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HPC Software

As of mid May 2021, the CQUniversity High Performance Computing system adopted the use of the easybuild HPC software building tool.  “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.” [https://easybuild.io/ - 22nd June 2021].

Since the installation of easybuild on the HPC system, over 160+ software packages have been installed within the first two month of being implemented – with over 660+ differing applications and versions of the same software being installed.  Due to not wanting easybuild software modules interfering with legacy or manually built HPC software, easybuild software modules are found in a different location on CQUniversity’s HPC facility.  Thus, if you were to issue the following command on the HPC system:

module avail

you would notice that legacy or manually built HPC software are located in

/apps/modules/modulefiles

whereas easybuild software modules are located in

/apps/easybuild/modules/all

Thus, if you are wanting to locate a particular software package, you will need to look at both lists to determine if it is available on the HPC system.

One thing you will notice is with Easybuild software is that to load it is slightly different to our legacy system.  To load software that has been created from easybuild, you will need to use the following syntax:

module load <Application Name>/<Version Number>

or

module load <Application Name>/<Version Number><-Tool Chain>

rather than just module load python, etc.

Note: some of the packages names are in Uppercase!

Due to the shear number of applications being installed via easybuild, a list of software install list is no longer manageable to detail on this website.  That being said, a list of legacy and manually installed software can be selected from the list below:

Software list

Bioinformatics
  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
Compilers
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
Data Mining and Analysis Applications
  • NCL (NCAR Command Language)
  • Ncview
  • NetCDF
  • NetCDF-Fortran
  • RapidMiner
  • STIR (Tomographic Imaging)
  • Weka
Development tools
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
Documentation Tools
  • Tex Live
  • Tex Info
Engineering Applications
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
Geospatial Tools
  • GDAL
  • GEOS
  • Panoply
Graphics Applications
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
Interpreters
  • Perl
  • Python (with many Modules Installed)
Mathematics and Statics
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
Run Time Environments
  • Java
Simulation Software
  • APSIM
Software Libraries
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS
Text Tools and Software
  • Flex