Day: January 11, 2022

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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