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The systems at the C entre for Advance Computing have a large amount of software pre-installed for use on our clusters. Here we give an overview of software installed on the Linux platform (CentOS). Note that software that was installed for the Solaris platform is not documented here, as that platform is being discontinued.


Table of Software on the Linux (CentOS) Platform

The following software can be accessed from the swlogin1 (login) node or through the abaqus.q queue of the Grid Engine scheduler. Most software may be accessed through usepackage entries which add software and libraries to your $PATH. As an example, "use anaconda3" replaces the default version of Python with the copy of Python provided by Anaconda. Which copy of software you are using may be verified with "which X", where X is the name of the executable. Note that some package entries are purely short cuts provided for convenience, and will add the default version of that software to your $PATH. The entries these short cuts "point to" are indicated in the "Points To" column.

NOTE: Unless explicitly specified here, it is generally best to run software using the usepackage entries (i.e. "use xxxxxxx") instead of attempting to call the software directly from its absolute location in /opt. The reason for this is that "use xxxxxxx" often loads required dependencies.

Software Name / Version Package Name Points To Usage Notes
Abaqus 64 bit current version abaqus abaqus-6.11 use abaqus
More information
Abaqus 6.10 64-bit version abaqus-6.10 use abaqus-6.10
More information
Abaqus 6.11 64-bit version abaqus-6.11 use abaqus-6.11
More information
Abinit (current version) 64 bit Abinit Abinit6.12.3_32bit use Abinit
More information
Abinit software (version 6.12.3, 32-bit) Abinit6.12.3_32bit use Abinit6.12.3_32bit
More information
Abinit software (version 6.12.3, 64-bit) Abinit6.12.3_64bit use Abinit6.12.3_64bit
More information
ABySS 1.9.0 abyss use abyss
AllPaths-LG (current version) allpaths-lg allpaths-lg-52488 use allpaths-lg
More information
AllPaths-LG (version 52488) allpaths-lg-52488 use allpaths-lg-52488
More information
Anaconda Python 2 distribution (includes numpy & scipy) anaconda2 anaconda20 use anaconda2
Anaconda Python 2 distribution (includes numpy & scipy) anaconda20 use anaconda20
Anaconda Python 3 distribution (includes numpy & scipy) anaconda3 use anaconda3
Fluent (Ansys 14 on Linux) ansys14 use ansys14
More information
Fluent (Ansys 16 on Linux) ansys16 use ansys16
More information
Autodock current version autodock autodock425 use autodock
Autodock 4.2.5 64-bit version autodock425 use autodock425
Initial Settings basic use basic
BEAST (current version) beast beast-1.8.2 use beast
BEAST 1.8.2 beast-1.8.2 use beast-1.8.2
BioPython Python package BioPython "use anaconda2"
BioScripts Python package BioScripts "use anaconda2" OR "use anaconda3"
Blast current version blast blast-2.2.30 use blast
More information
Blast 2.2.30+ blast-2.2.30 use blast-2.2.30
More information
Bowtie (VERSION 1!!!) bowtie bowtie-1.1.2 use bowtie
Bowtie 1.1.2 bowtie-1.1.2 use bowtie-1.1.2
Bowtie2 (current version) bowtie2 bowtie2-2.2.6 use bowtie2
Bowtie2 2.2.6 bowtie2-2.2.6 use bowtie2-2.2.6
BWA (current version) bwa bwa-0.7.12 use bwa
BWA 0.7.12 bwa-0.7.12 use bwa-0.7.12
CPMD (current version) 32 bit CPMD CPMD3.13.2_32bit use CPMD
More information
CPMD software (version 3.13.2, 32-bit) CPMD3.13.2_32bit use CPMD3.13.2_32bit
More information
CPMD software (version 3.13.2, 64-bit) CPMD3.13.2_64bit use CPMD3.13.2_64bit
More information
CPMD (current version) 64 bit CPMD_64bit use CPMD_64bit
More information
Cufflinks (current version) cufflinks cufflinks-2.2.1 use cufflinks
Cufflinks 2.2.1 cufflinks-2.2.1 use cufflinks-2.2.1
Cutadapt Cutadapt "use anaconda3" or "use anaconda2"
Discovar De Novo (current version) discovar-denovo discovar-denovo-52488 use discovar-denovo
Discovar De Novo (version 52488) discovar-denovo-52488 use discovar-denovo-52488
ESPReSso (current version) 32 bit espresso espresso3.1.1_32bit use espresso
ESPReSso software (version 3.1.1, 32-bit) espresso3.1.1_32bit use espresso3.1.1_32bit
ESPReSso software (version 3.1.1, 64-bit) espresso3.1.1_64bit use espresso3.1.1_64bit
ESPReSso (current version) 64 bit espresso_64bit use espresso_64bit
FastQC (current version) fastqc fastqc-0.11.4 use fastqc
FastQC 0.11.4 fastqc-0.11.4 use fastqc-0.11.4
FastX current version fastx fastx-0.0.13 use fastx
FastX 0.0.13 (64 bit) fastx-0.0.13 use fastx-0.0.13
FBAT 2.0.4 fbat-2.0.4 use fbat-2.0.4
Fire Dynamic Simulator (version 6) fds use fds
FoamExtend (current version) foam-extend foam-extend-3.1 use foam-extend
FoamExtend 3.1 foam-extend-3.1 use foam-extend-3.1
FreeFem++ current version freefem freefem-3.44 use freefem
More information
FreeFem++ 3.36-1 freefem-3.36 use freefem-3.36
More information
FreeFem++ 3.44 freefem-3.44 use freefem-3.44
More information
FreeSurfer freesurfer use freesurfer
More information
FSL 5.0.9 fsl use fsl
More information
Gamess (Dec 5 2014) gamess use gamess
More Information
Genome Analysis Toolkit (GATK) gatk java -jar /opt/gatk/3.5/GenomeAnalysisTK.jar <extra arguments here>
GNU compiler suite v4.1.2 gcc-4.1.2 use gcc-4.1.2
GNU compiler suite v4.8.2 gcc-4.8.2 use gcc-4.8.2
GNU compiler suite v4.8.3 gcc-4.8.3 use gcc-4.8.3
GNU compiler suite v4.9.2 gcc-4.9.2 use gcc-4.9.2
Gnuplot graphics software (latest version) gnuplot gnuplot_4.6.6 use gnuplot
Gnuplot graphics software (4.6.6) gnuplot_4.6.6 use gnuplot_4.6.6
Gromacs (current version) 32 bit Gromacs Gromacs4.0.7_32bit use Gromacs
More information
Gromacs software (version 4.0.7, 32-bit) Gromacs4.0.7_32bit use Gromacs4.0.7_32bit
More information
Gromacs software (version 4.0.7, 64-bit) Gromacs4.0.7_64bit use Gromacs4.0.7_64bit
More information
Gromacs software (version 4.6, 32-bit) Gromacs4.6_32bit use Gromacs4.6_32bit
More information
Gromacs software (version 4.6, 64-bit) Gromacs4.6_64bit use Gromacs4.6_64bit
More information
Gromacs software (version 5.0, 64-bit) Gromacs5.0.6 use Gromacs5.0.6
More information
Gromacs (current version) 64 bit Gromacs_64bit use Gromacs_64bit
More information
Gromacs (new, test) Gromacs_test use Gromacs_test
More information
Gurobi (newest version, 64-bit) gurobi use gurobi
More information
HMMER (current version) hmmer hmmer-3.1b2 use hmmer
HMMER 3.1b2 hmmer-3.1b2 use hmmer-3.1b2
HTSeq Python package HTSeq "use anaconda2"
Hypre hypre located in /opt/hypre
Intel Compiler Suite ics use ics
Intel Compiler Suite plus Intel MPI icsmpi use icsmpi
InStruct instruct use instruct
Java 7 Java 7 Already on PATH, simply type "java"
Java 8 java8 use java8
Jmol (current version) jmol jmol-14.2.7 use jmol
Jmol 14.2.7 jmol-14.2.7 use jmol-14.2.7
LAMMPS default version lammps lammps_64bit use lammps
More information
LAMMPS (Dec 2013) 64 bit Intel lammps_64bit use lammps_64bit
More information
LAMMPS (August 2015) 64 bit gcc/openmpi 1.8 lammps_aug15 use lammps_aug15
More information
matlab matlab use matlab ... Requires a user-supplied license
More information
matlab-2014a matlab-2014a use matlab-2014a ... Requires a user-supplied license
More information
migrate-n current version migrate-n migrate-n-3.6.8 use migrate-n
migrate-n-3.6.8 migrate-n-3.6.8 use migrate-n-3.6.8
MPICH-1 (newest) mpich-1 use mpich-1
mrtrix3 mrtrix use mrtrix
More information
MUSCLE v3.8.31 muscle use muscle
NAMD (current version) namd namd-2.10 use namd
NAMD 2.10 namd-2.10 use namd-2.10
NWChem (current) nwchem nwchem-6.1 use nwchem
More information
NWChem 6.1 nwchem-6.1 use nwchem-6.1
More information
octave (current version) octave octave-4.0.0 use octave
More information
GNU octave-4.0.0 MATLAB look-alike octave-4.0.0 use octave-4.0.0
More information
OpenFOAM (current version) openfoam openfoam-2.3.0 use openfoam
More information
OpenFOAM 2.1.1 openfoam-2.1.1 use openfoam-2.1.1
More information
OpenFOAM 2.3.0 openfoam-2.3.0 use openfoam-2.3.0
More information
OpenFOAM 3.0.0 openfoam-3.0.0 use openfoam-3.0.0
More information
openmpi (default version) openmpi openmpi-1.8 use openmpi
openmpi (development - v1.2) openmpi-1.2 use openmpi-1.2
openmpi (development - v1.8) openmpi-1.8 use openmpi-1.8
openmpi (development - v1.8.4) openmpi-1.8.4 use openmpi-1.8.4
orca (production - r2131) orca use orca
orca (production - r2360) orca-2360 use orca-2360
Paraview (current version) paraview paraview-4.3 use paraview
More information
Paraview (64 bit version 1.4) paraview-4.3 use paraview-4.3
More information
PEAR 0.9.6 pear use pear
Perl 5 (version 5.10) Perl 5 Already on PATH, simply type "perl"
PETSc scientific library (current version) petsc petsc-3.5.2 use petsc
More information
PETSc scientific library (version 3.5.2 using OpenMPI 1.8, gcc 4.4.6 petsc-3.5.2 use petsc-3.5.2
More information
PETSc scientific library (version 3.6.0 using Intel compilers and MPI petsc-3.6.0-intel use petsc-3.6.0-intel
More information
PETSc scientific library (current version, Intel compilers/MPI) petsc-intel use petsc-intel
More information
Picard Tools picardtools use java8
java -jar /opt/picardtools/2.0.1/picard.jar
PLINK 1.9 beta 3.30 plink-1.9 use plink-1.9
PLINK/SEQ 0.10 plink-seq use plink-seq
PyRx 0.9.2 Drug Screening Software PyRx use PyRx
More information
PyRx 0.9 Drug Screening Software PyRx-0.9 use PyRx-0.9
More information
Python (version 3.4.3) python-3.4 use python-3.4
Pyzo Python distribution (includes numpy & scipy) pyzo2015a use pyzo2015a
qespresso (current version) 64 bit qespresso qespresso5.2.1_64bit use qespresso
More information
Quantum Espresso software (version 5.0.2, 64-bit) qespresso5.0.2_64bit use qespresso5.0.2_64bit
More information
Quantum Espresso software (version 5.2.1, 64-bit) qespresso5.2.1_64bit use qespresso5.2.1_64bit
More information
R statistical software (system version) R R-3.2.3 use R
More information
R statistical software (older version, 32-bit) R-2.15.2 use R-2.15.2
More information
R statistical software (older version, 64-bit) R-2.15.2_64bit use R-2.15.2_64bit
More information
R version 3.2.3 (64-bit) R-3.2.3 use R-3.2.3
More information
samstat samstat use samstat
SAMtools (current version) samtools samtools-1.3 use samtools
SAMtools 0.1.19 samtools-0.1.19 use samtools-0.1.19
SAMtools 1.3 samtools-1.3 use samtools-1.3
samstat 1.5.1 samtstat use samtstat
seqtk (current version) seqtk use seqtk
Sun Grid Engine 6 sge6 use sge6
SRA Toolkit (current version) sratoolkit sratoolkit-2.5.7 use sratoolkit
SRA Toolkit 2.5.7 sratoolkit-2.5.7 use sratoolkit-2.5.7
Stacks (current version) stacks stacks-1.35 use stacks
Stacks 1.35 stacks-1.35 use stacks-1.35
STAR 2.5.1b star use star
Tophat2 (current version) tophat2 tophat2-2.1.0 use tophat2
Tophat2 2.1.0 tophat2-2.1.0 use tophat2-2.1.0
Trinity (current version) trinity trinity-2.1.1 use trinity
Trinity 2.1.1 trinity-2.1.1 use trinity-2.1.1
VisIt 2.10 visit visit use visit
More information
vsearch v1.9.10 vsearch use vsearch
Java based data mining (version 3.6) weka use weka

Language-specific software package installation

Certain programming languages require the use of multiple add-on packages to reach their full functionality. If we are missing a package you need, there are two options: either request it be installed email us at or perform a local install. Both methods will give you a working copy of the software package


To install Perl modules to a local directory, use the following bash commands to create a localized install of whatever modules you may need. It's actually not as complicated as it looks.

# install local::lib
tar -xzf local-lib-2.000018.tar.gz
cd local-lib-2.000018
perl Makefile.PL --bootstrap
make test && make install

# setting up appropriate environment variables so that perl knows about our new ~/perl5/lib directory
cd ~                
echo 'eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >> ~/.bashrc
source ~/.bashrc

# check that local::lib is indeed installing to the right directory, you should see a bunch of paths beginning with ~/perl5/lib/perl5/ get printed out
perl -e 'print "@INC"'

Installing Perl modules from CPAN will now allow you install whatever you need. For an example of using CPAN to install BioPerl, see below. This part requires a bit of baby-sitting, just hit enter whenever a prompt comes up.

install CJFIELDS/BioPerl-1.6.924.tar.gz


We highly recommend using one of the two Anaconda installations on the SW cluster. These already have a large number of pre-installed packages and will serve you well. However, if they are missing something you need, you can make a local install using the following instructions:

use anaconda3 #or "use anaconda2" for python 2.7
pip install --user packageName


When using R, make sure to use the centralized install first with "use R". The system R version on the login node has a slightly different set of installed libraries from the versions of R found on the production nodes, which can result in dependency issues. Adding "use R" to your scripts will avoid this.

When installing R packages from CRAN, it's easiest to manually specify the CRAN mirror to download from with:

install.packages("packageName", repos="mirrorURL")

where mirrorURL is one of the repositories listed at [1]. It will tell you at some point that the directory is not writeable and ask you if you want to make a local library instead- select 'yes'. The package should install normally and be ready for use.

When installing packages from Bioconductor:


If you see an error about "URLs are not supported", simply change any "https" URL to "http" and it will work. Again, it will ask you to make a "personal library", select 'yes'.

Using your own software

It's very easy to use software that is not pre-installed on the systems. Simply specify the absolute or relative path to your software in a script and it will run. For example, if you had a program called "test" located in ~/bin/, you could easily invoke it with "~/bin/test" in your scripts.