Olamide Isreal
f971fd0e21
- Nextflow pipeline using chai1 Docker image from Harbor - S3-based input/output paths (s3://omic/eureka/chai-lab/) - GPU-accelerated protein folding with MSA support Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
57 lines
1.8 KiB
Docker
Executable File
57 lines
1.8 KiB
Docker
Executable File
# Use NVIDIA CUDA base image with Ubuntu 22.04
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FROM nvidia/cuda:12.1.0-cudnn8-devel-ubuntu22.04
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# Set environment variables
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ENV DEBIAN_FRONTEND=noninteractive \
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LANG=C.UTF-8 \
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LC_ALL=C.UTF-8 \
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PYTHONUNBUFFERED=TRUE \
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PYTHONFAULTHANDLER=1 \
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PYTHONPYCACHEPREFIX='/tmp/.chai_pycache' \
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MYPY_CACHE_DIR='/tmp/.chai_mypy_cache'
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# Install system dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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git \
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wget \
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curl \
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ca-certificates \
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python3.10 \
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python3.10-dev \
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python3-pip \
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build-essential \
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&& rm -rf /var/lib/apt/lists/*
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# Set working directory
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WORKDIR /workspace
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# Upgrade pip
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RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel
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# Install chai_lab first (this will install older PyTorch)
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RUN pip3 install --no-cache-dir chai_lab==0.5.2
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# Force uninstall old PyTorch and related packages
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RUN pip3 uninstall -y torch torchvision torchaudio
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# Install PyTorch 2.6+ from main PyPI (has CUDA support built-in)
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RUN pip3 install --no-cache-dir torch torchvision torchaudio
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# Upgrade transformers to ensure compatibility
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RUN pip3 install --no-cache-dir --upgrade "transformers>=4.30.0"
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# Verify all installations
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RUN python3 -c "import torch; v=torch.__version__.split('+')[0]; print(f'PyTorch: {v}'); major,minor=map(int,v.split('.')[:2]); assert (major==2 and minor>=6) or major>2, f'PyTorch {v} is too old, need 2.6+'" && \
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python3 -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')" && \
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python3 -c "from transformers import EsmModel; print('transformers: OK')" && \
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python3 -c "import typer; print('typer: OK')" && \
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python3 -c "import chai_lab; print('chai_lab: OK')" && \
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chai --help
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# Add entry point script
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COPY entrypoint.sh /workspace/
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RUN chmod +x /workspace/entrypoint.sh
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# Set entry point
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ENTRYPOINT ["/workspace/entrypoint.sh"]
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