Cluster Software

This is a list of some of the major software installed on the cluster. Ask us if there is something that you need - it may already be on the cluster or we may be able to install it for you.

You can copy/compile/load your own code under your home directory for testing. This is immediately available across all the nodes.

This list updated: Monday, 26 June 2017

Editors

Package & Version Description Homepage URL
emacs   23.1 GNU Emacs text editor emacs
gedit   2.28.4 Text editor for the GNOME desktop gedit
nano   2.0.9 A small text editor nano
vim-enhanced   7.4.629 A version of the VIM editor which includes recent enhancements vim-enhanced

Version Control

Package & Version Description Homepage URL
bzr   2.1.1 Friendly distributed version control system bzr
cvs   1.11.23 A version control system cvs
git   1.7.12.4 Git core and tools git
subversion   1.6.11 A Modern Concurrent Version Control System subversion

Misc

Package & Version Description Homepage URL
dos2unix   3.1 Text file format converter  #
environment-modules   3.2.10 Provides dynamic modification of a user's environment environment-modules
gnuplot   4.2.6 A program for plotting mathematical expressions and data gnuplot
graphviz   2.26.0 Graph Visualization Tools graphviz
GraphicsMagick   1.3.25 An ImageMagick fork, offering faster image generation and better quality GraphicsMagick
ImageMagick   6.7.2.7 An X application for displaying and manipulating images ImageMagick
parallel   20141022 Shell tool for executing jobs in parallel parallel
rsync   3.0.6 A program for synchronizing files over a network rsync
sqlite   3.6.20 Library that implements an embeddable SQL database engine sqlite

Science

Package & Version Description Homepage URL
abinit-static   7.2.2 Full-featured atomic-scale first-principles simulation software abinit-static
BEDTools   2.15.0 A flexible suite of utilities for comparing genomic features BEDTools
blast   2.2.22 Legacy Blast from NCBI blast
bowtie1   1.0.0 An ultrafast, memory-efficient short read aligner bowtie1
bowtie2   2.1.0 An ultrafast, memory-efficient short read aligner bowtie2
ddscat   7.2.2 Calculating scattering and absorption of light by irregular particles Notes ddscat
fastqc   0.10.1 A quality control tool for high throughput sequence data. Notes fastqc
fasttree   2.1.3 FastTree -- inferring approximately-maximum-likelihood trees for large multiple sequence alignments fasttree
fastx_toolkit   0.0.13 FASTQ/A short-reads pre-processing tools fastx_toolkit
fftw   3.2.1 Fast Fourier Transform library fftw
fftw2   2.1.5 Fast Fourier Transform library (version 2) fftw2
flowgram_alignment   1.5.0 Flowgram Alignment is from the Qiime package flowgram_alignment
gdal   1.8.1 GIS file format library gdal
hdf   4.2.5 A general purpose library and file format for storing scientific data hdf
hdf5   1.8.5.patch1 A general purpose library and file format for storing scientific data hdf5
hmmer   3.1b2 HMMER: biosequence analysis using profile hidden Markov models. hmmer
lapack   3.2.1 Numerical linear algebra package libraries lapack
munkres   1.0.5.4 munkres algorithm for the Assignment Problem munkres
netcdf   4.1.1 Libraries for the Unidata network Common Data Form netcdf
proj   4.7.0 Cartographic projection software (PROJ.4) proj
proj-epsg   4.7.0 EPSG dataset for PROJ.4 proj-epsg
proj-nad   4.7.0 US and Canadian datum shift grids for PROJ.4 proj-nad
qhull   2003.1 General dimension convex hull programs qhull
rdp_classifier   2.2 RDP Classifier is a naive Bayesian classifier for taxonomic assignments rdp_classifier
samtools   0.1.18 Tools for nucleotide sequence alignments in the SAM format samtools
staden-io_lib   1.12.4 General purpose library to handle gene sequencing machine trace files staden-io_lib
siesta   462 Performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. siesta
shrimp   2.2.3 Software package for aligning genomic reads against a target genome. shrimp
trinity   2012_06_08 RNA-Seq De novo Assembly trinity
uclust   1.2.22 UCLUST is from the Qiime package uclust
usearch   5.2.32 High-throughput search and clustering usearch
viennarna   2.3.1 RNA Secondary Structure Prediction and Comparison viennarna

Languages and Debugging Tools

Package & Version Description Homepage URL
java-1.6.0-openjdk   1.6.0.41 OpenJDK Runtime Environment java-1.6.0-openjdk
java-1.7.0-openjdk   1.7.0.141 OpenJDK Runtime Environment java-1.7.0-openjdk
numpy   1.7.1 A fast multidimensional array facility for Python numpy
octave   3.4.3 A high-level language for numerical computations octave
perl   5.10.1 Practical Extraction and Report Language perl
python   2.6.6 An interpreted, interactive, object-oriented programming language python
python27   1 Package that installs python27  #
python33   1 Package that installs python33  #
R-core   3.4.0 The minimal R components necessary for a functional runtime R-core
rpy2   2.3.6 Python interface to the R language rpy2
ruby   1.8.7.374 An interpreter of object-oriented scripting language ruby
scipy   0.12.0 Scipy: Scientific Tools for Python scipy
sqlite   3.6.20 Library that implements an embeddable SQL database engine sqlite
tbb   2.2 The Threading Building Blocks library abstracts low-level threading details tbb
valgrind   3.8.1 Tool for finding memory management bugs in programs valgrind

Compilers and Libraries

Package & Version Description Homepage URL
armadillo   4.550.2 Fast C++ matrix library with interfaces to LAPACK and ATLAS armadillo
armadillo-devel   4.550.2 Development headers and documentation for the Armadillo C++ library armadillo-devel
arpack   3.1.3 Fortran 77 subroutines for solving large scale eigenvalue problems arpack
atlas   3.8.4 Automatically Tuned Linear Algebra Software atlas
atlas-devel   3.8.4 Development libraries for ATLAS atlas-devel
blacs-openmpi   2.0.2 BLACS libraries compiled against openmpi blacs-openmpi
blas   3.2.1 The Basic Linear Algebra Subprograms library blas
fftw   3.2.1 Fast Fourier Transform library fftw
fpc   2.4.0 Free Pascal Compiler fpc
gcc   4.4.7 Various compilers (C, C++, Objective-C, Java, ...) gcc
gcc-gfortran   4.4.7 Fortran support gcc-gfortran
gcc-c++   4.4.7 C++ support for GCC gcc-c++
lapack   3.2.1 Numerical linear algebra package libraries lapack
lapack-devel   3.2.1 LAPACK development libraries lapack-devel
mpfr   2.4.1 A C library for multiple-precision floating-point computations mpfr
openblas   0.2.19 An optimized BLAS library based on GotoBLAS2 openblas
QuantLib-devel   1.0.1 QuantLib development files QuantLib-devel
qrupdate   1.1.2 A Fortran library for fast updates of QR and Cholesky decompositions qrupdate
scalapack-openmpi   2.0.2 ScaLAPACK libraries compiled against openmpi scalapack-openmpi
suitesparse   3.4.0 A collection of sparse matrix libraries suitesparse