: install deps with uv (GPU-enabled)
+############################
+FROM python:3.11-slim AS builder
+
+# System deps (add more if you need: git, build-essential, etc.)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    git \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+# Install uv
+RUN pip install --no-cache-dir uv
+
+# Copy only dependency metadata first for better layer caching
+COPY pyproject.toml ./
+COPY uv.lock ./
+
+# Create a virtualenv and sync deps from lockfile, including CUDA extra
+# --frozen: fail if lockfile doesn't match pyproject
+RUN uv venv /opt/venv && \
+    . /opt/venv/bin/activate && \
+    uv sync --active --frozen --no-dev --extra cuda12
+
+############################
+# Runtime: copy venv + code
+############################
+FROM python:3.11-slim AS runtime
+
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONPATH=/app
+
+# NVIDIA runtime hints (GPU is still assigned at `docker run --gpus ...`)
+ENV NVIDIA_VISIBLE_DEVICES=all
+ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility
+
+WORKDIR /app
+
+# Copy venv from builder
+COPY --from=builder /opt/venv /opt/venv
+
+# Copy repo contents
+COPY . /app
+
+# Default help
+CMD ["python", "-c", "print('GPU container ready. Try: python scripts/measure_similarity.py')"]