We recommend all Phoenix users to contact us at the first instance for application enquiries. However, we are aware the diverse research requirement from various disciplines across the university, we are here to recommend a mechanism for our advanced cluster users to allow you to bypass the Phoenix administration to install many open source packages for your own research purposes. We are appreciate if you inform us your required packages at the first instance to allow us to provide the same packages access to other researchers.
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Installing Applications on the cluster[edit | edit source]
Phoenix cluster administrators use EasyBuild tool to install applications in a safe and reproducible fashion. You can also use this tool to install your required packages locally (in your home directory) for your own usage.
Loading EasyBuild[edit | edit source]
In order to use EasyBuild, you must load the module first:
> module load EasyBuild > eb --version This is EasyBuild 2.5.0 (framework: 2.5.0, easyblocks: 2.5.0) on host l01.phoenix.adelaide.edu.au
EasyBuild can easily install an application using a configure file for it. In many cases there is a configure file ready to use.
Now, it is time to install an application! e.g. We want to install Lua programming language. These are the steps to do so.
Searching with EasyBuild[edit | edit source]
Search for Lua configuration:
> eb -S Lua
The search result is:
== temporary log file in case of crash /tmp/eb-Tx0A_g/easybuild-Up59LX.log == Searching (case-insensitive) for 'lua' in /apps/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs CFGS1=/apps/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs/l
* $CFGS1/Lua/Lua-5.1.4-5-GCC-4.7.2.eb * $CFGS1/Lua/Lua-5.1.4-5-GCC-4.8.2.eb * $CFGS1/Lua/Lua-5.1.4-5-goolf-1.4.10.eb * $CFGS1/Lua/Lua-5.1.4-8-GCC-4.8.2.eb * $CFGS1/Lua/Lua-5.1.4-8-GCC-4.8.4.eb * $CFGS1/LuaJIT/LuaJIT-2.0.2-GCC-4.9.2.eb * $CFGS1/likwid/likwid-4.0.1-config-and-lua.patch
== Temporary log file(s) /tmp/eb-Tx0A_g/easybuild-Up59LX.log* have been removed. == Temporary directory /tmp/eb-Tx0A_g has been removed.
We have found 5 different versions of configuration files to install Lua. We can realise that there are two versions of lua: 5.1.4-5 and 5.1.4-8, and different toolchains.
To check any further dependency, it is a good practice first see the dependencies before installing. The argument -Dx does that:
> eb Lua-5.1.4-8-GCC-4.8.4.eb -Dx
== temporary log file in case of crash /tmp/eb-qlHVTV/easybuild-UivGqc.log Dry run: printing build status of easyconfigs and dependencies CFGS=/apps/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs * [ ] $CFGS/g/GCC/GCC-4.8.4.eb (module: GCC/4.8.4) * [ ] $CFGS/n/ncurses/ncurses-5.9-GCC-4.8.4.eb (module: ncurses/5.9-GCC-4.8.4) * [ ] $CFGS/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb (module: Lua/5.1.4-8-GCC-4.8.4) == Temporary log file(s) /tmp/eb-qlHVTV/easybuild-UivGqc.log* have been removed. == Temporary directory /tmp/eb-qlHVTV has been removed. > eb Lua-5.1.4-8-GCC-4.8.4.eb -Dx
The result shows that for installing lua using GCC-4.8.4 we need to install 2 additional applications. We need the GCC version 4.8.4 and ncurses library version 5.9. We can search what we actually have:
> module avail GCC GCC/4.9.3-binutils-2.25 GCC/5.1.0-binutils-2.25 > module avail ncurses ncurses/5.9-foss-2015b ncurses/5.9-intel-2015c
First of all, ncurses has been built by foss-2015b toolchain, which is the defacto toolchain on Phoenix. Therefore, we need to write a customised configuration to use foss/2015b as toolchain, but not from scratch. We can modify the found configuration:
Writing a configuration EasyBuild file[edit | edit source]
EasyBuild comes with many configuration files. They are located at: /apps/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs/. We can define a variable to help us:
> export EASYCONFIGHOME=/apps/software/EasyBuild/2.5.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.5.0-py2.7.egg/easybuild/easyconfigs/
> cp $EASYCONFIGHOME/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb Lua-5.1.4-8-foss-2015b.eb
Now we have a configuration file for Lua and foss toolchain, but we need to change its content. The copied file looks like:
easyblock = 'ConfigureMake'
name = "Lua"
version = "5.1.4-8"
homepage = "http://www.lua.org/"
description = """Lua is a powerful, fast, lightweight, embeddable scripting language.
Lua combines simple procedural syntax with powerful data description constructs based
on associative arrays and extensible semantics. Lua is dynamically typed,
runs by interpreting bytecode for a register-based virtual machine,
and has automatic memory management with incremental garbage collection,
making it ideal for configuration, scripting, and rapid prototyping."""
toolchain = {'name': 'GCC', 'version': '4.8.4'}
sources = ['lua-%s.tar.gz' % version.replace('-', '.')]
source_urls = ['http://sourceforge.net/projects/lmod/files/']
dependencies = [('ncurses', '5.9')]
sanity_check_paths = {
'files': ["bin/lua"],
'dirs': []
}
moduleclass = "lang"
After we have modified toolchain, the final version should look like:
easyblock = 'ConfigureMake'
name = "Lua"
version = "5.1.4-8"
homepage = "http://www.lua.org/"
description = """Lua is a powerful, fast, lightweight, embeddable scripting language.
Lua combines simple procedural syntax with powerful data description constructs based
on associative arrays and extensible semantics. Lua is dynamically typed,
runs by interpreting bytecode for a register-based virtual machine,
and has automatic memory management with incremental garbage collection,
making it ideal for configuration, scripting, and rapid prototyping."""
toolchain = {'name': 'foss', 'version': '2015b'}
sources = ['lua-%s.tar.gz' % version.replace('-', '.')]
source_urls = ['http://sourceforge.net/projects/lmod/files/']
dependencies = [('ncurses', '5.9')]
sanity_check_paths = {
'files': ["bin/lua"],
'dirs': []
}
moduleclass = "lang"
Installation[edit | edit source]
Now we can install the Lua in our personal home directory:
eb Lua-5.1.4-8-foss-2015b.eb
The installation output indicates what is going on...
== temporary log file in case of crash /tmp/eb-2LqRWW/easybuild-vCljJ5.log == processing EasyBuild easyconfig /home/a1634120/eb_tutorial/Lua-5.1.4-8-foss-2015b.eb == building and installing Lua/5.1.4-8-foss-2015b... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == testing... == installing... == taking care of extensions... == postprocessing... == sanity checking... == cleaning up... == creating module... == permissions... == packaging... == COMPLETED: Installation ended successfully == Results of the build can be found in the log file /home/a1634120/.local/easybuild/software/Lua/5.1.4-8-foss-2015b/easybuild/easybuild-Lua-5.1.4-8-20160303.110938.log == Build succeeded for 1 out of 1 == Temporary log file(s) /tmp/eb-2LqRWW/easybuild-vCljJ5.log* have been removed. == Temporary directory /tmp/eb-2LqRWW has been removed.
EasyBuild download the source files, load the toolchain, configure, build and install the application. Easy! The local installation directory is ~/.local/easybuild/
To use locally installed packages
module use ~/.local/easybuild/modules/all module load Lua