Singularity Set Home Directory
Our home directory path in /etc/passwd is a symlink in an automounted directory pointing to a path in another automounted directory. This allows thousands of user accounts to be referenced via a common logical path through a small disk partition. In the container runscript, you can change directories if you need to, use exec to run a script, etc. But by default for exec and shell it's going to just pass what the host working directory is for the working directory to start in. If you just want singularity to use somewhere else as home, you can set that via command line.
If you are not certain that your $home or singularity_cachedir filesystems support atomic rename, do not run singularity in parallel using remote container urls. Instead use singularity pull to create a local sif image, and then run this sif image in a parallel step. By default, the singularity software will create a set of folders in your $home directory for docker layers, singularity hub images, and docker metadata, respectively: $home/. singularity $home/. singularity/docker $home/. singularity/shub $home/. singularity/metadata Steps to reproduce behavior. $ singularity pull docker://ubuntu. Singularity containers support environment variables and labels that you can add to your container during the build process. This page details general information about defining environments and labels. If you are looking for specific environment variables for build time, see build environment. A home directory specification, it could be a source or destination path. The source path is the home directory outside the container and the destination overrides the home directory within the container. Singularity by default mounts your home directory. While this is great for seamless communication between your host and the container, it can introduce issues if you have software modules installed at $home. I would like to be able to run the container with /opt as the home directory, or somehow be able to run the container so that the home directory contains the files that already exist within the container. This maps a folder on the host as the home directory, rather than a folder in the container.
The source path is the home directory outside the container and the destination overrides the home directory within the container. Singularity by default mounts your home directory. While this is great for seamless communication between your host and the container, it can introduce issues if you have software modules installed at $home. I would like to be able to run the container with /opt as the home directory, or somehow be able to run the container so that the home directory contains the files that already exist within the container. This maps a folder on the host as the home directory, rather than a folder in the container. Some of the bind paths are automatically derived (e. g. A user’s home directory) and some are statically defined (e. g. Bind path in the singularity configuration file). Some bind paths are automatically derived (e. g. A user’s home directory) and some are statically defined (e. g. Bind paths in the singularity configuration file). In the default configuration, the directories $home , /tmp , /proc , /sys , /dev, and $pwd are. By default, singularity will create a set of folders in your $home directory for docker layers, cloud library images, and metadata, respectively: If you want to cache in a different directory, set singularity_cachedir to the desired path.
Some of the bind paths are automatically derived (e. g. A user’s home directory) and some are statically defined (e. g. Bind path in the singularity configuration file). Some bind paths are automatically derived (e. g. A user’s home directory) and some are statically defined (e. g. Bind paths in the singularity configuration file). In the default configuration, the directories $home , /tmp , /proc , /sys , /dev, and $pwd are. By default, singularity will create a set of folders in your $home directory for docker layers, cloud library images, and metadata, respectively: If you want to cache in a different directory, set singularity_cachedir to the desired path.
