软件的安装¶

安装 Docker¶

To build the Docker container, Docker need to be installed:

please refer to Docker Installation Homepage

quick installation

$ sudo apt-get update
$ sudo apt-get install apt-transport-https ca-certificates curl gnupg-agent
$ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
$ sudo apt-key fingerprint 0EBFCD88
$ sudo add-apt-repository    "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
    $(lsb_release -cs) \
    stable"
$ sudo apt-get update
$ sudo apt-get install docker-ce docker-ce-cli containerd.io

Note

if you have following error message:

$ docker images
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.40/images/json: dial unix /var/run/docker.sock: connect: permission denied

please do:

$ sudo groupadd docker
$ sudo usermod -aG docker ${USER}
$ You would need to loog out and log back (looks like reboot needed) in so that your group membership is re-evaluated

Note

if you get following error message:

$ docker container ls -a
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?

please do:

$ sudo service docker start

check if the docker installation is good

$ docker version
Client: Docker Engine - Community
 Version:           19.03.3
 API version:       1.40
 Go version:        go1.12.10
 Git commit:        a872fc2f86
 Built:             Tue Oct  8 00:58:10 2019
 OS/Arch:           linux/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          19.03.3
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.12.10
  Git commit:       a872fc2f86
  Built:            Tue Oct  8 00:56:46 2019
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.2.10
  GitCommit:        b34a5c8af56e510852c35414db4c1f4fa6172339
 runc:
  Version:          1.0.0-rc8+dev
  GitCommit:        3e425f80a8c931f88e6d94a8c831b9d5aa481657
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683

安装 Docker Compose¶

To build the Docker Compose:

please refer to Docker compose Homepage

quick installation (Please check the latest stable version number)

$ sudo curl -L "https://github.com/docker/compose/releases/download/1.25.4/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
$ sudo chmod +x /usr/local/bin/docker-compose
$ docker-compose --version
docker-compose version 1.24.1, build 4667896b

安装 Charliecloud¶

The whole system requires to be run with Charliecloud. To install Charliecloud:

please refer to Charliecloud Homepage
quick installation
Use Spack to install as a example ( Please refer to Spack package management )
$ spack install pkg-config # This is bug fix $ spack install charliecloud + builder
check if charliecloud installation is OK
$ ch-run --version 0.12~pre+59b5bfd

安装 Spack¶

了解详情，请点击这里

$ git clone https://github.com/spack/spack.git
# Add spack/bin to "PATH"
$ export PATH=/path/of/spack/bin:$PATH
$ . /path/of/spack/share/spack/setup-env.sh
$ spack --version
0.14.2-1486-b80d5e7

制作 Spack 镜像¶

如果本机（工作机器）无法连接互联网，需要找一台可以连入互联网的计算机，同样安装 Spack ，该台计算机将用于制作 Spack 的镜像软件仓库。

Note

两台计算机必须安装同样版本的 Spack！

在可以连入互联网的计算机上也安装好了 Spack 之后，开始在该计算机上下载安装 METplus 所需要的软件。

建立一个 specs.txt 文件，列出所需软件：

gcc@9.2.0
openmpi@3.1.6
netcdf-fortran@4.5.2%gcc@9.2.0 ^netcdf-c@4.7.3+parallel-netcdf ^hdf5@1.10.6+fortran
py-matplotlib@3.2.2
py-cartopy@0.17.0

制作需要软件的镜像

$ spack mirror create -D -f specs.txt

制作完成后，所需软件包下载到如下目录：

$ home/xinzhang> tree -L 1 /glade/u/home/xinzhang/spack/var/spack/cache
/glade/u/home/xinzhang/spack/var/spack/cache
├── autoconf
├── automake
├── gdbm
├── hdf5
├── hwloc
├── libiconv
├── libpciaccess
├── libsigsegv
├── libtool
├── libxml2
├── m4
├── ncurses
├── netcdf-c
├── netcdf-fortran
├── numactl
├── openmpi
├── parallel-netcdf
├── perl
├── pkgconf
├── readline
├── _source-cache
├── util-macros
├── xz
└── zlib

24 directories, 0 files

打包镜像目录，上传到需要安装软件的工作机器：

$ cd /glade/u/home/xinzhang/spack/var/spack
$ tar -zcvf spack_mirror.tgz cache

在工作机器上，设置 Spack 镜像目录

在工作机器上，将 spack_mirror.tgz 文件解压到一个目录，如：

$ mkdir -p /home/wrf/spack_mirror
$ cd /home/wrf/spack_mirror
$ tar xzvf ~/spack_mirror.tgz
$ rm ~/spack_mirror.tgz

设置 Spack 镜像目录

$ spack mirror add local_filesytem file:///home/wrf/spack_mirror/cache
$ spack mirror list
local_filesyetm    file:///home/wrf/home/wrf/spack_mirror/cache

安装 METplus¶

详细安装细节请参照 METplus文档

以3.0.2版本为例:

$ cd METplus-3.0.2
# 下载稳定版本的MET（v9.0.2) 到 MET 目录
$ cd build_components

编辑 env_vars.bash 如下

export TEST_BASE=/home/wrf/METplus-3.0.2/build_components
export COMPILER=gnu
export MET_SUBDIR=${TEST_BASE}
export MET_TARBALL=met.tar.gz
export MET_PYTHON_CC=-I/usr/include/python3.6m
export MET_PYTHON_LD="-L/usr/lib64 -lpython3.6m -lpthread -ldl -lutil -lm -Xlinker -export-dynamic"
#### Python version on your system
export PYTHON_MODULE=python_3.6.8
### Local system ${PYTHON_MODULE} install location for python libraries
export MET_PYTHON=/usr/local/python3.6
export PYTHON_MODULE_USE=1
export USE_MODULES=FALSE
export SET_D64BIT=TRUE

编辑 build_MET.sh 如下

#!/bin/bash
rm -fr met tar_files compile_MET_all.sh
### Grab the compenents source code from git using manage_externals
### Externals.cfg specifies what to checkout and where to put it
#../manage_externals/checkout_externals

## Grab the compile script
#wget https://dtcenter.org/sites/default/files/community-code/met/compile_scripts/compile_MET_all.sh.tgz
tar -xzvf compile_MET_all.sh.tgz

## Grab the external library tar file
#wget https://dtcenter.org/sites/default/files/community-code/met/compile_scripts/tar_files.tgz

## Stuff the contents into tar_files directory
tar -xzvf tar_files.tgz

## link the git hub source code directory to the current directory - serious hack for now
ln -s ../MET/met met

## Create a tarball which is what the compile script wants right now - hopefully change this later
tar -cvzhf tar_files/met.tar.gz met

### Source environment variables and run the compile_all script
source env_vars.bash
cd met
./bootstrap
cd ../
bash compile_MET_all.sh

手动下载

wget https://dtcenter.org/sites/default/files/community-code/met/compile_scripts/compile_MET_all.sh.tgz
wget https://dtcenter.org/sites/default/files/community-code/met/compile_scripts/tar_files.tgz

# 存入 build_components 目录下

Hack compile_MET_all.sh

删除替换 _64BIT_ 的 sed 语句，即：在编译 g2clib 中使用 -D__64BIT__ 选项

编译

$ ./build_MET.sh
$ ls -al bin
total 208648
drwxrwxr-x. 2 wrf wrf    4096 Jun 21 12:00 .
drwxrwxr-x. 7 wrf wrf    4096 Jun 21 12:35 ..
-rwxr-xr-x. 1 wrf wrf 7410728 Jun 21 12:00 ascii2nc
-rwxr-xr-x. 1 wrf wrf 8496616 Jun 21 12:00 ensemble_stat
-rwxr-xr-x. 1 wrf wrf 6106912 Jun 21 12:00 gen_vx_mask
-rwxr-xr-x. 1 wrf wrf  276400 Jun 21 12:00 gis_dump_dbf
-rwxr-xr-x. 1 wrf wrf  357208 Jun 21 12:00 gis_dump_shp
-rwxr-xr-x. 1 wrf wrf  293096 Jun 21 12:00 gis_dump_shx
-rwxr-xr-x. 1 wrf wrf 6357248 Jun 21 12:00 grid_diag
-rwxr-xr-x. 1 wrf wrf 8308912 Jun 21 12:00 grid_stat
-rwxr-xr-x. 1 wrf wrf 4920136 Jun 21 12:00 gsid2mpr
-rwxr-xr-x. 1 wrf wrf 4988592 Jun 21 12:00 gsidens2orank
-rwxr-xr-x. 1 wrf wrf 1368040 Jun 21 12:00 lidar2nc
-rwxr-xr-x. 1 wrf wrf 6909808 Jun 21 12:00 madis2nc
-rwxr-xr-x. 1 wrf wrf 9338144 Jun 21 12:00 mode
-rwxr-xr-x. 1 wrf wrf 3958560 Jun 21 12:00 mode_analysis
-rwxr-xr-x. 1 wrf wrf 6923192 Jun 21 12:00 modis_regrid
-rwxr-xr-x. 1 wrf wrf 7454832 Jun 21 12:00 mtd
-rwxr-xr-x. 1 wrf wrf 7426312 Jun 21 12:00 pb2nc
-rwxr-xr-x. 1 wrf wrf 5948184 Jun 21 12:00 pcp_combine
-rwxr-xr-x. 1 wrf wrf 6080464 Jun 21 12:00 plot_data_plane
-rwxr-xr-x. 1 wrf wrf 5770328 Jun 21 12:00 plot_point_obs
-rwxr-xr-x. 1 wrf wrf 6257480 Jun 21 12:00 point2grid
-rwxr-xr-x. 1 wrf wrf 8347488 Jun 21 12:00 point_stat
-rwxr-xr-x. 1 wrf wrf 6112088 Jun 21 12:00 regrid_data_plane
-rwxr-xr-x. 1 wrf wrf 6374800 Jun 21 12:00 rmw_analysis
-rwxr-xr-x. 1 wrf wrf 7936008 Jun 21 12:00 series_analysis
-rwxr-xr-x. 1 wrf wrf 5849264 Jun 21 12:00 shift_data_plane
-rwxr-xr-x. 1 wrf wrf 9326944 Jun 21 12:00 stat_analysis
-rwxr-xr-x. 1 wrf wrf 1794168 Jun 21 12:00 tc_dland
-rwxr-xr-x. 1 wrf wrf 8351096 Jun 21 12:00 tc_gen
-rwxr-xr-x. 1 wrf wrf 7153184 Jun 21 12:00 tc_pairs
-rwxr-xr-x. 1 wrf wrf 6650656 Jun 21 12:00 tc_rmw
-rwxr-xr-x. 1 wrf wrf 9035256 Jun 21 12:00 tc_stat
-rwxr-xr-x. 1 wrf wrf 8573648 Jun 21 12:00 wavelet_stat
-rwxr-xr-x. 1 wrf wrf 6598400 Jun 21 12:00 wwmca_plot
-rwxr-xr-x. 1 wrf wrf 6519248 Jun 21 12:00 wwmca_regrid

安装 METviewer¶

制作 METviewer Docker 镜像
在一台安装了Docker和又互联网连接的机器上，下载 METviewer Docker 镜像

制作 METviewer 的 Docker 镜像，存为 tar 文件
$ cd container-dtc-metviewer/METviewer $ docker image build -t metviewer . # 制作完成 $ docker image save metviewer -o metviewer.docker.image.tar

将该镜像文件上传到工作机器上（同时也需要准备mysql的镜像文件），然后加载该镜像

$ docker image load -i metviewer.docker.image.tar
0683de282177: Loading layer [==================================================>]  244.9MB/244.9MB
5714bb8688ee: Loading layer [==================================================>]    173MB/173MB
ec559b28281c: Loading layer [==================================================>]   1.65GB/1.65GB
3335b9f0667b: Loading layer [==================================================>]   2.56kB/2.56kB
1fa73ec3c2f2: Loading layer [==================================================>]  27.03MB/27.03MB
8872ec41f650: Loading layer [==================================================>]  13.93MB/13.93MB
989c6a32b856: Loading layer [==================================================>]  44.75MB/44.75MB
16fa149a25ac: Loading layer [==================================================>]  2.048kB/2.048kB
Loaded image: metviewer:latest

$ docker image load -i mysql5.7.docker.image.tar
13cb14c2acd3: Loading layer [==================================================>]  72.49MB/72.49MB
365386a39e0e: Loading layer [==================================================>]  338.4kB/338.4kB
c3f46b20a0d3: Loading layer [==================================================>]  9.539MB/9.539MB
66c45123fd43: Loading layer [==================================================>]    4.2MB/4.2MB
61cbb8ea6481: Loading layer [==================================================>]  1.536kB/1.536kB
44853bb67274: Loading layer [==================================================>]  53.75MB/53.75MB
3a2464d8e0c0: Loading layer [==================================================>]  6.656kB/6.656kB
91ae264962fb: Loading layer [==================================================>]  3.584kB/3.584kB
8f0182ef7c8c: Loading layer [==================================================>]  313.1MB/313.1MB
ac7657905788: Loading layer [==================================================>]  16.38kB/16.38kB
c90a34afcab0: Loading layer [==================================================>]  1.536kB/1.536kB
Loaded image: mysql:5.7

$ docker image ls -a
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
metviewer           latest              85b75697b9ee        9 days ago          2.11GB
mysql               5.7                 9cfcce23593a        11 days ago         448MB

在工作机器上，下载 container-dtc-nwp 和 METviewer Docker 镜像

新建工作目录：

$ cd container-dtc-metviewer
$ mkdir -p output
$ mkdir -p mysql

编辑 docker-compose 的配置文件

$ cd container-dtc-nwp/components/metviewer/
$ vi docker-compose.yaml

修改路径（请注意高亮处）：

db:
    image: mysql:5.7
    container_name: mysql_mv
    ports:
        - "6603:3306"
    volumes:
        - /home/wrf/container-dtc-metviewer/output/metviewer/mysql:/var/lib/mysql

    environment:
        MYSQL_ROOT_PASSWORD: mvuser
    tty: true
#
metviewer:
    image: metviewer
    container_name: metviewer
    ports:
    - "8080:8080"
    volumes:
      - /home/wrf/container-dtc-nwp/components/scripts:/scripts
      - /home/wrf/METout:/data
      - /home/wrf/container-dtc-metviewer/output/metviewer/output/xml:/opt/tomcat/webapps/metviewer_output/xml
      - /home/wrf/container-dtc-metviewer/output/metviewer/output/plots:/opt/tomcat/webapps/metviewer_output/plots
      - /home/wrf/container-dtc-metviewer/output/metviewer/output/data:/opt/tomcat/webapps/metviewer_output/data
      - /home/wrf/container-dtc-metviewer/output/metviewer/output/scripts:/opt/tomcat/webapps/metviewer_output/scripts
    links:
      - db:mysql_mv
    tty: true

启动 METviewer
$ cd container-dtc-nwp/components/metviewer/ $ docker-compose up -d Creating mysql_mv ... done Creating metviewer ... done
打开网页浏览器，输入网址：http://localhost:8080/metviewer/metviewer1.jsp 或 http://10.86.41.176:8080/metviewer/metviewer1.jsp

Note

在线图形显示可能有问题，请使用右上角的图形保持功能

软件的安装¶

安装 Docker¶

安装 Docker Compose¶

安装 Charliecloud¶

安装 Spack¶

制作 Spack 镜像¶

相关软件安装¶

安装 METplus¶

安装 METviewer¶