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Running Singularitry container

Let's practice a bit running one of the containers from the previous step. 

$ singularity pull lolcow.sif docker://godlovedc/lolcow
This will pull the Docker image in to A singularity container with name lolcow.sif.

Run the Singularity container

Executing the container file itself or a remote build will start will execute the commands defined in the %runscript section. This is equivalent to run singularity run ./lolcow.sif

$ ./lolcow.sif 
_________________________________________
/ You will stop at nothing to reach your  \
| objective, but only because your brakes |
\ are defective.                          /
 -----------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

$ singularity run ./lolcow.sif 
 _____________________________________
/ Don't relax! It's only your tension \
\ that's holding you together.        /
 -------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Getting a shell in the running container

$ singularity shell ./lolcow.sif 
Singularity>

If you try to list the files in your home folder with ls -l ~ you will see the content of your home folder. What about the root folder? List the content with ls -l / and compare the output from a different terminal.

Singularity binds the user home folder, /tmp and some other by default. If you are running on a computer with more users accounts than your own (like on a computer cluster) compare the content of ls -l /home from within the container and outside. You should not be able to see the other users' folders that are on the computer otherwise.

Execute program in the container

There is of course a way to start a different program than the default shell or the defined in the %runscript section.

$ singularity exec ./lolcow.sif fortune
Beauty and harmony are as necessary to you as the very breath of life.

$ singularity exec  ./lolcow.sif host
FATAL:   "host": executable file not found in $PATH

Keep in mind that running in the container you should be able to find the program inside or in the folders you have binded to the container i.e. the system tools and programs remain isolated.

Warning

If you have setup conda or pip installations in you profile folder, they get available in the container. This might conflict with the container setup which is unaware of programs installed in your home folder. To avoid such situations, you might need to run singularity with --cleanenv option i.e. singularity run -e ./lolcow.sif

Binding/mounting folders

By default, Singularity binds these folders from the host computer (your computer) to the container defined in /usr/local/etc/singularity/singularity.conf.

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mount home = yes

mount tmp = yes

#bind path = /etc/singularity/default-nsswitch.conf:/etc/nsswitch.conf
#bind path = /opt
#bind path = /scratch
bind path = /etc/localtime
bind path = /etc/hosts

On Rackham few more folders are automatically mounted for almost obvious reasons. 

- /scratch
- /sw
- /proj

Binding folders from the host to the container, allows you to

  • "Inject" any host folder as read/write folder in the container
    frequently used for external databases or standalone tools
  • Replace container's folder or file form the host
    usually used to provide external configuration files to replace default common.

More detailed online at User-defined bind paths