在CentOS上安装Singularity高性能容器
<h1 id="什么是singularity容器">什么是singularity容器</h1><p>Singularity是劳伦斯伯克利国家实验室专门为大规模、跨节点HPC和DL工作负载而开发的容器化技术。具备轻量级、快速部署、方便迁移等诸多优势，且支持从Docker镜像格式转换为Singularity镜像格式。除了兼容docker的镜像之外，singularity还有一个不太明显的优势：可以通过非root帐号来拉起容器，这样对于某些安全性要求比较高的场景来说还是有用途的。</p>
<h1 id="环境准备">环境准备</h1>
<p>目前singularity支持了redhat系列Linux发行版的二进制安装，这里我们使用的基础系统是CentOS：</p>
<pre><code class="language-bash"># cat /etc/redhat-release
CentOS Linux release 8.3.2011
</code></pre>
<h1 id="安装配置epel扩展源">安装配置epel扩展源</h1>
<p>首先我们需要更新所有的系统软件：</p>
<pre><code class="language-bash"># yum update -y
CentOS Linux 8 - AppStream 1.1 MB/s | 6.3 MB 00:05
CentOS Linux 8 - BaseOS 1.7 MB/s | 2.3 MB 00:01
Dependencies resolved.
Nothing to do.
Complete!
</code></pre>
<p>安装epel扩展源：</p>
<pre><code class="language-bash"># yum install -y epel-release
Last metadata expiration check: 0:00:22 ago on Wed 13 Jan 2021 09:24:36 AM UTC.
Dependencies resolved.
============================================================================================================================================================================================================================================
Package Architecture Version Repository Size
============================================================================================================================================================================================================================================
Installing:
epel-release noarch 8-8.el8 extras 23 k
Transaction Summary
============================================================================================================================================================================================================================================
Install1 Package
Total download size: 23 k
Installed size: 32 k
Downloading Packages:
epel-release-8-8.el8.noarch.rpm 140 kB/s |23 kB 00:00
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 34 kB/s |23 kB 00:00
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : epel-release-8-8.el8.noarch 1/1
Running scriptlet: epel-release-8-8.el8.noarch 1/1
Verifying : epel-release-8-8.el8.noarch 1/1
Installed:
epel-release-8-8.el8.noarch
Complete!
</code></pre>
<p>安装好epel源之后，需要再次更新系统软件：</p>
<pre><code class="language-bash"># yum update -y
Extra Packages for Enterprise Linux Modular 8 - x86_64 9.2 kB/s | 527 kB 00:57
Extra Packages for Enterprise Linux 8 - x86_64 10 kB/s | 8.8 MB 14:46
Last metadata expiration check: 0:00:19 ago on Wed 13 Jan 2021 09:26:09 AM UTC.
Dependencies resolved.
============================================================================================================================================================================================================================================
Package Architecture Version Repository Size
============================================================================================================================================================================================================================================
Upgrading:
epel-release noarch 8-10.el8 epel 22 k
Transaction Summary
============================================================================================================================================================================================================================================
Upgrade1 Package
Total download size: 22 k
Downloading Packages:
epel-release-8-10.el8.noarch.rpm 7.8 kB/s |22 kB 00:02
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 6.1 kB/s |22 kB 00:03
warning: /var/cache/dnf/epel-05da96c052a128d8/packages/epel-release-8-10.el8.noarch.rpm: Header V4 RSA/SHA256 Signature, key ID 2f86d6a1: NOKEY
Extra Packages for Enterprise Linux 8 - x86_64 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x2F86D6A1:
Userid : "Fedora EPEL (8) <epel@fedoraproject.org>"
Fingerprint: 94E2 79EB 8D8F 25B2 1810 ADF1 21EA 45AB 2F86 D6A1
From : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-8
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Running scriptlet: epel-release-8-10.el8.noarch 1/1
Upgrading : epel-release-8-10.el8.noarch 1/2
Cleanup : epel-release-8-8.el8.noarch 2/2
Running scriptlet: epel-release-8-8.el8.noarch 2/2
Verifying : epel-release-8-10.el8.noarch 1/2
Verifying : epel-release-8-8.el8.noarch 2/2
Upgraded:
epel-release-8-10.el8.noarch
Complete!
</code></pre>
<h1 id="配置epel国内镜像源">配置epel国内镜像源</h1>
<p>使用默认的源地址去下载软件的话，有可能会导致下载速度缓慢甚至下载失败。这里推荐使用华为的国内镜像源地址，配置方法如下：</p>
<pre><code class="language-bash"># sed -i "s/#baseurl/baseurl/g" /etc/yum.repos.d/epel.repo
# sed -i "s/metalink/#metalink/g" /etc/yum.repos.d/epel.repo
# sed -i "s@https\?://download.fedoraproject.org/pub@https://mirrors.huaweicloud.com@g" /etc/yum.repos.d/epel.repo
</code></pre>
<p>再次更新所有源：</p>
<pre><code class="language-bash"># yum update -y
Extra Packages for Enterprise Linux 8 - x86_64 5.9 MB/s | 8.8 MB 00:01
Last metadata expiration check: 0:00:02 ago on Wed 13 Jan 2021 09:55:51 AM UTC.
Dependencies resolved.
Nothing to do.
Complete!
</code></pre>
<h1 id="使用yum安装singularity">使用yum安装singularity</h1>
<p>到这里为止，基本的环境配置就完成了，可以正式开始singularity的安装：</p>
<pre><code class="language-bash"># yum install -y singularity
Last metadata expiration check: 0:00:59 ago on Wed 13 Jan 2021 09:55:51 AM UTC.
Dependencies resolved.
============================================================================================================================================================================================================================================
Package Architecture Version Repository Size
============================================================================================================================================================================================================================================
Installing:
singularity x86_64 3.7.0-1.el8 epel 42 M
Transaction Summary
============================================================================================================================================================================================================================================
Install1 Package
Total download size: 42 M
Installed size: 138 M
Downloading Packages:
singularity-3.7.0-1.el8.x86_64.rpm 3.4 MB/s |42 MB 00:12
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 3.4 MB/s |42 MB 00:12
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : singularity-3.7.0-1.el8.x86_64 1/1
Running scriptlet: singularity-3.7.0-1.el8.x86_64 1/1
Verifying : singularity-3.7.0-1.el8.x86_64 1/1
Installed:
singularity-3.7.0-1.el8.x86_64
Complete!
</code></pre>
<p>可以通过如下方式来验证singularity是否安装成功，并且查看版本号：</p>
<pre><code class="language-bash"># singularity --version
singularity version 3.7.0-1.el8
</code></pre>
<h1 id="singualrity的基本使用方法">singualrity的基本使用方法</h1>
<p>首先我们可以通过软件自身的help来查看软件支持的功能：</p>
<pre><code class="language-bash"># singularity --help
Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)
Usage:
singularity
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:
-c, --config string specify a configuration file (for root or
unprivileged installation only) (default
"/etc/singularity/singularity.conf")
-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
--version version for singularity
Available Commands:
build Build a Singularity image
cache Manage the local cache
capabilityManage Linux capabilities for users and groups
config Manage various singularity configuration (root user only)
delete Deletes requested image from the library
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 URI
remote Manage singularity remote endpoints, keyservers and OCI/Docker registry credentials
run Run the user-defined default command within a container
run-help Show the user-defined help for an image
search Search a Container Library for images
shell Run a shell within a container
sif siftool is a program for Singularity Image Format (SIF) file manipulation
sign Attach digital signature(s) 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/
</code></pre>
<p>这里可以看到跟docker的接口还是有较大区别的，但是容器的本质还是基于namespace和cgroup的隔离方案，这点上都是大同小异。由于本文的主要目的在于介绍singularity的安装，这里不详细展开singularity的使用介绍，仅简单介绍一个使用的案例：适用singularity搭建一个ubuntu的容器环境。</p>
<ul>
<li>首先我们创建一个容器沙箱，这里用的基础镜像还是从dockerhub获取的ubuntu基础镜像</li>
</ul>
<pre><code class="language-bash"># singularity build --sandbox ubuntu docker://ubuntu
INFO: Starting build...
Getting image source signatures
Copying blob da7391352a9b done
Copying blob 14428a6d4bcd skipped: already exists
Copying blob 2c2d948710f2 [--------------------------------------] 0.0b / 0.0b
Copying config aa23411143 done
Writing manifest to image destination
Storing signatures
2021/01/14 01:20:39info unpack layer: sha256:da7391352a9bb76b292a568c066aa4c3cbae8d494e6a3c68e3c596d34f7c75f8
2021/01/14 01:20:39info unpack layer: sha256:14428a6d4bcdba49a64127900a0691fb00a3f329aced25eb77e3b65646638f8d
2021/01/14 01:20:39info unpack layer: sha256:2c2d948710f21ad82dce71743b1654b45acb5c059cf5c19da491582cef6f2601
INFO: Creating sandbox directory...
INFO: Build complete: ubuntu
</code></pre>
<ul>
<li>在执行结束后可以在当期目录下生成一个名为<code>ubuntu</code>的目录，通过拉起该目录为容器，可以修改镜像配置，制作自己的容器镜像</li>
</ul>
<pre><code class="language-bash"># singularity shell -w ubuntu
</code></pre>
<ul>
<li>修改完配置之后，可以将该沙箱<code>build</code>成一个镜像文件</li>
</ul>
<pre><code class="language-bash"># singularity build ubuntu-base.sif ubuntu/
INFO: Starting build...
INFO: Creating SIF file...
INFO: Build complete: ubuntu-base.sif
</code></pre>
<ul>
<li>创建好<code>sif</code>镜像之后，会在本地生成一个sif文件，可通过该sif文件拉起一个容器，这里我们可以用一个非root帐号来拉起</li>
</ul>
<pre><code class="language-bash"># singularity shell ubuntu.sif
</code></pre>
<p>这里我们不过多赘述容器的使用方法，后续会出一些源码安装的方案以及更多的使用和配置场景。</p>
<h1 id="版权声明">版权声明</h1>
<p>本文首发链接为：https://www.cnblogs.com/dechinphy/p/singularity-install.html<br>
作者ID：DechinPhy<br>
更多原著文章请参考：https://www.cnblogs.com/dechinphy/</p>
<h1 id="参考链接">参考链接</h1>
<ol>
<li>北大超算集群使用教程</li>
<li>singularity开源地址</li>
</ol><br><br>
来源：https://www.cnblogs.com/dechinphy/p/singularity-install.html
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