Gridware: Usage Example¶

Creating and Using Ecosystem¶

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

To install and use gridware:

Activate the flight system

Create the gridware installation for the user:

[flight@gateway1 ~]$ flight env create gridware
Creating environment gridware@default
   > ✅ Verifying prerequisites
   > ✅ Fetching prerequisite (modules)
   > ✅ Extracting prerequisite (modules)
   > ✅ Building prerequisite (modules)
   > ✅ Installing prerequisite (modules)
   > ✅ Fetching prerequisite (gridware)
   > ✅ Extracting prerequisite (gridware)
   > ✅ Installing prerequisite (gridware)
   > ✅ Configuring repo: main
   > ✅ Configuring repo: volatile
   > ✅ Creating environment (gridware@default)
Environment gridware@default has been created

Activate the gridware ecosystem:

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

Check that gridware can be run:

<gridware> [flight@gateway1 ~]$ gridware --version
gridware 1.5.1

Installing and Running Perl¶

An example workflow using perl is demonstrated below.

View available versions:

<gridware> [flight@gateway1 ~]$ gridware search perl
2 repositories need to update ...
Updating repository: main
          Update ... OK (At: 55916fd)
Updating repository: volatile
          Update ... OK (At: 61cc544)
main/apps/bismark/0.16.3                  main/apps/bismark/0.17.0                  main/apps/cegma/2.5.0
main/apps/clusterflow/0.6.0-20170502      main/apps/clusterflow/0.6.0-20170530      main/apps/forks/0.36
main/apps/ihrsr/1.5                       main/apps/perl/5.20.2                     main/apps/python/2.7.8
<-- snip -->
volatile/apps/perl/5.16.1                 volatile/apps/perl/5.16.3                 volatile/apps/perl/5.18.0
volatile/apps/perl/5.20.2                 volatile/apps/python/2.7.3                volatile/apps/python/2.7.5
<-- snip -->

Install specific version:

<gridware> [flight@gateway1 ~]$ gridware install main/apps/perl/5.20.2
Preparing to install main/apps/perl/5.20.2
Installing main/apps/perl/5.20.2

 > Preparing package sources
        Download --> perl-5.20.2.tar.gz ... OK
          Verify --> perl-5.20.2.tar.gz ... OK
        Packaged --> CPAN-Config.pm     ... OK
        Packaged --> CPAN-MyConfig.pm   ... OK

 > Preparing for installation
           Mkdir ... OK (/home/flight/.cache/flight/env/build/gridware/src/apps/perl/5.20.2/gcc-4.8.5)
         Extract ... OK

 > Proceeding with installation
         Compile ... OK
           Mkdir ... OK (/home/flight/.local/share/flight/env/gridware+default/depots/23cd1570/el7/pkg/apps/perl/5.20.2/gcc-4.8.5)
         Install ... OK
          Module ... OK

Installation complete.

Check installation location:

<gridware> [flight@gateway1 ~]$ module load apps/perl
apps/perl/5.20.2/gcc-4.8.5
 | -- libs/gcc/system
 |    * --> OK
 |
 OK
<gridware> [flight@gateway1 ~]$ which perl
~/.local/share/flight/env/gridware+default/depots/23cd1570/el7/pkg/apps/perl/5.20.2/gcc-4.8.5/bin/perl

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

<gridware> [flight@gateway1 ~]$ cpan File::Slurp
Reading '/home/flight/gridware/share/perl/5.20.2/cpan/Metadata'
  Database was generated on Tue, 10 Sep 2019 01:17:03 GMT
Running install for module 'File::Slurp'
<-- snip -->
Appending installation info to /home/flight/gridware/share/perl/5.20.2/lib/5.20.2/x86_64-linux/perllocal.pod
  CAPOEIRAB/File-Slurp-9999.27.tar.gz
  /usr/bin/make install INSTALLMAN3DIR=/home/flight/gridware/share/perl/5.20.2/man/man3 INSTALLMAN1DIR=/home/flight/gridware/share/perl/5.20.2/man/man1 -- O

Check installation worked:

<gridware> [flight@gateway1 ~]$ cpan File::Slurp
Reading '/home/flight/gridware/share/perl/5.20.2/cpan/Metadata'
  Database was generated on Tue, 10 Sep 2019 01:17:03 GMT
File::Slurp is up to date (9999.27).