cc_staff
156
edits
Singularity: Difference between revisions
Added text for running Singularity interactively
m (use tt rather than pre for non-command text) |
(Added text for running Singularity interactively) |
||
| Line 189: | Line 189: | ||
===Creating/Updating an Image Interactively and Manually=== | ===Creating/Updating an Image Interactively and Manually=== | ||
This section is incomplete and will be completed later. | TODO: This section is incomplete and will be completed later. | ||
===Is sudo Needed or Not Needed?=== | ===Is sudo Needed or Not Needed?=== | ||
| Line 228: | Line 228: | ||
===Running Commands Interactively=== | ===Running Commands Interactively=== | ||
Singularity can be used interactively by using its shell command, e.g., | |||
<source lang="console">$ singularity shell --help</source> | |||
will give help on shell command usage. The following: | |||
<source lang="console">$ singularity shell -B /home -B /project -B /scratch -B /localscratch myimage.simg</source> | |||
will do the following within the container image <code>myimage.simg</code>: | |||
* bind mount <code>/home</code> so that all home directories can be accessed (subject to your account's permissions) | |||
* bind mount <code>/project</code> so that project directories can be accessed (subject to your account's permissions) | |||
* bind mount <code>/scratch</code> so that the scratch directory can be accessed (subject to your account's permissions) | |||
* bind mount <code>/localscratch</code> so that the localscratch directory can be accessed (subject to your account's permissions) | |||
* run a shell (e.g., <code>/bin/bash</code>) | |||
If this command is successful, you can interactively run commands from within your container while still being able to access your files in home, project, scratch, and localscratch. :-) | |||
* NOTE: When done, type "exit" to exit the shell. | |||
In some cases, you will not want the pollution of shell environment variables from your Compute Canada shell. You can run a "clean environment" shell by adding a <code>-e</code> option, e.g., | |||
<source lang="console">$ singularity shell -e -B /home -B /project -B /scratch -B /localscratch myimage.simg</source> | |||
but know you may need to define some shell environment variables such as <code>$USER</code>. | |||
Finally, if you are using Singularity interactively on your own machine, in order for your changes to the image to be written to the disk, you must: | |||
* be using a Singularity "sandbox" image (i.e., be using a directory not the read-only .simg file) | |||
* be using the <code>-w</code> option, and, | |||
* be using <code>sudo</code> | |||
e.g., first create your sandbox image: | |||
<source lang="console">$ sudo singularity build -s myimage-dir myimage.simg</source> | |||
and then engage with Singularity interactively: | |||
<source lang="console">$ sudo singularity shell -w myimage-dir</source> | |||
When done, you can build a new/updated simg file, with the command: | |||
<source lang="console">$ sudo singularity build myimage-new.simg myimage-dir/</source> | |||
and upload myimage-new.simg to a cluster in order to use it. | |||
===Running a Single Command=== | ===Running a Single Command=== | ||