Singularity Usage Example

Singularity is high-performance container technology specifically designed to enhance Enterprise Performance Computing by building containers that support HPC, analytics, artificial intelligence, machine learning, and deep learning to provide "intelligence anywhere".

Creating and Using Ecosystem

Flight Env provides quick setup methods to create a singularity software ecosystem.

To install and use singularity:

Warning

If installing singularity for a user then there are a number of restrictions and additional steps to consider in configuring the environment. See the Personal Environment section of flight env info singularity.

Activate the flight system.

Create the singularity installation for the user:

[flight@chead1 ~]$ flight env create singularity
Creating environment singularity@default
   > ✅ Verifying prerequisites
   > ✅ Fetching prerequisite (squashfs)
   > ✅ Extracting prerequisite (squashfs)
   > ✅ Building prerequisite (squashfs)
   > ✅ Installing prerequisite (squashfs)
   > ✅ Fetching prerequisite (go)
   > ✅ Extracting prerequisite (go)
   > ✅ Fetching prerequisite (singularity)
   > ✅ Extracting prerequisite (singularity)
   > ✅ Building prerequisite (singularity)
   > ✅ Installing prerequisite (singularity)
   > ✅ Creating environment (singularity@default)
Environment singularity@default has been created

Activate the singularity ecosystem:

[flight@chead1 ~]$ flight env activate singularity
<singularity> [flight@chead1 ~]$

Check that singularity can be run:

<singularity> [flight@chead1 ~]$ singularity --version
singularity version 3.2.1

Installing and Running Perl

An example workflow using perl is demonstrated below.

Note

The perl container is built from a docker container which can be searched for in the docker hub. To search the singularity container library, use singularity search SEARCHTERM.

Install specific version:

<singularity> [flight@chead1 ~]$ singularity build --sandbox perl_5.30.simg docker://perl:5.30
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:4ae16bd4778367b46064f39554128dd2fda2803a5747fddeff74059f353391c9
 48.05 MiB / 48.05 MiB [====================================================] 0s
Copying blob sha256:bbab4ec87ac4f89eaabdf68dddbd1dd930e3ad43bded38d761b89abf9389a893
 7.44 MiB / 7.44 MiB [======================================================] 0s
<-- snip -->
Writing manifest to image destination
Storing signatures
INFO:    Creating sandbox directory...
INFO:    Build complete: perl_5.30.simg

Check installation location:

<singularity> [flight@chead1 ~]$ singularity exec perl_5.30.simg which perl
/usr/local/bin/perl

Install perl library (this may prompt for initial cpan configuration, once configuration is complete then the library will be installed):

<singularity> [flight@chead1 ~]$ singularity exec -w perl_5.30.simg cpan File::Slurp
INFO:    Convert SIF file to sandbox...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "en_GB.UTF-8",
    LANG = "en_GB.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Sep 2019 13:29:02 GMT
Running install for module 'File::Slurp'
<-- snip -->

Check installation worked:

<singularity> [flight@chead1 ~]$ singularity exec perl_5.30.simg cpan File::Slurp
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "en_GB.UTF-8",
    LANG = "en_GB.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Sep 2019 13:29:02 GMT
File::Slurp is up to date (9999.27).