The documented method to build a Singularity container image requires using sudo privilege. In this owhow-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 then install your own Linux virtual machine with the Singularity rpm, giving yourself root/sudo privilege on that VM. This will allows allow you to build an image. The solution works for both Windows, Mac and Linux desktop/laptop.
- Even easier than using Virtual Box directly: Use Vagrant. Vagrant uses Virtual Box to spin up VMs, but it's automated and very fast. The advantage to Vagrant is that the OS install does not need to be done – Vagrant downloads preinstalled images, so you can run "vagrant up" and then ssh into your VM in seconds, and use sudo there.
- Similarly, one can install Docker on your desktop or laptop. Then 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 makes significant changes. The follows following are the steps to do this, assuming you are on a SLAC CentOS 7 public login node (centos7.slac.stanford.edu), you your current directory is /tmp, and you want to build a CentOS based Singularity container image:
- Download and save a base CentOS image from Docker with the following command. This command download downloads the image to /tmp/centos_centos7.7.1908.sif. The image contains a very basic set of CentOS 7 operating system. It does include yum and rpm commands so that one can install more rpmsRPMs.
singularity pull docker://centos:centos7.7.1908
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- Unpack CentOS 7 operating system files from the squashfs image. This will create a sub-directory squashfs-root and put all the files there. All files under this directory are own by you, not root.
/binsbin/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 RPMs via yum in the image. So do this:
- Fix a few directory permission issueissues:
cd /tmp/squashfs-root; find usr bin lib* etc root var -type d -exec chmod u+w {} \;
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:param base: a :class:`yum.Yumbase` object. :raises: :class:`cli.CliError` """ # if base.conf.uid != 0: # base# base.logger.critical(_('You need to be root to perform this command.')) # raise # raise cli.CliError
- After the above changes, you can start using the image, installing rpms RPMs or do other customization, such as
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- When you are done, you can create a squashfs image, which can be use by Singularity at other places.
cd /tmp/squashfs-root; /sbin/mksquashfs . /tmp/my-container.img
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