Flight Env

Overview

The breadth of application of HPC environments can be intimidating. There are many different users and workflows for every application.

This part of the documentation aims to provide some suitable examples to demonstrate the ease of establishing consistent workflows and the flexibility provided by the flight tools in assisting with workflow creation.

Traditionally, administrators handle a lot of workflow creation. From manually compiling applications all the way through to assisting users launching their workflows. With this in mind, these documents should be able to assist both admins and users to establish their own customised solutions with minimal disruption.

Flight Env Command Usage

Viewing Available Ecosystems

Various package-ecosystems are available for managing software on your research environment. These can be viewed by using the env subcommand:

flight env avail

Creating a Local Ecosystem

A local ecosystem is only available to the user that creates it. All of the packages and libraries are installed to the users home directory.

To install a package ecosystem, use the create command as follows (replacing easybuild with your desired package ecosystem):

flight env create easybuild

Once a package ecosystem has been installed, it needs to be activated for the session to be able to manage software with it:

[flight@chead1 (mycluster1) ~]$ flight env activate easybuild
<easybuild> [flight@chead1 (mycluster1) ~]$

Your preferred software ecosystem can be set to automatically activate for your user within the flight system by running flight env set-default easybuild, replacing easybuild with your chosen software ecosystem

Creating a Global Ecosystem

A global ecosystem is available to all users on the system. All of the packages and libraries are installed to a shared storage directory. The global directories can be configured in /opt/flight/opt/env/etc/config.yml with the global_depot_path: and global_build_cache_path keys.

The user requires suitable write permissions to the configured global depot paths in order to be able to create a global ecosystem

To install a global package ecosystem, use the create command with the global option flag:

flight env create -g easybuild

Once the global ecosystem has been installed, it needs to be activated for the session to be able to monitor software with it:

[root@chead1 (mycluster1) ~]$ flight env activate easybuild@global
<easybuild@global> [flight@chead1 (mycluster1) ~]$

Custom Ecosystem Names

When installing an ecosystem, a custom alias can be added by appending @mycustomname to the end of creation command. For example, to create a local gridware installation with the alias test:

flight env create easybuild@test

To activate this environment, the alias will need to be specified in the activation command:

[flight@chead1 (mycluster1) ~]$ flight env activate easybuild@test
<easybuild@test> [flight@chead1 (mycluster1) ~]$

Ecosystems

The Flight Env command provides streamlined installation of many popular software management ecosystems. These can be seen below along with the features they provide.

	Conda	Easybuild	Modules	Singularity	Spack
Dependency Management	✅	✅	❌	✅	✅
Compilation	✅	✅	❌	❌	✅
Preconfigured Binaries	❌	✅	❌	✅	◆
Multiple Versions	◆	✅	✅	✅	✅

More information on the features:

• Dependency Management - The ecosystem automatically resolves and installs dependencies
• Compilation - The ecosystem builds software from source for optimised functionality on the system (Note: these sorts of installations will take a long time)
• Preconfigured Binaries - The ecosystem provides binaries of the available software for quicker installation to get applications installed quickly
• Multiple Versions - The ecosystem allows for installation of multiple versions of software which can be toggled between

◆ is for partial support. Technically these features are supported in certain use cases and with additional work. This is not considered full support as multiple versions may require undocumented or uncommon use-cases of the tool

Conda Usage Example

Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.

Creating and Using Ecosystem

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

To install and use conda:

• Activate the flight system.
• Create the conda installation for the user:

[flight@chead1 ~]$ flight env create conda
Creating environment conda@default
   > ✅ Verifying prerequisites
   > ✅ Fetching prerequisite (miniconda)
   > ✅ Creating environment (conda@default)
Environment conda@default has been created

• Activate the conda ecosystem:

[flight@chead1 ~]$ flight env activate conda
(base) <conda> [flight@chead1 ~]$

• Check that conda can be run:

(base) <conda> [flight@chead1 ~]$ conda --version
conda 4.7.10

Installing and Running Perl

An example workflow using perl is demonstrated below.

• View available versions:

(base) <conda> [flight@chead1 ~]$ conda search perl
Loading channels: done
# Name                       Version           Build  Channel
perl                          5.26.0      hae598fd_0  pkgs/main
perl                          5.26.2      h14c3975_0  pkgs/main

• Install specific version:

(base) <conda> [flight@chead1 ~]$ conda install perl=5.26.2
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/flight/.local/share/flight/env/conda+default

  added / updated specs:
    - perl=5.26.2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.5.15  |                1         134 KB
    certifi-2019.6.16          |           py37_1         156 KB
    conda-4.7.11               |           py37_0         3.0 MB
    perl-5.26.2                |       h14c3975_0        10.5 MB
    ------------------------------------------------------------
                                           Total:        13.7 MB

The following NEW packages will be INSTALLED:

  perl               pkgs/main/linux-64::perl-5.26.2-h14c3975_0

The following packages will be UPDATED:

  ca-certificates                               2019.5.15-0 --> 2019.5.15-1
  certifi                                  2019.6.16-py37_0 --> 2019.6.16-py37_1
  conda                                       4.7.10-py37_0 --> 4.7.11-py37_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
conda-4.7.11         | 3.0 MB    | ############################################################################################ | 100%
certifi-2019.6.16    | 156 KB    | ############################################################################################ | 100%
perl-5.26.2          | 10.5 MB   | ############################################################################################ | 100%
ca-certificates-2019 | 134 KB    | ############################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
    Executing transaction: done

• Check installation location:

(base) <conda> [flight@chead1 ~]$ which perl
~/.local/share/flight/env/conda+default/bin/perl

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

(base) <conda> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Mon, 09 Sep 2019 15:17:03 GMT
Running install for module 'File::Slurp'
<-- snip -->

• Check installation worked:

(base) <conda> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Mon, 09 Sep 2019 15:17:03 GMT
File::Slurp is up to date (9999.27).

Easybuild Usage Example

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.

Creating and Using Ecosystem

Flight Env provides quick setup methods to create an easybuild software ecosystem.

To install and use easybuild:

• Activate the flight system
• Create the easybuild installation for the user:

[flight@chead1 ~]$ flight env create easybuild
Creating environment easybuild@default
   > ✅ Verifying prerequisites
   > ✅ Fetching prerequisite (lua)
   > ✅ Extracting prerequisite (lua)
   > ✅ Building prerequisite (lua)
   > ✅ Installing prerequisite (lua)
   > ✅ Fetching prerequisite (tcl)
   > ✅ Extracting prerequisite (tcl)
   > ✅ Building prerequisite (tcl)
   > ✅ Installing prerequisite (tcl)
   > ✅ Fetching prerequisite (lmod)
   > ✅ Extracting prerequisite (lmod)
   > ✅ Configuring prerequisite (lmod)
   > ✅ Installing prerequisite (lmod)
   > ✅ Fetching prerequisite (easybuild)
   > ✅ Bootstrapping EasyBuild environment (easybuild@default)
Environment easybuild@default has been created

• Activate the easybuild ecosystem:

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

• Check that easybuild can be run:

<easybuild> [flight@chead1 ~]$ module load EasyBuild
<easybuild> [flight@chead1 ~]$ eb --version
This is EasyBuild 3.9.4 (framework: 3.9.4, easyblocks: 3.9.4) on host chead1.pri.basic.cluster.local.

Installing and Running Perl

An example workflow using perl is demonstrated below.

• View available versions:

<easybuild> [flight@chead1 ~]$ eb -S perl
CFGS1=/home/flight/.local/share/flight/env/easybuild+default/software/EasyBuild/3.9.4/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.4-py2.7.egg/easybuild/easyconfigs
 * $CFGS1/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb
 * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-foss-2017b-Perl-5.26.0.eb
 * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-foss-2018b-Perl-5.28.0.eb
 * $CFGS1/b/Bio-DB-HTS/Bio-DB-HTS-2.11-intel-2017b-Perl-5.26.0.eb
<-- snip -->
 * $CFGS1/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb
 * $CFGS1/p/Perl/Perl-5.26.1-foss-2018a-bare.eb
 * $CFGS1/p/Perl/Perl-5.26.1-foss-2018a.eb
 * $CFGS1/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb
 * $CFGS1/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb
<-- snip -->
 * $CFGS1/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb
 * $CFGS1/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb

Note: 9 matching archived easyconfig(s) found, use --consider-archived-easyconfigs to see them

• Install specific version:

<easybuild> [flight@chead1 ~]$ eb Perl-5.28.1-GCCcore-8.2.0.eb --robot
== temporary log file in case of crash /tmp/eb-MdohD2/easybuild-J6tjhZ.log
== resolving dependencies ...
== processing EasyBuild easyconfig /home/flight/.local/share/flight/env/easybuild+default/software/EasyBuild/3.9.4/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.4-py2.7.egg/easybuild/easyconfigs/m/M4/M4-1.4.18.eb
== building and installing M4/1.4.18...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
<-- snip -->

• Check installation location:

<easybuild> [flight@chead1 ~]$ which perl

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

<easybuild> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Mon, 09 Sep 2019 15:47:03 GMT
Running install for module 'File::Slurp'
<-- snip -->

• Check installation worked:

<easybuild> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Mon, 09 Sep 2019 15:47:03 GMT
File::Slurp is up to date (9999.27).

Modules Usage Example

Modules provides simple environment management. Tools and software to be used with modules will be compiled or installed outside of the modules environment.

Creating and Using Ecosystem

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

To install and use modules:

• Activate the flight system
• Create the modules installation for the user:

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

• Activate the modules ecosystem:

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

• Check that modules can be run:

<modules> [flight@chead1 ~]$ module --version
Modules Release 4.3.0 (2019-07-26)

Installing Software - General Overview

Unlike the other package ecosystems, Modules provides the ecosystem management tool but not any package management tools. Therefore, with the Modules ecosystem, you are free to compile and install software in a Module compatible manner.

Module files can be installed to ~/.local/share/flight/env/modules+default/modulefiles (for local Modules ecosystems) or to /opt/apps/flight/env/modules+global/modulefiles (for global modules ecosystems).

If the Modules ecosystem has been installed with a custom ecosystem name then the path will not be modules+default/modules+global but instead modules+mycustomname

For more information on building software for Modules, see the modulefile reference and build documentation for the chosen software.

Installing and Running Perl

Compile Perl from Source

• Download perl 5.30.1 source:

<modules> [flight@chead1 ~]$ wget https://www.cpan.org/src/5.0/perl-5.30.1.tar.gz

• Decompress the source files:

<modules> [flight@chead1 ~]$ tar -xzf perl-5.30.1.tar.gz

• Configure the software to install to a localperl directory:

<modules> [flight@chead1 ~]$ cd perl-5.30.1
<modules> [flight@chead1 ~]$ ./Configure -des -Dprefix=$HOME/localperl

• Compile and install perl:

<modules> [flight@chead1 ~]$ make
<modules> [flight@chead1 ~]$ make install

Create Modulefile and Test

• Create the perl modulefile:

<modules> [flight@chead1 ~]$ cat << EOF > ~/.local/share/flight/env/modules+default/modulefiles/perl-5.30.1
#%Module1.0
proc ModulesHelp { } {
global dotversion

puts stderr "\tPerl 5.30.1"
}

module-whatis "Perl 5.30.1"
conflict perl
prepend-path PATH ~/localperl/bin
prepend-path LD_LIBRARY_PATH ~/localperl/lib
prepend-path LIBRARY_PATH ~/localperl/lib
prepend-path MANPATH ~/localperl/man
EOF

• Check install location:

<modules> [flight@chead1 ~]$ module load perl-5.30.1
<modules> [flight@chead1 ~]$ which perl
~/localperl/bin/perl

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

<modules> [flight@chead1 ~]$ cpan File::Slurp
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Mar 2020 15:29:03 GMT
<-- snip -->
Appending installation info to /home/flight/localperl/lib/5.30.1/x86_64-linux/perllocal.pod
  CAPOEIRAB/File-Slurp-9999.30.tar.gz
  /usr/bin/make install  -- OK

• Check installation worked:

<modules> [flight@chead1 ~]$ cpan File::Slurp
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Mar 2020 15:29:03 GMT
File::Slurp is up to date (9

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:

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.

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).

Spack Usage Example

Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

Creating and Using Ecosystem

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

To install and use spack:

• Activate the flight system
• Create the spack installation for the user:

[flight@chead1 ~]$ flight env create spack
Creating environment spack@default
   > ✅ Verifying prerequisites
   > ✅ Fetching prerequisite (spack)
   > ✅ Extracting Spack hierarchy (spack@default)
   > ✅ Bootstrapping Spack environment (spack@default)
Environment spack@default has been created

• Activate the spack ecosystem:

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

• Check that spack can be run:

<spack> [flight@chead1 ~]$ spack --version
spack 0.12.1

Installing and Running Perl

An example workflow using perl is demonstrated below.

• View available versions:

<spack> [flight@chead1 ~]$ spack list perl
==> 148 packages.
perl                          perl-extutils-pkgconfig     perl-math-cdf                    perl-sub-uplevel
perl-algorithm-diff           perl-file-copy-recursive    perl-math-cephes                 perl-svg
perl-app-cmd                  perl-file-listing           perl-math-matrixreal             perl-swissknife
perl-array-utils              perl-file-pushd             perl-module-build                perl-task-weaken
perl-b-hooks-endofscope       perl-file-sharedir-install  perl-module-implementation       perl-term-readkey
<-- snip -->

<spack> [flight@chead1 ~]$ spack info perl
Package:   perl

Description:
    Perl 5 is a highly capable, feature-rich programming language with over
    27 years of development.

Homepage: http://www.perl.org

Tags:
    None

Preferred version:
    5.26.2     http://www.cpan.org/src/5.0/perl-5.26.2.tar.gz

Safe versions:
    5.28.0     http://www.cpan.org/src/5.0/perl-5.28.0.tar.gz
    5.26.2     http://www.cpan.org/src/5.0/perl-5.26.2.tar.gz

• Install specific version:

<spack> [flight@chead1 ~]$ spack install perl@5.26.2
==> Installing pkgconf
==> Searching for binary cache of pkgconf
==> Warning: No Spack mirrors are currently configured
==> No binary for pkgconf found: installing from source
==> Fetching http://distfiles.alpinelinux.org/distfiles/pkgconf-1.4.2.tar.xz
<-- snip -->
==> Successfully installed perl
  Fetch: 0.83s.  Build: 2m 31.21s.  Total: 2m 32.04s.
[+] /home/flight/.local/share/flight/env/spack+default/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.26.2-wavwojlef7lshvx2awf4zze2lrx5l7l4

• Check installation location:

<spack> [flight@chead1 ~]$ module load perl-5.26.2-gcc-4.8.5-wavwojl
<spack> [flight@chead1 ~]$ which perl
~/.local/share/flight/env/spack+default/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.26.2-wavwojlef7lshvx2awf4zze2lrx5l7l4/bin/perl

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

<spack> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Sep 2019 14:41:02 GMT
Running install for module 'File::Slurp'
<-- snip -->

• Check installation worked:

<spack> [flight@chead1 ~]$ cpan File::Slurp
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/flight/.cpan/Metadata'
  Database was generated on Wed, 11 Sep 2019 14:41:02 GMT
File::Slurp is up to date (9999.27).