| Quick Start These docs are for Singularity Version 2.5.2. For older versions, see our archive This guide is intended for running Singularity on a computer where you have root (administrative) privileges. If you are learning about Singularity on a system where you lack root privileges, you can still complete the steps that do not require the sudo command. If you need to request an installation on your shared resource, check out our requesting an installation help page for information to send to your system administrator.InstallationThere are many ways to install Singularity but this quick start guide will only cover one.git clone https://github.com/singularityware/singularity.gitcd singularity./autogen.sh./configure --prefix=/usr/localmakesudo make installSingularity must be installed as root to function properly.Overview of the Singularity InterfaceSingularity’s command line interface allows you to build and interact with containers transparently. You can run programs inside a container as if they were running on your host system. You can easily redirect IO, use pipes, pass arguments, and access files, sockets, and ports on the host system from within a container.The --help option gives an overview of Singularity options and subcommands as follows:$ singularity --helpUSAGE: singularity [global options...] [command options...] ...GLOBAL OPTIONS: -d|--debug Print debugging information -h|--help Display usage summary -s|--silent Only print errors -q|--quiet Suppress all normal output --version Show application version -v|--verbose Increase verbosity +1 -x|--sh-debug Print shell wrapper debugging informationGENERAL COMMANDS: help Show additional help for a command or container selftest Run some self tests for singularity install CONTAINER USAGE COMMANDS: exec Execute a command within container run Launch a runscript within container shell Run a Bourne shell within container test Launch a testscript within container CONTAINER MANAGEMENT COMMANDS: apps List available apps within a container bootstrap *Deprecated* use build instead build Build a new Singularity container check Perform container lint checks inspect Display a container's metadata mount Mount a Singularity container image pull Pull a Singularity/Docker container to $PWD COMMAND GROUPS: image Container image command group instance Persistent instance command group CONTAINER USAGE OPTIONS: see singularity help For any additional help or support visit the Singularitywebsite: http://singularity.lbl.gov/Singularity uses positional syntax. Global options follow the singularity invocation and affect the way that Singularity runs any command. Then commands are passed followed by their options.For example, to pass the --debug option to the main singularity command and run Singularity with debugging messages on:$ singularity --debug run shub://GodloveD/lolcowAnd to pass the --containall option to the run command and run a Singularity image in an isolated manner:$ singularity run --containall shub://GodloveD/lolcowTo learn more about a specific Singularity command, type one of the following:$ singularity help $ singularity --help $ singularity -h $ singularity --help$ singularity -hUsers can also write help docs specific to a container or for an internal module called an app. If those help docs exist for a particular container, you can view them like so.$ singularity help container.simg # See the container's help, if provided$ singularity help --app foo container.simg # See the help for foo, if providedDownload pre-built imagesYou can use the pull and build commands to download pre-built images from an external resource like Singularity Hub or Docker Hub. When called on a native Singularity images like those provided on Singularity Hub, pull simply downloads the image file to your system.$ singularity pull shub://vsoch/hello-world # pull with default name, vsoch-hello-world-master.simg$ singularity pull --name hello.simg shub://vsoch/hello-world # pull with custom nameSingularity images can also be pulled and named by an associated GitHub commit or content hash.You can also use pull with the docker:// uri to reference Docker images served from a registry. In this case pull does not just download an image file. Docker images are stored in layers, so pull must also combine those layers into a usable Singularity file.$ singularity pull docker://godlovedc/lolcow # with default name$ singularity pull --name funny.simg docker://godlovedc/lolcow # with custom namePulling Docker images reduces reproducibility. If you were to pull a Docker image today and then wait six months and pull again, you are not guaranteed to get the same image. If any of the source layers has changed the image will be altered. If reproducibility is a priority for you, try building your images from Singularity Hub.You can also use the build command to download pre-built images from an external resource. When using build you must specify a name for your container like so:$ singularity build hello-world.simg shub://vsoch/hello-world$ singularity build lolcow.simg docker://godlovedc/lolcowUnlike pull, build will convert your image to the latest Singularity image format after downloading it.build is like a “Swiss Army knife” for container creation. In addition to downloading images, you can use build to create images from other images or from scratch using a recipe file. You can also use build to convert an image between the 3 major container formats supported by Singularity. We discuss those image formats below in the Build images from scratch section.Interact with ImagesOnce you have an image, you can interact with it in several ways. For these examples we will use a hello-world.simg image that can be downloaded from Singularity Hub like so.$ singularity pull --name hello-world.simg shub://vsoch/hello-worldShellThe shell command allows you to spawn a new shell within your container and interact with it as though it were a small virtual machine.$ singularity shell hello-world.simgSingularity: Invoking an interactive shell within container...# I am the same user inside as outside!Singularity hello-world.simg:~/Desktop> whoamivanessaSingularity hello-world.simg:~/Desktop> iduid=1000(vanessa) gid=1000(vanessa) groups=1000(vanessa),4(adm),24,27,30(tape),46,113,128,999(input)shell also works with the shub:// and docker:// URIs. This creates an ephemeral container that disappears when the shell is exited.$ singularity shell shub://vsoch/hello-worldExecuting CommandsThe exec command allows you to execute a custom command within a container by specifying the image file. For instance, to list the root (/) of our hello-world.simg image, we could do the following:$ singularity exec hello-world.simg ls /anaconda-post.log etc lib64 mnt root singularity tmpbin home lost+found opt run srv usrdev lib media proc sbin sys varexec also works with the shub:// and docker:// URIs. This creates an ephemeral container that executes a command and disappears.$ singularity exec shub://singularityhub/ubuntu cat /etc/os-releaseRunning a containerSingularity containers contain “runscripts”. These are user defined scripts that define the actions a container should perform when someone runs it. The runscript can be triggered with the run command, or simply by calling the container as though it were an executable.$ singularity run hello-world.simg$ ./hello-world.simgrun also works with shub:// and docker:// URIs. This creates an ephemeral container that runs and then disappears.$ singularity run shub://GodloveD/lolcowWorking with FilesFiles on the host are reachable from within the container.$ echo |