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Singularity runs on Linux natively and can also be run on Windows and Macthrough virtual machines (VMs). Here we cover several different methods ofinstalling Singularity (>=v3.0.0) on Linux and also give methods for downloadingand running VMs with singularity pre-installed from Vagrant Cloud.

To enjoy bash completion with Singularity commands and options, source the bashcompletion file like so. Add this command to your ~/.bashrc file so that bashcompletion continues to work in new shells. (Obviously adjust this path if youinstalled the bash completion file in a different location.)

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Singularity is available on Debian and derivative distributions starting withDebian stretch and the Ubuntu 16.10 releases. The package is calledsingularity-container. For more recent releases of singularity andbackports for older Debian and Ubuntu releases, it is recommended that you usethe NeuroDebian repository.

The epel (Extra Packages for Enterprise Linux) repos contain Singularity. Thesingularity package is actually split into two packages calledsingularity-runtime (which simply contains the necessary bits to runsingularity containers) and singularity (which also gives you the ability tobuild Singularity containers).

I use a Singularity/Apptainer container (build from a definition file) to build the code of my project.The way I use it is to run the container with singularity shell my_container.sif such that my workspace is mounted in the container and then run the command for building there.

For the build to work, I first need to source a configuration file which sets up the environment, creates some aliases, etc. This configuration file is part of the container. So currently inside the container I do the following:

I am wondering if there is a way to make Singularity/Apptainer automatically source that /setup.bash file when I run the container with singularity shell. I tried with the %environment section in the definition file but it does not seem possible to create aliases there.

Singularity began as an open-source project in 2015, when a team of researchers at Lawrence Berkeley National Laboratory, led by Gregory Kurtzer, developed the initial version written in the C programming language and released it[8] under the BSD license.[9]

In May 2020 Gregory Kurtzer left Sylabs but retained leadership of the Singularity open source project.[25] In May 2021 Sylabs made a fork of the project[26] and called it SingularityCE.[27][28] In November 2021 the Singularity open source project joined the Linux Foundation[29] and was renamed to Apptainer.[30]

Using other enterprise container solutions like Docker in HPC systems would require modifications to the software.[35]Docker containers can be automatically converted to stand-alone singularity files which can then be submitted to HPC resource managers.[36]

Has anyone had success sourcing a root built in singularity, not from binaries?

The build succeeds, and it can be used normally with singularity shell root.sif, but running the entrypoint, or exec commands fail to source thisroot.sh, citing failure on line 168:

The following binaries are found on $PATH during build time when./mconfig is run, and their location is added to thesingularity.conf configuration file. At runtime this configuredlocation is used. To specify an alternate executable, change therelevant path entry in singularity.conf.

mksquashfs from squashfs-tools 4.3+ is used to create thesquashfs container filesystem that is embedded into SIF containerimages. The mksquashfs procs and mksquashfs mem directives insingularity.conf can be used to control its resource usage.

To allow Singularity to locate the host (i.e. CentOS / Debian) GPUlibraries correctly, set ldconfig path in singularity.conf topoint to the host ldconfig. I.E. it should be set to/sbin/ldconfig or /sbin/ldconfig.real rather than a Nix or Guixrelated path.

Singularity will cache SIF container images generated from remotesources, and any OCI/docker layers used to create them. The cache iscreated at $HOME/.singularity/cache by default. The location of thecache can be changed by setting the SINGULARITY_CACHEDIR environmentvariable.

If you are not certain that your $HOME or SINGULARITY_CACHEDIRfilesystems support atomic rename, do not run singularity in parallelusing remote container URLs. Instead use singularity pull to createa local SIF image, and then run this SIF image in a parallel step. Analternative is to use the --disable-cache option, but this willresult in each Singularity instance independently fetching thecontainer from the remote source, into a temporary location.

To support the SIF image format, automated networking setup etc., andolder Linux distributions without user namespace support, Singularitymust be make install``ed as root or with ``sudo, so it can installthe libexec/singularity/bin/starter-setuid binary with rootownership and setuid permissions for privileged operations. If you needto install as a normal user, or do not want to use setuid functionalitysee below.

In a standard installation of Singularity 3.0.1 and beyond (whenbuilding from source), the command sudo make install lists all thefiles as they are installed. You must remove all of these files anddirectories to completely remove Singularity.

The new result shows that black holes gain mass in a way consistent with them containing vacuum energy, providing a source of dark energy and removing the need for singularities to form at their centre.

Study first author Duncan Farrah, University of Hawai`i Astronomer and former Imperial PhD student, said: We're really saying two things at once: that there's evidence the typical black hole solutions don't work for you on a long, long timescale, and we have the first proposed astrophysical source for dark energy.

What that means, though, is not that other people haven't proposed sources for dark energy, but this is the first observational paper where we're not adding anything new to the Universe as a source for dark energy: black holes in Einstein's theory of gravity are the dark energy.''

A study in Neuron took a first step. Thanks to Xbox and some virtual mall shopping, a team led by Dr. Arne Ekstrom from the University of Arizona dug deep into what drives theta waves. The study recruited people with epilepsy who already had electrodes implanted into their brains to hunt down the source of seizures.

Some people are just outright unreasonable: they refuse to adapt to the world and, instead, try to adapt the world to themselves. Marcin Jakubowski is one of those crazy people who has been trying to open source a civilization starter kit from the ground up. Now, as we know, most unreasonable people fail. But those who make it through end up changing the world. And I sure hope Marcin is one of those. So I could not pass the opportunity to have him on Singularity 1on1 and talk about being unreasonable and the work that he does.

OpenCog Hyperon is a long-term project to implement a complete, scalable, and open-source general artificial intelligence system based on the principles of OpenCog. It is an open-sourced platform where different AI strategies and methods such as Neuro Symbolic AI, Evolutionary Learning systems, Economic Attention Allocation, Machine Learning, and other AI approaches can collaborate based on a shared knowledge metagraph (Atomspace).

Lead by Dr. Ben Goertzel, our team includes seasoned scientists, researchers, engineers, designers, entrepreneurs and community leaders. To support our mission we are looking for talented individuals that will help us build toward a positive technological singularity.

If you want support for tab completion of Singularity commands, you need to source the appropriate file and add it to the bash completion directory in /etc so that it will be sourced automatically when you start another shell.

If everything went according to plan, you now have a working installation of Singularity.Simply typing singularity will give you a summary of all the commands you can use.Typing singularity help will give you more detailed information about running an individual command.

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.

The landscape of scientific computing is fluid. Over the past decade and a half, virtualization has gone from an engineering toy to a global infrastructure necessity, and the evolution of related technologies has thus flourished. The currency of files and folders has changed to applications and operating systems. The business of Supercomputing Centers has been to offer scalable computational resources to a set of users associated with an institution or group [1]. With this scale came the challenge of version control to provide users with not just up-to-date software, but multiple versions of it. Software modules [2, 3], virtual environments [4, 5], along with intelligently organized file systems [6] and permissions [7] were essential developments to give users control and reproducibility of work. On the administrative side, automated builds and server configuration [8, 9] have made maintenance of these large high-performance computing (HPC) clusters possible. Job schedulers such as SLURM [10] or SGE [11] are the metaphorical governors to control these custom analyses at scale, and are the primary means of relay between administrators and users. The user requires access to consume resources, and the administrator wants to make sure that the user has the tools and support to make the most efficient use of them. ff782bc1db