From f66132fcd01005896ebb23dc0acd88683e7e1e8c Mon Sep 17 00:00:00 2001
From: mm644706215 <ze.ga@qq.com>
Date: Sat, 18 Jan 2025 22:42:10 +0800
Subject: [PATCH] fist add

---
 Dockerfile.4.pyautofep         |  9 +++----
 docker-compose_4_pyautofep.yml | 47 ++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 5 deletions(-)
 create mode 100644 docker-compose_4_pyautofep.yml

diff --git a/Dockerfile.4.pyautofep b/Dockerfile.4.pyautofep
index 7856abe..5aa256a 100644
--- a/Dockerfile.4.pyautofep
+++ b/Dockerfile.4.pyautofep
@@ -1,15 +1,14 @@
-# syntax=docker/dockerfile:1.3-labs
-# NOTE: Building this image requires Docker version >= 23.0.
-
-# Stage 1: Build environment
 ARG TAG_VERSION
 ARG BASE
-FROM ${BASE}:${TAG_VERSION} AS build-env
+FROM ${BASE}:${TAG_VERSION}
 
 # Install PyAutoFEP
+WORKDIR /root
 RUN <<EOT
 #!/bin/bash
 git clone https://github.com/luancarvalhomartins/PyAutoFEP.git
+micromamba create -n PyAutoFEP -c conda-forge -y rdkit openbabel matplotlib networkx pip
+micromamba run -n PyAutoFEP python -m pip install pymbar alchemlyb==0.6.0 matplotlib biopython mdanalysis
 EOT
 
 # Install AmberTools and Amber
diff --git a/docker-compose_4_pyautofep.yml b/docker-compose_4_pyautofep.yml
new file mode 100644
index 0000000..78692b2
--- /dev/null
+++ b/docker-compose_4_pyautofep.yml
@@ -0,0 +1,47 @@
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.4.pyautofep
+      args: 
+        CACHEBUST: 1
+        BASE: "hotwa/gromacs"
+        TAG_VERSION: "gromacs"
+        PLUMED_VERSION: "2.9.2"
+        FFTW_VERSION: "3.3.10"
+        GROMACS_VERSION: "2021.7"
+        CUDA_ARCH: "75;86;89"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    container_name: cuda_4
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:pyautofep
+    # privileged: true
+    # cap_add:
+    #   - ALL
+    #   - CAP_SYS_PTRACE
+    # shm_size: '16gb'
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    # ports:
+    #   - "53322:2222" 
+    # network_mode: host
+    # command: ["/usr/sbin/sshd", "-D"]
+    command: ["tail", "-f", "/dev/null"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]