The documented method to build a Singularity container image requires using sudo privilege. In the how-to document, we outline how to work with this constraint. Obviously if you have sudo somewhere that you can use to build a Singularity container image, your problem is solved. For those who don't, here are some of the options:
- Install an Oracle Virtual Box on your desktop or laptop. You can them install your own Linux virtual machine with the Singularity rpm, giving yourself root/sudo privilege on that VM. This will allows you to build an image. The solution works for both Windows, Mac and Linux desktop/laptop.
- Similarly, one can install Docker on your desktop or laptop. The install / pull a Linux Docker container and install Singularity rpm in the container. The rest is the same as above.
- Build what you need in a Docker image and upload to Docker Hub, and on a SLAC Linux host, use command "singularity pull your_docker_image" to convert and save it as a Singularity image.
If you want to do none of the above, you have an option to build a Singularity container image without root on a SLAC CentOS 7 machine. This method is a bit of hacking so it may not work in the future when Singularity make significant changes. The follows are the steps to do this, assuming you are on a SLAC CentOS 7 public login node, you current directory is /tmp, and you want to build a CentOS based Singularity container image:
- Download and save a basic CentOS image from Docker with the following command. This command will save a file /tmp/centos_centos7.7.1908.sif to /tmp.
singularity pull docker://centos:centos7.7.1908
- Extract the squashfs image from the saved .sif file. A .sif has several objects inside, which you can exam by using "
singularity sif list /tmp/centos_centos7.7.1908.sif"command. The squashfs image we need is usually the 3rd object. Extract and save it with command
singularity sif dump 3 /tmp/centos_centos7.7.1908.sif > /tmp/centos_centos7.7.1908.sqsh
- Unpack the files from the squashfs image. This will create a sub-directory squashfs-root, which contains the OS files. All files under this directory are own by you, not root.
/bin/unsquashfs \-no-xattrs /tmp/centos_centos7.7.1908.sqsh
- Singularity can use the files in /tmp/squashfs-root as an "image" (Singularity sandbox image). But one needs to change a few things in order to install additional rpms via yum in the image. So do this:
- Fix a few directory permission issue:
cd /tmp/squashfs-root; find usr bin lib* etc root var -type d -exec chmod u+w {} \;
- By default, yum checks if the user is root, and will refuse to install anything if it is not. So edit /tmp/squashfs-root/usr/share/yum-cli/yumcommands.py and change the following code and comment out the relevant code (in red)
def checkRootUID(base): """Verify that the program is being run by the root user.
:param base: a :class:`yum.Yumbase` object. :raises: :class:`cli.CliError` """ # if base.conf.uid != 0: # base.logger.critical(_('You need to be root to perform this command.')) # raise cli.CliError
- After the above change, you can start using the image and installing rpms, such as
singularity shell /tmp/squashfs-root
singularity exec \-w --no-home /tmp/squashfs-root yum install git
Step-by-step guide
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