Changes between Version 15 and Version 16 of cypress/Singularity


Ignore:
Timestamp:
08/30/2026 07:52:50 PM (4 days ago)
Author:
Carl Baribault
Comment:

Added details - SIF, verification, user space, architecture

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  • cypress/Singularity

    v15 v16  
    1111You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters like Cypress.
    1212
    13 Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system and system.
     13Your container is a single file - normally with file extension '''.sif''', and you don’t have to worry about how to install all the software you need on each different operating system and system.
    1414
    15 === Caveat: linux, architecture ===
     15=== Caveats For Using Containers ===
    1616
    17 There are a couple of caveats for running your container image file on other machines.
    18 
    19 * The target machine must be running a linux operating system (OS) and have Singularity (or Apptainer - using the same '''.sif''' image file format) installed.
    20 * Your image file may not run on the target machine's architecture, x86/amd64 (for Intel/AMD) or arm64 (for Apple), if it is not the same as that of the machine on which the image file was constructed.
     17* '''SIF Compatibility''' - The target machine must be running a linux operating system (OS) and have Singularity or Apptainer installed - using the same version of the '''.sif''' image file format. (See  [https://apptainer.org/docs/user/main/singularity_compatibility.html#sif-image-compatibility| SIF Image Compatibility] in Apptainer documentation.)
     18* '''Machine Architecture''' - Your image file may not run on the target machine's architecture, x86/amd64 (for Intel/AMD) or arm64 (for Apple), if it is not the same as that of the machine on which the image file was constructed.
     19 * For linux platform architecture, use the command '''uname -m'''.
     20 * For linux kernel version use, use the command '''uname -r'''.
     21* '''Container Verification''' - Because Singularity runs entirely inside your user space (see [https://www.linfo.org/user_space.html| User Space Definition]), the container instantly inherits your identity, your permissions, and your network access. This includes your Cypress account's access to files and internet. (See the command '''singularity help verify'''.)
    2122
    2223=== More about containers ===
     
    2526
    2627== Possible uses for Singularity on Cypress ==
    27 * Run an application built for a different distribution of Linux than Cypress OS (Centos).
     28* Run an application built for a different distribution or '''flavor''' (for example [SingularityDockerhub#Example1:BuildingacontainerforUbuntu Ubuntu]) of Linux than Cypress OS (Centos).
    2829* Reproduce an environment to run a workflow created by someone else.
    2930* Run a series of applications (a 'pipeline') that includes applications built on different platforms.