项目结构 For single-host with Docker Compose 1 2 3 4 5 6 7 8 9 10 cluster ├── Dockerfile # Image specification ├── project # Sample program source code │ └── mpi_hello_world.c ├── ssh # keys for accessing │ ├── id_rsa # (could generate your own) │ └── id_rsa.pub ├── .env # General configuration ├── docker-compose.yml # Container orchestration └── cluster.sh # Commands wrapper ultility
接下来逐个文件解析项目
cluster.sh 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 set -e # 如果不带任何参数 直接运行set，会显示所有环境变量和shell函数 # set -x 用来在运行结果之前，先输出执行的那一行命令,set -e表示脚本执行出错就立即退出，避免错误的积累 # shellcheck disable=SC1091 . ./.env ####################### # TASK INDICATORS COMMAND_UP=0 COMMAND_DOWN=0 COMMAND_RELOAD=0 COMMAND_SCALE=0 COMMAND_LOGIN=0 COMMAND_EXEC=0 COMMAND_LIST=0 COMMAND_CLEAN=0 # Default values if providing empty SIZE=4 ############################################# usage () { echo " Alpine MPICH Cluster (for Docker Compose on single Docker host)" echo "" echo " USAGE: ./cluster.sh [COMMAND] [OPTIONS]" echo "" echo " Examples of [COMMAND] can be:" echo " up: start cluster" echo " ./cluster.sh up size=10" echo "" echo " scale: resize the cluster" echo " ./cluster.sh scale size=30" echo "" echo " reload: rebuild image and distribute to nodes" echo " ./cluster.sh reload size=15" echo "" echo " login: login to Docker container of MPI master node for interactive usage" echo " ./cluster.sh login" echo "" echo " exec: execute shell command at the MPI master node" echo " ./cluster.sh exec [SHELL COMMAND]" echo "" echo " down: shutdown cluster" echo " ./cluster.sh down" # echo "" # echo " clean: remove images in the system" # echo " ./cluster.sh clean" echo "" echo " list: show running containers of cluster" echo " ./cluster.sh list" echo "" echo " help: show this message" echo " ./cluster.sh help" echo "" echo " " } HEADER=" __v_ (.___\\/{ ~^~^~^~^~^~^~^~^~^~^~^~^~" down_all () { printf "\\n\\n===> CLEAN UP CLUSTER" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose down" printf "\\n" docker-compose down } up_registry () { printf "\\n\\n===> SPIN UP REGISTRY" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose up -d registry" printf "\\n" docker-compose up -d registry } generate_ssh_keys () { if [ -f ssh/id_rsa ] && [ -f ssh/id_rsa.pub ]; then return 0 fi printf "\\n\\n===> GENERATE SSH KEYS \\n\\n" echo "$ mkdir -p ssh/ " printf "\\n" mkdir -p ssh/ echo "$ ssh-keygen -f ssh/id_rsa -t rsa -N ''" printf "\\n" ssh-keygen -f ssh/id_rsa -t rsa -N '' } build_and_push_image () { printf "\\n\\n===> BUILD IMAGE" printf "\\n%s\\n" "$HEADER" echo "$ docker build -t \"$REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME\" ." printf "\\n" docker build -t "$REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME" . printf "\\n" printf "\\n\\n===> PUSH IMAGE TO REGISTRY" printf "\\n%s\\n" "$HEADER" echo "$ docker push \"$REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME\"" printf "\\n" docker push "$REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME" } up_master () { printf "\\n\\n===> SPIN UP MASTER NODE" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose up -d master" printf "\\n" docker-compose up -d master } up_workers () { printf "\\n\\n===> SPIN UP WORKER NODES" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose up -d worker" printf "\\n" docker-compose up -d worker printf "\\n" printf "\\n%s\\n" "$HEADER" NUM_WORKER=$((SIZE - 1)) echo "$ docker-compose scale worker=$NUM_WORKER" printf "\\n" docker-compose scale worker=${NUM_WORKER} } down_master () { printf "\\n\\n===> TORN DOWN MASTER NODE" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose stop master && docker-compose rm -f master" printf "\\n" docker-compose stop master && docker-compose rm -f master } down_workers () { printf "\\n\\n===> TORN DOWN WORKER NODES" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose stop worker && docker-compose rm -f worker" printf "\\n" docker-compose stop worker && docker-compose rm -f worker } list () { printf "\\n\\n===> LIST CONTAINERS" printf "\\n%s\\n" "$HEADER" echo "$ docker-compose ps" printf "\\n" docker-compose ps } exec_on_mpi_master_container () { # shellcheck disable=SC2046 docker exec -it -u mpi $(docker-compose ps | grep 'master'| awk 'NR==1{print $1}') "$@" } prompt_ready () { printf "\\n\\n===> CLUSTER READY \\n\\n" } show_instruction () { echo ' ## . ' echo ' ## ## ## == ' echo ' ## ## ## ## ## === ' echo ' /"""""""""""""""""\___/ === ' echo ' ~~~ {~~ ~~~~ ~~~ ~~~~ ~~~ ~ / ===- ~~~ ' echo ' \______ o __/ ' echo ' \ \ __/ ' echo ' \____\_______/ ' echo ' ' echo ' Alpine MPICH Cluster ' echo '' echo ' More info: https://github.com/NLKNguyen/alpine-mpich' echo '' echo '==============================================================' echo '' echo "To run MPI programs in an interative shell:" echo " 1. Login to master node:" echo " Using Docker through command wrapper:" echo " $ ./cluster.sh login" echo "" echo " Or using SSH with keys through exposed port:" echo " $ ssh -o \"StrictHostKeyChecking no\" -i ssh/id_rsa -p $SSH_PORT mpi@localhost" echo ' where [localhost] could be changed to the host IP of master node' echo "" echo " 2. Execute MPI programs inside master node, for example:" echo " $ mpirun hostname" echo " *----------------------------------------------------*" echo " | Default hostfile of connected nodes in the cluster |" echo " | is automatically updated at /etc/opt/hosts |" echo " | To obtain hostfile manually: $ get_hosts > hosts |" echo " * ---------------------------------------------------*" echo "" echo "" echo "To run directly a shell command at master node:" echo " $ ./cluster.sh exec [COMMAND]" echo "" echo " Example: " echo " $ ./cluster.sh exec mpirun hostname" echo "" } ############################################# while [ "$1" != "" ]; do PARAM=$(echo "$1" | awk -F= '{print $1}') VALUE=$(echo "$1" | awk -F= '{print $2}') case $PARAM in help) usage exit ;; -i) show_instruction exit ;; login) COMMAND_LOGIN=1 ;; exec) COMMAND_EXEC=1 shift # the rest is the shell command to run in the node SHELL_COMMAND="$*" break # end while loop ;; up) COMMAND_UP=1 ;; down) COMMAND_DOWN=1 ;; reload) COMMAND_RELOAD=1 ;; scale) COMMAND_SCALE=1 ;; list) COMMAND_LIST=1 ;; clean) COMMAND_CLEAN=1 ;; size) [ "$VALUE" ] && SIZE=$VALUE ;; *) echo "ERROR: unknown parameter \"$PARAM\"" usage exit 1 ;; esac shift done if [ $COMMAND_UP -eq 1 ]; then down_all up_registry generate_ssh_keys build_and_push_image up_master up_workers prompt_ready show_instruction elif [ $COMMAND_DOWN -eq 1 ]; then down_all elif [ $COMMAND_CLEAN -eq 1 ]; then echo "TODO" elif [ $COMMAND_SCALE -eq 1 ]; then down_master down_workers up_master up_workers prompt_ready show_instruction elif [ $COMMAND_RELOAD -eq 1 ]; then down_master down_workers build_and_push_image up_master up_workers prompt_ready show_instruction elif [ $COMMAND_LOGIN -eq 1 ]; then exec_on_mpi_master_container /bin/sh elif [ $COMMAND_EXEC -eq 1 ]; then exec_on_mpi_master_container ash -c "${SHELL_COMMAND}" elif [ $COMMAND_LIST -eq 1 ]; then list else usage fi
dockerfile 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 FROM nlknguyen/alpine-mpich:onbuild # # ------------------------------------------------------------ # # Build MPI project # # ------------------------------------------------------------ # Put all build steps and additional package installation here # Note: the current directory is ${WORKDIR:=/project}, which is # also the default directory where ${USER:=mpi} will SSH login to # Copy the content of `project` directory in the host machine to # the current working directory in this Docker image COPY project/ . # Normal build command RUN mpicc -o mpi_hello_world mpi_hello_world.c # RUN sudo chmod 777 -R /project && cd /project/NPB3.3.1/NPB3.3-MPI && make IS CLASS=A NPROCS=4 # #################### # For Docker beginner: # After Docker syntax `RUN`, you can execute any command available in # the current shell of the image. # To switch to root: USER root # To switch back to default user: USER ${USER}
docker-compose.yml 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 version: "2" services: registry: image: registry ports: - "${REGISTRY_PORT}:5000" master: image: $REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME user: root entrypoint: ["mpi_bootstrap", "role=master", "mpi_master_service_name=master", "mpi_worker_service_name=worker"] ports: - "${SSH_PORT}:22" networks: - net worker: image: $REGISTRY_ADDR:$REGISTRY_PORT/$IMAGE_NAME user: root entrypoint: ["mpi_bootstrap", "role=worker", "mpi_master_service_name=master", "mpi_worker_service_name=worker"] networks: - net networks: net:
NPB测试的使用 进入home/hadoop/alpine-mpich/cluster文件夹下
1 2 3 4 5 6 7 8 9 10 make IS CLASS=B NPROCS=8 make: execvp: sys/print_header: Permission denied Makefile:68: recipe for target 'header' failed make: *** [header] Error 127 需要更改权限，可以使用 sudo chmod 777 -R /project
docker怎么进入一个正在运行的容器内部 1 2 3 sudo docker exec -it 775c7c9ee1e1 /bin/bash sudo docker exec -it 775c7c9ee1e1 /bin/sh
我的宿主机没有安装MPICH但是仍然能够在容器中进行编译和运行，但是在宿主机上是不能编译的，所以文献中的兼容性问题，我认为是想现在主机上进行编译，编译完之后在各个容器之间进行分发，这样在主机编译后的代码需要在容器的环境下能够运行
参照默认dockerfile定制化 定制化后在虚拟机上 运行mpirun -np 1 is.A.4
仍然出现以下错误:
ERROR: compiled for 4 processes
npb 测试集 mpi run -np， np这个参数得和编译所用的参数相一致才不会退出
怎么查看docker容器的运行状态 1 2 3 4 5 6 7 8 9 docker top grafana 得出grafana二进制文件目录； 得出grafana配置文件地址； 得出grafana日志文件地址 docker inspect grafana
“LogPath”: “/var/lib/docker/containers/c7f8a384fc1b647989b5b78336feb67fbc7002d713156a49d33f87aadebc44a1/c7f8a384fc1b647989b5b78336feb67fbc7002d713156a49d33f87aadebc44a1-json.log”
docker 怎么把容器保存为本地镜像 commit 命令
怎么给docker 容器重命名 容器在运行的时候可以利用以下语句进行重命名
1 sudo docker rename discourse_app disc_app
docker run的参数解释 1 2 3 4 5 -a attach 表示追加 - i 表示交互方式 - t --privileged=false， 指定容器是否为特权容器，特权容器拥有所有的capabilities
指定容器名称
1 2 3 docker run --name [container name] -t -i [image ID | Repository:TAG] /bin/bash sudo docker run --name sql5.7 -it mysql:5.7 /bin/bash
删除容器的镜像 直接 sudo docker rmi mysql的时候会报错，因为还有容器依赖于该镜像，所以正常情况下是先删除容器再删除容器依赖的镜像
docker删除所有none镜像
1 2 docker rmi `docker images | grep '<none>' | awk '{print $3}'`
docker数据映射 什么是挂载
当在 Linux 系统中使用这些硬件设备时，只有将Linux本身的文件目录与硬件设备的文件目录合二为一，硬件设备才能为我们所用。合二为一的过程称为“挂载”。
挂载，指的就是将设备文件中的顶级目录连接到 Linux 根目录下的某一目录（最好是空目录），访问此目录就等同于访问设备文件
当插入了新硬盘，分了新磁盘区sdb1。它现在还不属于/。
我们虽然可以在一些图形桌面系统里找到他的位置，浏览管理里面的文件，但在命令行却不知怎么访问它的目录，比如无法使用cd或者ls。也无法在编程时指定一个目录对它操作。
当我们使用了 mount /dev/sdb1 /Share/ ，把新硬盘的区sdb1挂载到工作目录的/Share/文件夹下，之后访问这个~/Share/文件夹就相当于访问这个硬盘2的sdb1分区了。对/Share/的任何操作，都相当于对sdb1里文件的操作。
所以Linux下，mount挂载的作用，就是将一个设备（通常是存储设备）挂接到一个已存在的目录上。访问这个目录就是访问该存储设备。
插入CD，系统其实自动执行了 mount /dev/cdrom /media/cdrom。所以可以直接在/media/cdrom中对CD中的内容进行管理
纠正一个误区，并不是根目录下任何一个目录都可以作为挂载点，由于挂载操作会使得原有目录中文件被隐藏，因此根目录以及系统原有目录都不要作为挂载点，会造成系统异常甚至崩溃，挂载点最好是新建的空目录
语法：docker run –dit –v /src:/dst centos:latest bash
例1：把物理机上的/var/ww/html映射到docker实例的/var/www/html
能不能对同一个docker容器建立两个以上的互动窗口 如何打开多个终端进入Docker容器
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