toxtransformer/Dockerfile.cuda at main · biobricks-ai/toxtransformer · GitHub

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# Multi-stage build to avoid disk space issues
# Stage 1: Build CUDA extension with full devel image
FROM nvidia/cuda:12.8.0-devel-ubuntu20.04 AS builder

ENV DEBIAN_FRONTEND=noninteractive

# Install minimal build dependencies
RUN apt-get update && apt-get install -y \
    python3.9 \
    python3-pip \
    python3.9-dev \
    git \
    && rm -rf /var/lib/apt/lists/*

RUN ln -s /usr/bin/python3.9 /usr/bin/python
RUN python -m pip install --upgrade pip

# Install PyTorch (needed for building extension)
RUN pip install torch torchvision torchaudio

# Copy and build CUDA extension
COPY csrc /tmp/csrc
COPY setup_cpp.py /tmp/setup_cpp.py
RUN cd /tmp && python setup_cpp.py install

# Stage 2: Runtime image (smaller, no devel tools)
FROM nvidia/cuda:12.8.0-runtime-ubuntu20.04

ENV DEBIAN_FRONTEND=noninteractive

# Install system dependencies
RUN apt-get update && apt-get install -y \
    python3.9 \
    python3-pip \
    python3.9-dev \
    git \
    libxrender1 \
    && rm -rf /var/lib/apt/lists/*

RUN ln -s /usr/bin/python3.9 /usr/bin/python
RUN python -m pip install --upgrade pip

# Install PyTorch and dependencies
RUN pip install \
    torch torchvision torchaudio \
    pandas scikit-learn pyarrow \
    biobricks dvc tqdm \
    matplotlib dask[distributed] \
    rdkit

# Install Flask app requirements
COPY flask_cvae/requirements.txt requirements.txt
RUN pip install --trusted-host pypi.python.org -r requirements.txt

# Copy CUDA extension from builder
COPY --from=builder /usr/local/lib/python3.9/dist-packages/toxtransformer_cuda-0.0.0-py3.9-linux-x86_64.egg /usr/local/lib/python3.9/dist-packages/

# Add PyTorch libs to LD_LIBRARY_PATH
ENV LD_LIBRARY_PATH=/usr/local/lib/python3.9/dist-packages/torch/lib:$LD_LIBRARY_PATH

# Copy application code
RUN mkdir -p app
COPY flask_cvae app/flask_cvae
COPY cvae app/cvae

# Create data directories (mounted at runtime)
RUN mkdir -p app/brick app/cache

# Set up Flask
ENV FLASK_APP=flask_cvae.app
ENV ROOT_URL=http://localhost:6515

EXPOSE 6515

WORKDIR /app
CMD ["gunicorn", "-b", "0.0.0.0:6515", "--timeout", "480", "--graceful-timeout", "480", \
    "--workers", "1", "--threads", "8", "--worker-class", "gthread", "--keep-alive", "300", "flask_cvae.app:app"]