Available Software

In the table below is a list of all software that is currently installed on the cluster. You can also directly see a real-time list of all available modules using the command below.

module avail

How To Use

Once you identify the software and version you want to run by looking at the table below, you will need to enable it by using our module system. Once loaded, you'll be able to run the software using the commands you typically use for your calculations.

module load software/version

If you don't have a need for a specific version, then you can just load the software by only its name instead.

module load software

Once you are done using a module, you can use "module unload software" to disable it.

Examples

PythonRGaussian

module load python-libs    # Load Python Module
conda activate tensorflow-2.11-gpu  # Load custom Python environment (if needed)
python my-script.py        # Run Python Script

module load R/4.4.0    # Load R (4.4.0)
Rscript input-file.R   # Run R Script

module load gaussian/16 # Load Gaussian 16
g16 < input-file > output-file.log  # Run the Gaussian program

Installed Software

Software	BGSC	BOSE	Description
ADMIXTURE [ User Guide ]	admixture/1.3.0	admixture/1.3.0	Used to estimate individual ancestry from single nucleotide polymorphism (SNP) data sets.
Adaptive Poisson-Boltzmann Solver (APBS) [ User Guide ]	apbs/3.0.0 apbs/3.1.4	apbs/3.1.3 apbs/3.4.1	Solves the equations of continuum electrostatics for large biomolecular assemblages.
Apptainer [ User Guide ]	apptainer/latest (1.2.5) apptainer/1.2.5		Popular HPC software for running scientific programs inside portable containers.
Autoconf [ User Guide ]	2.69*	2.69* autoconf/2.72	Tool used for generating configure scripts for building software from source code.
Bayesian Analysis of Macroevolutionary Mixtures (BAMM) [ User Guide ]	bamm/2.5.0		Program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees.
BLAST+ [ User Guide ]		blast/2.15.0	Basic Local Alignment Search Tool used to compare nucleotide or protein sequences to databases.
CFOUR [ User Guide ]	cfour-parallel/2.1 cfour/2.1 cfour/2.1.2	cfour-parallel/2.1 cfour-parallel/2.1-par-1 cfour/2.1	Used to perform high-level quantum chemical calculations on atoms and molecules.
CUDA Toolkit [ User Guide ]	cuda/10.2 cuda/11.4	cuda/10.0 cuda/11.4 cuda/12.6	Development environment used to support GPU-acceleration in software.
DMTCP [ User Guide ]		dmtcp/2.6.0	Distributed MultiThreaded Checkpointing
DSuite [ User Guide ]	DSuite/0.4	DSuite/0.4	Fast D‐statistics and related admixture evidence from VCF files
Gaussian [ User Guide ]	gaussian/09 gaussian/16	gaussian/16	General purpose computational chemistry software
gcc [ User Guide ]	gcc/9.3.0	8.3.1* gcc/9.3.0 gcc/10.3.0 gcc/11.1.0	General purpose compiler
git [ User Guide ]	git/2.28.0	2.27.0*	Universally-used version control
Globus [ User Guide ]			File transferring service for organizations and their users
Globus CLI [ User Guide ]	globus-cli/3.24.0	globus-cli/3.24.0	File transferring service for organizations and their users; adapted to command line
GNU Octave [ User Guide ]		octave/7.3.0	Mathematics oriented scientific programming language largely compatibile with Matlab
GNU Parallel [ User Guide ]	parallel/20220622	parallel/20220622	Executes commands in parallel
gnuplot [ User Guide ]		gnuplot/5.4.1	Graphing program for 2D and 3D plotted graphs
go [ User Guide ]		go/1.16.4	Go programming language
GROMACS [ User Guide ]		test-gromacs/2024.3	A software suite for high-performance molecular dynamics and output analysis
Gurobi Optimizer [ User Guide ]		gurobi/11.0.0	Solver for mathematical models
IBM ILOG CPLEX Optimization Studio [ User Guide ]		cplex-studio/22.1.1	Decision optimization software
ifort [ User Guide ]	ifort/2013splu2		Fortran compiler
ImageMagick [ User Guide ]		imagemagick/7.1.0	Image processing + conversions
ImageJ / Fiji [ User Guide ]		imagej/1.53 imagej-fiji/2.15.0	GUI-based program used to process and analyze scientific images and videos.
Intel oneAPI Base + HPC Toolkit [ User Guide ]		oneapi, oneapi-*	Intel oneAPI is a collection of tools (compilers, MPI, mkl, etc) from Intel in a single package. By loading the 'oneapi' module, you'll be given access to all the oneapi modules when you type 'module avail'. Every module started with 'oneapi-XX'
jre [ User Guide ]	jre/1.8.0_291		Java runtime environment
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [ User Guide ]	lammps-parallel/2020-03-03 lammps/2020-03-03	lammps/2Aug2023	Molecular dynamics simulator
Maple [ User Guide ]	maple/2017		Symbolic/numeric computing environment and programming language
MedeA		3.7.2*	Software package to hook into VASP, LAMMPS, and Gaussian. Note: License required for use.
MESA [ User Guide ]	mesa/r15140	mesa/24.03.1 mesa/r23051 mesa/r15140	Stellar evolution simulator
MRCC [ User Guide ]		test-mrcc/20230828	Quantum chemistry program suite for high-accuracy electronic structure calculations
Music21 [ Website ]	music21/8.1.0	music21/8.1.0	Python-based music analysis software
Nanoscale Molecular Dynamics (NAMD) [ User Guide ]	namd/2.13 namd/2.13-cuda	namd/2.14 namd/2.14-cuda test-namd/3.0 test-namd/3.0-cuda	Molecular dynamics simulator
Network Simulator (NS) [ User Guide ]		netsim/2.35	Network traffic simulator
OneDrive Client for Linux	onedrive/2.4.15 onedrive/2.4.23	onedrive/2.4.23	Command-line tool for used for syncing files with a Microsoft OneDrive account.
openBabel	openbabel/3.1.1	openbabel/3.1.1	A chemical toolbox project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
openJDK	openjdk/11 openjdk/16		Open-source implimentation of the java platform
Open MPI	openmpi/1.10.0_ifort openmpi/4.0.3 openmpi/4.0.3_ifort	openmpi/1.10.7 openmpi/2.1.6 openmpi/4.1.1 cray-openmpi/4.1.1 openmpi/5.0.3	Open-source message passing interface
PhyML	phyml/3.3.20200621		Analyzes allignments of nucleotide or amino acid sequences using statistical approach
Prokka [ User Guide ]		prokka/1.14.5	Rapid prokaryotic genome annotation
Psi4 [ User Guide ]		psi4/1.9.1	Open-Source Quantum Chemistry – an electronic structure package
Python [ User Guide ]	python/2.7.18 python/3.9.2	python/3.9.2	General-purpose high-level programming language This module not is recommended for use, see "Python Libraries (Conda)" below.
Python Libraries (Conda) [ User Guide ]	python-libs	python-libs	Conda is the primary package system used for installing Python, its libraries, and creating shared environments for research groups.
p7zip		p7zip/16.02	For compressing and extracting .7z files
Q-Chem [ User Guide ]	qchem-mpi/5.2-MPI qchem/5.2	qchem/5.2	General-purpose electronic structure package
QGIS [ User Guide ]		test-qgis/latest (3.22.16) test-qgis/3.22.16 Also Via OnDemand	Free and open-source geographic information systems (GIS) application
QIIME 2 [ User Guide ]		qiime2/2024.5	Microbiome multi-omics bioinformatics and data science platform
R [ User Guide ]	R/3.4.4 R/3.6.3 R/4.0.2 R/4.4.0	R/4.0.4 R/4.0.5 R/4.2.1 R/4.3.1 R/4.4.0	Programming language for statistical computing
RAxML Next Generation [ User Guide ]	raxml-ng/0.9.0	raxml-ng/1.1.0	Phylogenetic tree inference tool
Rclone	rclone/1.62.2	rclone/1.62.2	Command-line tool allowing files to be synced between cloud providers, such as OneDrive, Google Drive, and Dropbox.
redmd/redmdstream [ User Guide ]		redmd/2.3 redmdstream/1.0	Tools for modeling biomolecular systems. Stream is for model development, and redmd is a simulation engine.
Roary [ User Guide ]		roary/3.13.0	High speed pan-genome pipeline
RStudio [ User Guide ]		2023.09.1 - Via OnDemand	A Integrated Development Environment (IDE) for the R programming language.
Ruby	ruby/2.7.1	ruby/2.7.1	General-purpose high-level programming language
Stacks [ User Guide ]	stacks/2.57		software pipeline for building loci from short-read sequences
Structure/Faststructure [ User Guide ]		structure/2.3.3 faststructure/1.0.4	Variational framework for inferring population structure from SNP genotype data
Subversion (SVN)	svn/1.10.6 svn/1.14.0		Version and revision control software
VCFTools		vcftools/0.1.16	Program package for working with .vcf files. Also included in this module: Tabix, BCFtools, BGZip, Fixref plugin for VCFtools
VMD [ User Guide ]		vmd/1.9.3 vmd/1.9.4	Program used to visualize molecules and analyze molectular structure

* These are installed by default and do not need a module to use them.

Need Something Installed?

We have an eForm for you to fill out the detail of a requested software, whether it is unavailable in the cluster, or a specific version.

Start Form Now

Please note that software requests are subject to approval and if your software requires a license, you must already have access to the license for your group.