失败人士的Singularity安装失败经历

Posted on Edited on

官网上便有一些过时的失败教程

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$ git clone https://github.com/singularityware/singularity.git
$ cd singularity
$ ./autogen.sh
$ ./configure --prefix=/usr/local --sysconfdir=/etc
$ make
$ sudo make install

如果满足于安装旧版本，能成功

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VERSION=2.5.2
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
sudo make install

测试

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$ singularity
Increasing verbosity level (2)
Singularity version: 2.5.2-dist
USAGE: singularity [global options...] <command> [command options...] ...

但用着用着发现2.5.2这个版本太低了，有些bug

开启万能卸载重安装大法

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sudo apt-get autoremove singularity

移除旧版本

https://singularity.lbl.gov/docs-installation#remove-an-old-version

之前将Singularity安装在/usr/local，需要移除它们

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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

如果对系统配置目录做过修改，移除singularity.conf文件

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$ ls /etc/*.conf

发现我没有配置过这个文件，那就不管了

如果只是将singularity安装在一个平常的文件目录下，移除那个文件目录即可（真不错，可惜我属于前一种情况）。比如--prefix=/some/temp/dir，则

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$ sudo rm -rf /some/temp/dir

新版本

原来v3的安装教程在这里 https://sylabs.io/guides/3.6/admin-guide/installation.html#installation-on-linux

安装dependency

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$ 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

安装GO

Singularity v3主要是用Go编写的，需要安装Go 1.13或更高版本才能从源代码进行编译。

下载解压到/usr/local

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$ export VERSION=1.13.5 OS=linux ARCH=amd64 && \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz

设置Go环境变量

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$ echo 'export PATH=/usr/local/go/bin:${PATH}' >> ~/.bashrc && \
    source ~/.bashrc

源代码安装

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export VERSION=3.6.3 && # adjust this as necessary \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
    tar -xzf singularity-${VERSION}.tar.gz && \
    cd singularity
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$ ./mconfig && \
    make -C ./builddir && \
    sudo make -C ./builddir install

版本>=3.6.4也可用git checkout安装

然而，真是可恶，GO被墙了，而且由于GO DEP不走proxy，可恶……

https://github.com/goproxy/goproxy.cn/issues/29

反正服务器上有，不弄了，哼！