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There are three main ways to run a Singularity image on OSCAR. As an interactive shell, using the exec command, or building a runscript and using the run command. |
The most likely usage of your singularity environment will be via utilizing either singularity exec or singularity run. These can be directly executed via a batch script or through an interactive job in place of your traditional execution scripts. For more information about the methods of running a singularity image, the Singularity quickstart guide is pretty handy.
{% hint style="info" %} Treat the running of a singularity container like any other executable or codebase on OSCAR. Do not run singularity containers directly on the login nodes. Instead, they should be run either via an interactive or batch job, or via the terminal within a VNC session. {% endhint %}
This will launch an interactive shell within a singularity instance based on the designated image. This should be used when you are testing/debugging the image or intend to use it via the interact/VNC methods.
$ singularity shell <imagePath>
This method is only applicable when working with an interact slurm job, or via the terminal within a VNC session.
The next method is to launch the image with a defined set of instructions. This will launch the singularity image, and execute whatever commands are defined by the user.
$ singularity exec <imagePath> <commands>
Here, the commands can range from running a script, loading modules, or piping multiple instructions together. To see an example of this process, see the Example - Tensorflow section where we execute a script to run within the singularity image.
The last method we will go over here is via singularities run command, which will execute a series of instructions provided to the image in the form of a runscript. This script will automatically execute if the image is either launch using the run command, or if the singularity image is directly executed.
$ singularity run <imagePath>
or
./<imagePath>
In both cases, we are executing the container’s “runscript” (the executable /singularity at the root of the image).
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For more information about singularity run and the associated runscript, we recommend the run documentation using singularity run help or visiting the singularity run documentation.
{% endhint %}