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    The following points are related to the installation of software for use on the HPC cluster or compute VMs.
    1. Generally, software is installed/upgraded upon request only.
    2. The latest stable version of the requested software will be installed unless a specific version is provided.
    3. HPC will generally only hold two (2) versions of any given software at any given time.  In some cases, it is only possible to have one version of a given piece of software installed.  Researchers should contact HPC after they have successfully tested new software (even if only an upgrade) to confirm that it either works or isn't working as expected.
    4. Software will not be installed/upgraded if there is a risk of system/service failure afterward.  For example, overwriting the OS distributed perl or python with an unsupported version will likely lead to a "broken" system.
    5. A snapshot of installed software (Jan-2012) is given below. A better method of determining what software is available is to ssh to zodiac.hpc.jcu.edu.au and issue one of the following commands:

      Command

      Result

      module avail

      A list of available software is displayed

      module help <software>

      Version number and brief synopsis is displayed for <software>

    6. The environment for a given software package is generally setup using the command:

      module load <software>
    1. Environment module files are located in /sw/modules
    2. Most scientific software is installed in /sw/<software>/<version>/
    3. Components used by programmers (e.g., stand-alone libraries) are generally installed in /sw/common/
      Installation of frequently required libraries is additionally done onto local system disks (using yum), if libraries are available in repositories.
    4. Live upgrades of software should only be performed when no login/compute node is using the software. Compute nodes should be reimaged rather than have live upgrades performed. The login node may need to be live upgraded, due to jobs always running on this system.
    5. Some packages (e.g., BLCR) are rebuilt from source RPMs.  BLCR, in particular, needs to be recompiled for each new kernel installed.

    The following table provides information about operating systems used on physical servers managed (in some way) by HPC staff.

    Operating SystemPrimary service(s) providedTypically accessed from
    RedHat Enterprise Linux 6.x

    HPC login nodes

    HPC compute nodes

    Desktop or Laptop computers

    HPC login nodes

    SUSE Linux Enterprise Server 11.x

    CIFS fileshares

    NFS fileshares

    Desktop or Laptop computers

    HPC login and compute nodes

    Windows 2012 ServerCIFS filesharesDesktop or Laptop computers (Cairns)

    Vendors usually require an enterprise O/S be installed on physical servers if you have purchased maintenance.

    JCU researchers wishing to host servers/storage in a datacentre must contact ITR management before purchasing is even considered.

    All virtual machines (VMs) offered by HPC are, by default, provided as Infrastructure as a Service (IaaS).  VM owners are responsible for daily maintenance operations on their VMs.  For security reasons, all systems are registered for application of automatic updates.  HPC staff will apply patches/updates (from RedHat and EPEL repositories only) to VMs where the automatic update process fails.

    Internal (conducted by ITR) and external security audits take place on all publicly visible systems at times determined by ITR management.  VM owners are responsible for fixing any security concerns identified in these audits.  HPC staff may be consulted or be asked to provide assistance with such fixes.

    Software Catalogue

      Software

      Access Command

      Related Website

      4ti2

      module load 4ti2

      http://www.4ti2.de/

      Software

      Access Command

      Related Website

      ABySS

      module load abyss

      http://www.bcgsc.ca/platform/bioinfo/software/abyss

      ariadne

      module load ariadne

      http://www.well.ox.ac.uk/ariadne/

      Arlequin

      module load arlequin

      http://anthro.unige.ch/software/arlequin/software/

      ASAP

      module load asap

      http://svn.atnf.csiro.au/trac/asap

      ATLAS

       

      http://math-atlas.sourceforge.net

      Software

      Access Command

      Related Website

      DX

       

      http://www.opendx.org/index2.php

      Software

      Access Command

      Related Website

      DX

       

      http://www.opendx.org/index2.php

      ELPH

       

      http://www.cbcb.umd.edu/software/ELPH/

      EMBOSS

      module load EMBOSS

      http://emboss.sourceforge.net/

      ENMTools

      module load enmtools

      http://enmtools.blogspot.com/

      Software

      Access Command

      Related Website

      fasta

      module load fasta

      http://www.csc.fi/english/research/sciences/bioscience/programs/fasta/fasta3x.doc

      fastme

      module load fastme

      http://atgc.lirmm.fr/fastme/

      fftw

       

      http://www.fftw.org/

      Software

      Access Command

      Related Website

      HDF

       

      http://www.hdfgroup.org/

      hmmer

       

      http://hmmer.wustl.edu

      Software

      Access Command

      Related Website

      IMa2

      module load ima2

      http://genfaculty.rutgers.edu/hey/software#IMa2

      Software

      Access Command

      Related Website

      jmodeltest

      module load jmodeltest

      http://darwin.uvigo.es/software/jmodeltest.html

      MATLAB Components/Toolboxes

      Component

      License allows

      Toolbox

      License allows

      MATLAB

      50 user connections

      Control System

      50 user connections

      MATLAB Coder

      50 user connections

      Optimization

      50 user connections

      Simulink

      50 user connections

      Signal Processing

      50 user connections

      Simulink Coder

      50 user connections

      Symbolic Math

      50 user connections

      Simulink Control Design

      50 user connections

      System Identification

      50 user connections

       

       

      Mapping

      5 user connections

       

       

      Neural Network

      5 user connections

       

       

      Statistics

      5 user connections

       

       

      Distributed Computing

      4 user connections

       

       

      Fuzzy Logic

      4 user connections

       

       

      Global Optimization

      4 user connections

       

       

      Image Processing

      4 user connections

       

       

      MATLAB Compiler

      4 user connections

       

       

      Wavelet

      4 user connections

      Software

      Access Command

      Related Website

      oases

      module load oases

      http://www.ebi.ac.uk/~zerbino/oases/

      octave

       

      http://www.gnu.org/software/octave/

      ogdi

       

      http://ogdi.sourceforge.net/

      openmpi

      module load openmpi

      http://www.open-mpi.org/

      Software

      Access Command

      Related Website

      pari

      module load pari

      http://pari.math.u-bordeaux.fr/

      paup

      module load paup

      http://paup.csit.fsu.edu/

      proj

       

      http://proj.osgeo.org

      pvm

      module load pvm

      http://www.epm.ornl.gov/pvm/pvm_home.html

      Software

      Access Command

      Related Website

      R

      module load R

      http://www.r-project.org/

      r8s

      module load r8s

      http://loco.biosci.arizona.edu/r8s/

      RainbowCrack

      module load rainbowcrack

      http://www.project-rainbowcrack.com/

      RPFITS

      module load rpfits

      http://www.atnf.csiro.au/computing/software/rpfits.html

      R Packages

      A: abind, acepack, actuar, ade4, ade4TkGUI, adehabitat, AER, akima, alr3, anchors, ape
      B: base, bdsmatrix, biglm, BIOMOD, Biobase, bitops, boot, BufferedMatrix
      C: car, caTools, chron, CircStats, class, clim.pact, cluster, coda, codetools, coin, colorspace, compiler, CompQuadForm, coxme, cubature
      D: DAAG, datasets, DBI, degreenet, deldir, Design, digest, diptest, DynDoc, dynlm
      E: e1071, Ecdat, effects, ellipse, ergm, evaluate, expm
      F: fBasics, fCalendar, fEcofin, fields, flexmix, foreach, foreign, Formula, fSeries, fts, fUtilities
      G: gam, gbm, gclus, gdata, gee, geoR, geoRglm, ggplot2, gpclib, gplots, graphics, grDevices, grid, gtools
      H: hdf5, hergm, hexbin, Hmisc, HSAUR
      I: igraph, ineq, inline, ipred, iquantitator, ISwR, iterators, itertools, its
      K: kernlab, KernSmooth, kinship
      L: latentnet, lattice, leaps, limma, lme4, lmtest, locfit, logspline
      M: mapproj, maps, maptools, mAr, marray, MASS, Matrix, matrixcalc, MatrixModels, maxLik, mboost, mclust, MCMCpack, mda, MEMSS, methods, mgcv, mice, misc3d, miscTools, mitools, mix, mlbench, mlmRev, mlogit, modeltools, moments, MPV, msm, multcomp, multicore, mutatr, mvtnorm
      N: ncdf, network, networksis, nlme, nnet, nor1mix, np, numDeriv, nws
      O: oz
      P: parallel, party, PBSmapping, permute, pixmap, plm, plyr, png, prabclus, proto, pscl
      Q: qtl, quadprog, quantreg
      R: RandomFields, randomForest, RANN, RArcInfo, raster, rbenchmark, rcolony, RColorBrewer, Rcpp, RcppArmadillo, ReadImages, relevent, reshape, rgdal, rgenoud, rgeos, rgl, Rglpk, rjags, rlecuyer, rmeta, robustbase, ROCR, RODBC, rpanel, rpart, RSQLite, RUnit
      S: sampleSelection, sandwich, scatterplot3d, SDMTools, sem, sfmisc, sgeostat, shapefiles, shapes, slam, sm, sna, snow, snowFT, sp, spam, SparseM, spatial, SpatialTools, spatstat, spdep, splancs, splines, statmod, statnet, stats, stats4, stringr, strucchange, subselect, survey, survival, systemfit
      T: tcltk, tcltk2, TeachingDemos, testthat, timeDate, timeSeries, tis, tkrplot, tools, tree, tripack, truncreg, trust, TSA, tseries, tweedie
      U: urca, utils
      V: vcd, vegan, VGAM, VIM
      W: waveslim, wavethresh, widgetTools
      X: XML, xtable, xts
      Z: Zelig, zoeppritz, zoo

       

      Software

      Access Command

      Related Website

      TargetP

      module load targetp

      http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=targetp

      TMAP

      module load tmap

      http://math.berkeley.edu/~dustin/tmap/

      TMHMM

      module load tmhmm

      http://www.cbs.dtu.dk/services/TMHMM-2.0/TMHMM2.0b.guide.php

      TOPALi

      module load topali

      http://www.topali.org/

      Towhee

      module load openmpi

      http://towhee.sourceforge.net/

      trans-ABySS

      module load trans-abyss

      http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

      Trinitymodule load trinityrnaseqhttp://trinityrnaseq.sourceforge.net/

      Software

      Access Command

      Related Website

      UDUNITS

       

      http://www.unidata.ucar.edu/software/udunits/

      Software

      Access Command

      Related Website

      Velvet

      module load velvet

      http://www.ebi.ac.uk/~zerbino/velvet/

      Software

      Access Command

      Related Website

      WCSLIB

      module load wcslib

      http://www.atnf.csiro.au/people/Mark.Calabretta/WCS/index.html

      Wine

       

      http://www.winehq.org/

      Wise2

      module load wise2

      http://www.ebi.ac.uk/Tools/Wise2/doc_wise2.html

      wwatch3

      module load wwatch3

       

      Software

      Access Command

      Related Website

      Xfig

       

      http://epb.lbl.gov/xfig/

      Software

      Access Command

      Related Website

      yasm

      module load yasm

      http://yasm.tortall.net/

      Software

      Enabling Command

      zlibmodule load zlib

      zonation

      module load zonation

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