MATLAB Components/Toolboxes

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

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.

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.