add docker

docker/Dockerfile

@@ -0,0 +1,39 @@
+
+ARG CUDA_VERSION='12.4.1'
+FROM mambaorg/micromamba:cuda${CUDA_VERSION}-ubuntu22.04
+ARG ROOT_PASSWD="micromamba"
+ENV ROOT_PASSWD=${ROOT_PASSWD}
+ARG HTTPS_PROXY=""
+ARG HTTP_PROXY=""
+ENV HTTP_PROXY=${HTTP_PROXY}
+ENV HTTPS_PROXY=${HTTPS_PROXY}
+
+USER root
+RUN <<EOT
+#!/bin/bash
+apt update
+apt install -y vim git sudo bash-completion wget curl htop jq bzip2 npm unzip libz-dev libgomp1 libblas-dev liblapack-dev libzmq3-dev libjpeg-dev zlib1g-dev libpng-dev libfreetype6-dev libcairo2-dev pkg-config
+echo "mambauser ALL=(ALL) NOPASSWD: ALL" | sudo tee -a /etc/sudoers > /dev/null
+echo "mambauser:${ROOT_PASSWD}" | chpasswd
+EOT
+
+USER mambauser
+WORKDIR /app
+ARG MAMBA_ENV_NAME="SIME"
+ENV MAMBA_ENV_NAME=${MAMBA_ENV_NAME}
+ARG PYTHON_VERSION="3.8"
+ENV PYTHON_VERSION=${PYTHON_VERSION}
+RUN <<EOT
+#!/bin/bash
+echo "alias conda=micromamba" >> /home/mambauser/.bashrc
+echo "alias mamba=micromamba" >> /home/mambauser/.bashrc
+micromamba create -n ${MAMBA_ENV_NAME} python=${PYTHON_VERSION} -y
+echo "mamba activate ${MAMBA_ENV_NAME}" >> /home/mambauser/.bashrc
+git clone https://github.com/hotwa/SIME
+cd /app/SIME
+micromamba run -n ${MAMBA_ENV_NAME} pip install -r requirements.txt
+micromamba run -n ${MAMBA_ENV_NAME} pip install ipython rdkit
+EOT
+
+WORKDIR /app/SIME
+# ENTRYPOINT ["micromamba", "run", "-n", "SIME", "python", "main.py"]

docker/docker-compose.yml

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+version: '3'
+services:
+  app:
+    build: 
+      context: .
+      dockerfile: Dockerfile
+      args: 
+        CUDA_VERSION: 12.4.1
+        # HTTPS_PROXY: http://127.0.0.1:10809
+        # HTTP_PROXY: http://127.0.0.1:10809
+    image: hotwa/sime:latest
+    container_name: smi_mol
+    volumes:
+      - ../test:/app/SIME/test
+    # profiles:
+    #   - production
+    #   - testing
+    ports:
+      - 5000:5000
+    command: >
+      micromamba run -n SIME python main.py
+
+# docker-compose --profile production up -d
+# docker-compose --profile production -f docker-compose.yml build
+# docker-compose --profile production -f docker-compose.yml up -d