Basic Usage of Singularity (Part 2)

The information can be taken from https://github.com/NIH-HPC/Singularity-Tutorial. I’m just documenting what I understand step-by-step

EXEC Command

Using the exec command, we can run commands within the container from the host system.

[user1@node ~]$ singularity exec lolcow_latest.sif cowsay 'How is today?'
 _______________
< How is today? >
 ---------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

RUN Command

Sometimes you can run a container

 [user1@node ~]$ singularity run lolcow_latest.sif
 _____________________________________
/ Fine day to work off excess energy. \
\ Steal something heavy.              /
 -------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

A special script “runscript” is activated when the “run” command is exercised. To have a closer look

[user1@node ~]$ singularity inspect --runscript lolcow_latest.sif
#!/bin/sh

    fortune | cowsay | lolcat

runscript consists of three simple commands with the output of each command piped to the subsequent command. Altenatively, you can do a

[user1@node ~]$ ./lolcow_latest.sif

Pipes and Redirection

Singularity allows piping services so that the host system can interact with the container. Here we are executing a command in the container and piping the output out into a file called output.txt

[user1@node ~]$ singularity exec lolcow_latest.sif cowsay moo > output.txt

You will notice that the output has been pushed to output.txt. Make sure you create output.txt prior

[user1@node ~]$ vim output.txt

Inside output.txt

 How are you >
 -------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Let’s say we create a file called HelloThere and put in a text called “Shame On You”. The command is then fed into cowsay.

% cat HelloThere | singularity exec lolcow_latest.sif cowsay -n
______________
< Shame on You >
 --------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

References:

  1. https://github.com/NIH-HPC/Singularity-Tutorial

Basic Usage of Singularity (Part 1)

The article is taken from https://github.com/NIH-HPC/Singularity-Tutorial. I’m personally learning much from the systematic rich contents and below are my learning points……

Popular Sites

There are popular sites for Singularity Download that has pre-build containers

Downloading the Containers

% singularity pull library://godlovedc/funny/lolcow
INFO:    Downloading library image
89.2MiB / 89.2MiB [========================================================================================================================================================] 100 % 5.4 MiB/s 0s
WARNING: integrity: signature not found for object group 1
WARNING: Skipping container verification

Singularity File

The Singularity File has a .sif extension something like this

lolcow_latest.sif

Entering the Shell of Singularity

% singularity shell lolcow_latest.sif
Singularity> cat /etc/os-release
NAME="Ubuntu"
VERSION="16.04.5 LTS (Xenial Xerus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.5 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial

You will notice the container is running Ubuntu…… although the Host OS could be different

Interesting Observations

a. The user remains the same inside and outside of the container.

Singularity> whoami
admin

b. The hostname remains the same inside and outside the container

Singularity> hostname
node1

c. Running the application within the containers

Singularity> cowsay moo
 _____
< moo >
 -----
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

d. Exiting the Application

Singularity > exit

References:

  1. https://github.com/NIH-HPC/Singularity-Tutorial
  2. https://github.com/sylabs/singularity

Compiling Singularity-CE-3.9.2 on CentOS-7

The Official Documentation can be found at https://sylabs.io/guides/3.0/user-guide/installation.html

Prerequisites 1 – Yum

If you are using CentOS, you may want to put the necessary libraries and dependencies in first.

yum install -y && \
yum groupinstall -y 'Development Tools' && \
yum install -y \
openssl-devel \
libuuid-devel \
libseccomp-devel \
wget \
squashfs-tools

Prerequisites 2 – Go

Go to the Download Page https://go.dev/dl/ to download the Linux Version.

Extract the archive you downloaded into /usr/local, creating a Go tree in /usr/local/go.

This step below will remove a previous installation at /usr/local/go, if any, prior to extracting. Please back up any data before proceeding.

% rm -rf /usr/local/go && tar -C /usr/local -xzf go1.17.5.linux-amd64.tar.gz

Add /usr/local/go/bin to the PATH environment variable. You can do this by adding the following line to your $HOME/.profile or /etc/profile (for a system-wide installation):

export PATH=$PATH:/usr/local/go/bin

Verify the Installation with the command

% go version

Compiling Singularity

To download Singularity, do visit the download site. Singularity uses a build system called makeit. mconfig is called to generate Makefile and them make is used to compile and install

% cd singularity
% ./mconfig
 --prefix=/usr/local/singularity-ce-3.9.2
% cd build
% make
% make install

Source bash-completion file

To enjoy bash completion with Singularity commands and options, source the bash-completion file. you need to source the appropriate file and add it to the bash-completion directory in /etc so that it will be sourced automatically when you start another shell.

% . /usr/local/singularity-ce-3.9.2/etc/bash_completion.d/singularity
% cp /usr/local/singularity-ce-3.9.2/etc/bash_completion.d/singularity /etc/bash_completion.d/

Testing

As long as you see a cow your installation is working properly…….

singularity run library://godlovedc/funny/lolcow
/ Q: What is the difference between a \
\ duck? A: One leg is both the same.  /
 -------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

References

  1. https://sylabs.io/guides/3.0/user-guide/installation.html
  2. https://github.com/NIH-HPC/Singularity-Tutorial