Using Singularity containers to run commands
Overview
Teaching: 10 min
Exercises: 5 minQuestions
How do I run different commands within a container?
How do I access an interactive shell within a container?
Objectives
Learn how to run different commands when starting a container.
Learn how to open an interactive shell within a container environment.
Running specific commands within a container
We saw earlier that we can use the singularity inspect
command to see the run script that a container is configured to run by default. What if we want to run a different command within a container?
If we know the path of an executable that we want to run within a container, we can use the singularity exec
command. For example, using the lolcow.sif
container that we’ve already pulled from Singularity Hub, we can run the following within the test
directory where the lolcow.sif
file is located:
remote$ singularity exec lolcow.sif /bin/echo "Hello, world"
Hello, world
Here we see that a container has been started from the lolcow.sif
image and the /bin/echo
command has been run within the container, passing the input Hello, world
. The command has echoed the provided input to the console and the container has terminated.
Note that the use of singularity exec
has overriden any run script set within the image metadata and the command that we specified as an argument to singularity exec
has been run instead.
Basic exercise: Running a different command within the “hello-world” container
Can you run a container based on the
lolcow.sif
image that prints the current date and time?Solution
remote$ singularity exec lolcow.sif /bin/date
Fri Jun 26 15:17:44 BST 2020
Difference between singularity run
and singularity exec
Above, we used the singularity exec
command. In earlier episodes of this
course we used singularity run
. To clarify, the difference between these
two commands is:
-
singularity run
: This will run the default command set for containers based on the specified image. This default command is set within the image metadata when the image is built (we’ll see more about this in later episodes). You do not specify a command to run when usingsingularity run
, you simply specify the image file name. As we saw earlier, you can use thesingularity inspect
command to see what command is run by default when starting a new container based on an image. -
singularity exec
: This will start a container based on the specified image and run the command provided on the command line followingsingularity exec <image file name>
. This will override any default command specified within the image metadata that would otherwise be run if you usedsingularity run
.
Opening an interactive shell within a container
If you want to open an interactive shell within a container, Singularity provides the singularity shell
command. Again, using the lolcow.sif
image, and within our test
directory, we can run a shell within a container from the hello-world image:
remote$ singularity shell lolcow.sif
Singularity> whoami
[<your username>]
Singularity> ls
lolcow.sif
Singularity>
As shown above, we have opened a shell in a new container started from the lolcow.sif
image. Note that the shell prompt has changed to show we are now within the Singularity container.
Use the exit
command to exit from the container shell.
Key Points
The
singularity exec
is an alternative tosingularity run
that allows you to start a container running a specific command.The
singularity shell
command can be used to start a container and run an interactive shell within it.