Singularity: Usage Example

Creating and Using Ecosystem

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

To install and use singularity:

Note

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@gateway1 ~]$ 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@gateway1 ~]$ flight env activate singularity
  <singularity> [flight@gateway1 ~]$
  

• Check that singularity can be run:

  <singularity> [flight@gateway1 ~]$ 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@gateway1 ~]$ 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@gateway1 ~]$ 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@gateway1 ~]$ 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@gateway1 ~]$ 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).