Singularity
Singularity用于GUI应用的容器发布是非常方便的，另外一个场景是拥有HPC MPI并行计算求解器发布。
1 安装
参考: https://sylabs.io/guides/3.8/admin-guide/installation.html
1.1 Ubuntu /CentOS环境依赖
=====Ubuntu 系统=====
$ sudo apt-get update && sudo apt-get install -y \
build-essential \
uuid-dev \
libgpgme-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup-bin
=====CentOS系统=====
$ sudo yum update -y && \
sudo yum groupinstall -y 'Development Tools' && \
sudo yum install -y \
openssl-devel \
libuuid-devel \
libseccomp-devel \
wget \
squashfs-tools \
cryptsetup
1.2 安装golang环境
参考：https://golang.org/doc/install
Step0:下载golang
$ wget https://files.michaelapp.com/install/go1.16.5.linux-amd64.tar.gz
Step1:删除旧版本，解压到指定目录.
$ rm -rf /usr/local/go && tar -C /usr/local -xzf go1.16.5.linux-amd64.tar.gz
Step2:在环境命令文件（/etc/profile）中最后一行添加下面这两行:
export PATH=$PATH:/usr/local/go/bin
export GOPROXY=https://goproxy.cn,direct
Step3:检查是否生效
$ go version
go version go1.16.5 linux/amd64
1.3 下载和编译singularity
源码安装
$ mkdir install
$ cd install
$ wget https://files.michaelapp.com/install/singularity-ce-3.8.0.tar.gz
$ tar zxvf singularity-ce-3.8.0.tar.gz
$ cd singularity-ce-3.8.0
$ ./mconfig #默认安装在/usr/local,如果为其他路径 ./mconfig --prefix=/opt/singularity
======================没有这一步，下面的步骤会很慢=============
$ vim .builddir/Makefile,修改下面这行
将
GOPROXY := https://proxy.golang.org
改为
GOPROXY := https://goproxy.cn,direct
=========================================================
$ make -C ./builddir
$ sudo make -C ./builddir install
安装完成，验证一下
$ singularity version
3.8.0
2 Singularity简单使用
2.1 拉取预编译镜像
1）拉取ubuntu镜像
$ singularity pull docker://ubuntu:20.04
2）拉取centos镜像
$ singularity pull docker://centos:7
2.2 运行镜像
交互式运行
$ sudo singularity run ubuntu_20.04.sif
执行命令并退出
$ sudo singularity run ubuntu_20.04.sif pwd
$ sudo singularity run ubuntu_20.04.sif ls /bin
2.3 挂载外部目录
$ sudo singularity run -B /opt:/opt ubuntu_20.04.sif
2.4 其他命令
比如 sudo singularity instance start xxx / sudo singularity instance stop xxxx
比如 sudo singularity shell 等
3 定制镜像功能
Singularity 从原始镜像，添加自己的内容，然后打包成自己的镜像并运行
3.1 定制CentOS镜像，并运行GUI 程序
思路：通过sandbox的方式制作可运行图像程序的镜像。从CentOS原始镜像开始，通过安装gnome桌面支持GUI.
(1) 以root身份创建一个centos的sandbox
$ sudo singularity build --sandbox centos_gui/ centos_7.sif
(2) 以root用户可以写的方式运行sandbox容器，并且安装桌面环境
$ sudo singularity shell --writable centos_gui/
Singularity> yum groupinstall -y "GNOME Desktop"
运行完成后，CTRL+C退出容器。
(3) 打包带GUI的容器centos_gui.sif
$ sudo singularity build centos_gui.sif centos_gui/
(4) 测试1：运行 gedit程序
$ singularity run centos_gui.sif gedit
即可看到gedit gui应用运行起来了，比docker运行gui要简单容易的多。
(5) 测试2：运行 firefox程序
$ singularity run centos_gui.sif firefox
备注：如果运行gui出现错误."cannot open display: :0". 先执行xhost +，然后再执行相应的命令即可运行GUI应用
4 通过镜像定义文件（.def）创建Redis镜像
备注：类似Docker里的dockerfile, singularity也支持通过文件定义流程，创建镜像
4.1 Redis 镜像文件定义，redis.def配置如下
Bootstrap:docker
From: ubuntu:20.04
%help
Singularity container running Redis 5.0.0 for Ubuntu20.04
%post
#Update and install dependencies
apt-get update
apt-get install -y wget build-essential
#Get redis and install it
wget http://download.redis.io/releases/redis-5.0.0.tar.gz
tar xzf redis-5.0.0.tar.gz
cd redis-5.0.0
make
%environment
export PAHT=$PATH:/opt/bin
%startscript
#Start the server daemon with this command
/redis-5.0.0/src/redis-server
%runscript
#Start the Redis client with this command
/redis-5.0.0/src/redis-cli
其中，%startscript 指容器启动时的运行命令，启动redis服务
%runscript 指容器执行时运行的命令，run 命令或者exec命令
$ sudo singularity build redis.sif redis.def
4.2 启动 redis server,并命名为redis001
$ singularity instance start redis.sif redis001
4.3 查看redis的实例
$ singularity instance list
如何要连入镜像，singularity shell instance://redis001
4.4 运行redis client
$ singularity run redis.sif
4.5 停止实例
$ singularity instance stop redis001
5、通过镜像定义文件（.def）创建QT应用镜像
详细见代码仓库: https://github.com/panyingyun/qtclientsingularity
5.1 创建qtclient.def文件
其目的是用于创建singularity镜像
# qtclient.def
BootStrap: docker
From: ubuntu:20.04
%labels
Author panyingyun
Version qtclient 0.1
# run、entrypoint 执行的命令
%runscript
exec /usr/local/bin/qtclient
# 从宿主机实现文件拷贝到容器镜像目标路径中
%files
./qtclient /opt
# post之后执行的环境变量与操作
%environment
export LANG="zh_CN.UTF-8"
export LANGUAGE="zh_CN:zh:en_US:en"
# 安装依赖
%post
echo "Basic Configuration of Ubuntu 20.04"
# Replace Official Repository with 163 Repository (in China needed)
sed -i 's/archive.ubuntu.com/mirrors.huaweicloud.com/g' /etc/apt/sources.list
sed -i 's/security.ubuntu.com/mirrors.huaweicloud.com/g' /etc/apt/sources.list
apt update
export DEBIAN_FRONTEND=noninteractive
# Install Base System Utilities
apt install -y vim curl wget git net-tools build-essential cmake tzdata
# Install X11 and OpenGL Related
apt install -y libgl1-mesa-dev mesa-common-dev libx11-dev libxt-dev
# Install Qt Library
apt install -y qt5-default qtcreator libqt5x11extras5-dev libqt5charts5-dev
# Installl zh font
echo "Asia/Shanghai" > /etc/timezone
dpkg-reconfigure -f noninteractive tzdata
apt install -y language-pack-zh-han* language-pack-gnome-zh-han*
apt install -y $(check-language-support)
locale-gen
export LANG="zh_CN.UTF-8"
export LANGUAGE="zh_CN:zh:en_US:en"
echo "Install qtclient"
cd /opt/qtclient && sh auto_build_linux.sh && cp build/qtclient /usr/local/bin/
chmod 755 /usr/local/bin/qtclient
echo "Clean files"
rm -rf /opt/qtclient
echo "qtclient install successful."
%help
singularity run-help qtclient.sif
use-
singularity exec qtclient.sif [command] [params]
example-
singularity exec qtclient.sif
5.2 打包singularity镜像
$ sudo singularity build qtclient.sif qtclient.def
5.3 运行镜像，可看到GUI
$ singularity run qtclient.sif
参考文献
1. 官方用户手册
- https://sylabs.io/guides/3.8/user-guide/build_a_container.html
- https://sylabs.io/guides/3.8/user-guide/definition_files.html
2. 官方用户手册-MPI支持
- https://sylabs.io/guides/3.8/user-guide/mpi.html
3. singularity容器中运行GUI程序
- https://blog.csdn.net/kongxx/article/details/98101081
4. singularity通过def打包的案例
- https://github.com/sylabs/examples
5. redis def打包镜像案例
- https://blog.csdn.net/kongxx/article/details/100550919
6. singularity容器优缺点
- http://blog.zxh.site/2018/05/15/Singularity/