charmmのdockerでのbuild

code:Dockerfile

# CHARMM Dockerfile with CUDA 11.8, OpenMPI, FFTW3, and Python (uv)

FROM nvidia/cuda:11.8.0-devel-ubuntu22.04

# Set environment variables to avoid interactive prompts

ENV DEBIAN_FRONTEND=noninteractive

ENV CUDA_HOME=/usr/local/cuda

ENV PATH=${CUDA_HOME}/bin:${PATH}

ENV LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}

# Install system packages and build tools

RUN apt-get update && apt-get install -y \

build-essential \

cmake \

gfortran \

wget \

curl \

git \

python3 \

python3-pip \

libopenmpi-dev \

openmpi-bin \

libfftw3-dev \

&& rm -rf /var/lib/apt/lists/*

# Install NVIDIA utilities for nvidia-smi (required for Apptainer)

# This installs nvidia-smi and related utilities

# Note: If a specific version is needed, check your host driver version:

# nvidia-smi --query-gpu=driver_version --format=csv,noheader

RUN apt-get update && \

(apt-get install -y --no-install-recommends nvidia-utils-535 2>/dev/null || \

apt-get install -y --no-install-recommends nvidia-utils 2>/dev/null || \

echo "Warning: nvidia-utils installation failed, nvidia-smi may not be available") && \

rm -rf /var/lib/apt/lists/*

# Install uv (Python package manager)

ENV PATH="/root/.cargo/bin:${PATH}"

# Set working directory

WORKDIR /opt

# Copy CHARMM source code

COPY . /opt/charmm

# Create build directory and configure CHARMM with DOMDEC_GPU

RUN mkdir -p /opt/charmm-build && \

cd /opt/charmm-build && \

../charmm/configure \

--prefix=/usr/local \

--domdec_gpu

# Build CHARMM with reduced parallelism to avoid resource exhaustion

# Using -j4 instead of -j$(nproc) to prevent OOM and cancellation issues

RUN cd /opt/charmm-build && \

make -j4 && \

make install

# Set environment variables for runtime

ENV PATH=/usr/local/bin:${PATH}

ENV LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/openmpi/lib:/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}

# Set default command

code:bash

docker build -t charmm-cuda11.8 .

apptainer build charmm-cuda11.8.cif docker-daemon://charmm-cuda11.8:latest