singularity 安装
安装依赖
在ubuntu上
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config
在centos上
sudo yum update -y && \
sudo yum groupinstall -y 'Development Tools' && \
sudo yum install -y \
openssl-devel \
libuuid-devel \
libseccomp-devel \
wget \
squashfs-tools
安装Go
Singularity 3.0以上版本主要用Go编写，因此需要安装Go来从源代码编译
首先，访问Go下载页面，并选择相应的Go版本（版本选择1.11.1以上）
export VERSION=1.11 OS=linux ARCH=amd64
cd /tmp
wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz
将Go安装包解压缩到/usr/local
sudo tar -C /usr/local -xzf go$VERSION.$OS-$ARCH.tar.gz
最后设置Go环境变量
echo 'export GOPATH=${HOME}/go' >> ~/.bashrc
echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc
source ~/.bashrc
下载singularity
先创建Go的编译目录
mkdir -p $GOPATH/src/github.com/sylabs
cd $GOPATH/src/github.com/sylabs
git clone https://github.com/sylabs/singularity.git
安装Go依赖项
使用Deo管理依赖关系，用go get安装
go get -u -v github.com/golang/dep/cmd/dep
编译安装
必须以root身份安装
cd $GOPATH/src/github.com/sylabs/singularity
./mconfig
make -C builddir
sudo make -C builddir install
验证安装是否成功
singularity help
Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)
Usage:
singularity [global options...]
Description:
Singularity containers provide an application virtualization layer enabling
mobility of compute via both application and environment portability. With
Singularity one is capable of building a root file system that runs on any
other Linux system where Singularity is installed.
Options:
-d, --debug print debugging information (highest verbosity)
-h, --help help for singularity
--nocolor print without color output (default False)
-q, --quiet suppress normal output
-s, --silent only print errors
-v, --verbose print additional information
Available Commands:
apps List available apps within a container
build Build a Singularity image
cache Manage the local cache
capability Manage Linux capabilities for an image
exec Run a command within a container
help Help about any command
inspect Show metadata for an image
instance Manage containers running as services
key Manage OpenPGP keys
oci Manage OCI containers
plugin Manage singularity plugins
pull Pull an image from a URI
push Upload image to the provided library (default is "https://library.sylabs.io")
remote Manage Sylabs Cloud endpoints
run Run the user-defined default command within a container
run-help Show the help for an image
search Search a Library for images
shell Run a shell within a container
sign Attach a cryptographic signature to an image
test Run the user-defined tests within a container
verify Verify cryptographic signatures attached to an image
version Show the version for Singularity
Examples:
$ singularity help <command> [<subcommand>]
$ singularity help build
$ singularity help instance start
For additional help or support, please visit https://www.sylabs.io/docs/
删除旧版本
sudo rm -rf /usr/local/libexec/singularity
sudo rm -rf /usr/local/etc/singularity
sudo rm -rf /usr/local/include/singularity
sudo rm -rf /usr/local/lib/singularity
sudo rm -rf /usr/local/var/lib/singularity/
sudo rm /usr/local/bin/singularity
sudo rm /usr/local/bin/run-singularity
sudo rm /usr/local/etc/bash_completion.d/singularity
sudo rm /usr/local/man/man1/singularity.1
singularity 使用
创建镜像/沙盒
可以通过build命令直接创建一个镜像
singularity build centos.img docker://centos:latest
build命令可以直接创建镜像或者singularity默认的sif容器文件，还可以是simg
也可以通过build命令直接创建一个沙盒
singularity build --sandbox centos/ docker://centos:latest
build命令加上 --sandbox可以直接创建沙盒，沙盒可以直观的看到容器内的目录，直观方便
以上实际上是将Container Library或者Docker Hub上的镜像download下来用作容器。
以library:// 开头的URI，表示是从Container Library构建
以docker:// 开头的URI，表示是从Docker Hub构建
以shub:// 开头的URI，表示是从Singularity Hub构建
同样可以用singularity自定义文件(例如Singularity 或者singularity.def)来建立容器
Bootstrap: docker
From: ubuntu:16.04
%post
apt-get -y update
apt-get -y install fortune cowsay lolcat
%environment
export LC_ALL=C
export PATH=/usr/games:$PATH
%runscript
fortune | cowsay | lolcat
sudo singularity build lolcow.sif lolcow.def
与容器进行交互
通过shell —writable来对容器进行操作
singularity shell --writable centos/ #此时是对沙盒进行操作
Singularity centos:~/centos>
安装软件环境
接下来以安装vasp为例
安装intel编译器
下载好tgz包和有效的license文件后，进入容器
tar -zxvf parallel_studio_xe_2017_update5.tgz
cd parallel_studio_xe_2017_update5
./install.sh #卸载操作也是执行这个文件
安装过程有7步，其中第三步骤选择
I want to activate my product using a serial number
cat 查看license里的序列号后输入即可
intel编译器会默认安装在/opt/intel目录下。安装完成后需要添加PATH到环境变量中。 vim ～/.bashrc ，修改单个用户。vim /etc/profile，修改全局。插入如下代码
source /opt/intel/compilers_and_libraries_2017.5.239/linux/bin/compilervars.sh intel64
source /opt/intel/compilers_and_libraries_2017.5.239/linux/bin/iccvars.sh intel64
source /opt/intel/compilers_and_libraries_2017.5.239/linux/bin/ifortvars.sh intel64
source /opt/intel/compilers_and_libraries_2017.5.239/linux/mkl/bin/mklvars.sh intel64
source /opt/intel/impi/2017.4.239/bin64/mpivars.sh
以上操作都是在singularity沙盒目录中执行的操作，处于容器环境中，是可以同时看见容器中的文件和本机系统的文件的。例如此时名为centos的沙盒目录的位置是本机的
/root目录下，那么容器里的/root目录实际路径是 ·/root/centos/root也就是说，在名为 centos 容器中，Intel编译器默认安装的真实路径实际上是
/root/centos/opt/intel但是由于在容器中是完全隔离的，因此不需要考虑这个真实路径，在配置环境变量的时候依然是opt/intel
修改环境变量完成后
source ~/.bashrc #或者 source /etc/profile
使用接下来的命令查看环境变量是否添加成功
which icc ifort icpc mpiifort
如果此时退出容器，那么下次进入容器后需要重新
source /etc/profile否则会报
which: no icc in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
which: no ifort in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
which: no icpc in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
which: no mpiifort in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
安装VASP
解压VASP压缩包, 进入文件夹复制makefile.include
cd vasp.5.4.4
cp arch/makefile.include.linux_intel makefile.include
修改makefile.include中的OBJECTS
OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o /opt/intel/compilers_and_libraries_2017.5.239/linux/mkl/interfaces/fftw3xf/libfftw3xf_intel.a
安装
make all 2>&1 | tee make.log
添加环境变量，vim ~/.bashrc 或者 vim /etc/profile
PATH=/root/vasp.5.4.1/build/std:$PATH
source ~/.bashrc #或者 source /etc/profile
将沙盒打包成镜像或者sif文件
在对容器环境编写好之后，需要将其打包成sif文件或者是镜像的话，同样使用build命令来建立相应的文件
singularity build centos.img centos/
同样可以用 singularity shell --writable centos.img 进入容器
