update add PyAutoFEP

docker-compose_plumed_autofep.yml

@@ -0,0 +1,60 @@
+version: '3.8'
+
+services:
+  gromacs:
+    build: 
+      context: .
+      dockerfile: Dockerfile.gromacs
+      args: 
+        CACHEBUST: 1
+        TAG_VERSION: "12.4.1"
+        PLUMED_VERSION: "2.9.1"
+        FFTW_VERSION: "3.3.10"
+        BUILDKIT_INLINE_CACHE: 1
+    # env_file:
+    #   - .env
+    volumes:
+      - ./data:/data
+      - /dev/shm:/dev/shm
+      - /var/tmp:/var/tmp 
+      - ./script:/root/script
+    container_name: gromacs
+    pull_policy: if_not_present
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    restart: unless-stopped
+    image: hotwa/gromacs:latest
+    privileged: true
+    cap_add:
+      - ALL
+      - CAP_SYS_PTRACE
+    shm_size: '64gb'
+    # devices:
+    #   - /dev/infiniband/rdma_cm
+    #   - /dev/infiniband/uverbs0
+    #   - /dev/infiniband/uverbs1
+    #   - /dev/infiniband/uverbs2
+    #   - /dev/infiniband/uverbs3
+    #   - /dev/infiniband/uverbs4
+    #   - /dev/infiniband/uverbs5
+    #   - /dev/infiniband/uverbs6
+    #   - /dev/infiniband/uverbs7
+    #   - /dev/infiniband/uverbs8
+    environment:
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=compute,utility
+      - TMPDIR=/var/tmp
+    ports:
+      - "53322:2222" 
+      # - UCX_NET_DEVICES=mlx5_0:1,mlx5_1:1,mlx5_2:1,mlx5_4:1,mlx5_5:1,mlx5_6:1,mlx5_7:1,mlx5_8:1
+    # network_mode: host
+    command: ["/usr/sbin/sshd", "-D"]
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]