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:

• 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.

• 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).