Software Library

This inventory includes major software packages available on our compute systems. If you would like us to install a package not listed here, please let us know.

Available Software

Materials Science and Computational Chemistry
ABINIT 8.10.1

Materials Modeling and Electronic Structure Calculations

ADF 2016.101

Amsterdam Density Functional

atsas 2.8.4

A program suite for small-angle scattering data analysis from biological macromolecules

Charmm 41

A Computational Chemistry program for Molecular Modeling and Simulation

Chimera 1.8.1

Molecular modeling system

Crystal17 Crystal17/1.0.2

Software computing electronic wave function and properties of periodic systems

Desmond 3.4.0.2

Simulation Software for Molecular Dynamics

FPLO14.00 49

A Solver for the Kohn-Sham Equations on Regular Lattices

Gaussian v09

An application that provides state-of-the-art capabilities for electronic structure modeling

GROMACS 2020

GROMACS is a versatile package to perform molecular dynamics

GULP 5.1

Program for performing a variety of types of simulations on materials

LAMMPS 20181212

Large-scale Atomic/Molecular Massively Parallel Simulator

libxc 4.3.0

A DFT Exchange and Correlation Functionals Library

moltemplate 2.1.2

A general text-based molecule builder for LAMMPS.

NAMD 2.13

A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

nbo6 6.0

The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions.

NWChem 6.8.1

Application for high performance computational chemistry

ORCA 4.0.0.2

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties

P4VASP 0.3.30

An Open-Source Visualization Tool for VASP

PyMOL 1.6

A molecular visualization system on an open-source Python foundation

python-ase 3.19.1

ASE is an Atomistic Simulation Environment written in Python

Quantum ESPRESSO 6.3

Nanoscale electronic-structure calculations and materials modeling

VASP 5.4.1

The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling.

Bioinformatics
ABySS 2.1.5

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

bcl2fastq 2.20.0.422

A Program to Convert BCL Data to FASTQ Format

Beagle 2.1

Beagle is a High-Performance Bayesian and Maximum Likelihood Bioinformatics Library

BEAST 1.10.4

BEAST is a Bayesian Analysis program for Building and Analyzing Phylogenetic Trees

BEST 2.3.1

BEST is a Phylogenetics Program design to estimate Phylogenetic Trees

Biopython 1.68

Python library for computational molecular biology.

BLAT 34

A Low-Memory Footprint Genetic Sequence Alignment Tool

Bowtie 1.0.1

Bowtie is an ultrafast, memory-efficient short read aligner

Bowtie2 2.3.2

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

BWA 0.7.17

Software package for mapping low-divergent sequences

Clustal W 2.1

A Program for Alignment of Multiple Genetic or Protein Sequences

Clustal X 2.1

A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W)

Cufflinks 2.1.1

Transcript assembly, differential expression, and differential regulation for RNA Sequencing

ELPH 0.1.5

Motif Finding by Gibbs Sampling in DNA and Protein Sequences

FASTA 36.3.8e

Searching Biological Sequence Data for Regions of Similarity

FASTQC 0.11.8

A quality control tool for high throughput sequence data.

FreeSurfer 7.1.1, 6.0.0

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

gemBS-rs 4.0.0

gemBS-rs is a rewrite of the gemBS pipeline using Rust. gemBS itself is a powerful high-throughput pipeline for DNA Methylation sequencing analysis.

Glimmer 3.02b

An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes

HTSeq 0.6.1

A Python Package for Analysis of High-Throughput Genetic Sequence Data

MAFFT 7.407

A Program for Aligning Multiple Sets of Genetic Sequence Data

Mauve 2.4.0

Aligning Multiple Genome Sequences with Large-Scale Evolutionary Events

migrate-n 3.6.11, 4.4.0

Estimates effective population sizes and past migration rates

MrBayes 3.2.1

A Bayesian MCMC Program for Inferring Phylogenetic Models

MUMmer 3.23

An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data

RNA-STAR 2.4.1d

Ultrafast universal RNA sequencing aligner

SAMtools 0.1.19

Flexible generic format for storing nucleotide sequence alignment

STAR 2.5.3a

A Program for Ultrafast RNA-seq Sequence Alignments

TopHat 2.1.1

A spliced read mapper for RNA Sequencing

Trans-ABySS 1.5.5

RNA-Seq Transcript Assembly using the ABySS Algorithm

Trimmomatic 0.36

A flexible read trimming tool for Illumina NGS data

VMD 1.9.1

VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software

Libraries
ALPS 2.1

Algorithms and Libraries for Physics Simulations

Armadillo C++ Library 9.860.2

A high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

ARPACK 3.7.0

A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems

BLAS 3.2.1

Linear Algebra Library

Boost 1.69.0

Boost - A Powerful, Multipurpose library of C++ Tools

DAQ 2.0.6

The Data Acquisition Library for the Snort IDS

FFTW 3.3.8, 2.1.5

C library to compute the discrete Fourier transforms

FIAT 1.6.0.dev0

An Automatic Basis Function Tabulator for the Finite Element Package FEniCS

fonttools 3.8.0

A Python library to Work With Text Font Files

FSL 6.0.2

FMRIB Software Library

GSL 1.6, 2.3, 2.6

The GNU Scientific Library (GSL) is a powerful library of common numerical and scientific functions intended for use in C and C++ software. It serves as an important backend in many software packages.

h5py 2.8.0

An API for the HDF5 Data Format for Python

HDF4 4.2.15

Tools and File Structures for Storing and Analyzing Scientific Data

HDF5 1.10.4

unique technology suite that makes possible the management of large and complex data

Hypre 2.18.2

Library for solving large, sparse linear systems of equations on massively parallel computers

LAPACK 3.8.0

Standard software library for linear algebra

MPI for Python 3.0.0

An Implementation of MPI Bindings for Python

MVAPICH2 2.3

A Highly Scalable MPI Implementation for High-End Computer Systems

netCDF 4.8.0(gcc/intel) 4.3.1(netcdf-cxx) 4.5.3 (fortran)

libraries for representing scientific data

OpenBLAS 0.3.5

A Highly Optimized Linear Algebra Library based on GotoBLAS

OpenCV 3.4.6

A Powerful Library for Computer Vision Applications

OpenMPI 4.0.0

An MPI Implementation for Parallel Computing

PyTorch 1.3.1

A powerful machine learning library for Python

ScaLAPACK 2.0.2

A High-Performance Linear Algebra Library

SuperLU 5.4.0, 5.2.1

Library for the direct solution of large, sparse, nonsymmetric systems of linear equations.

TensorFlow 2.2.0

A Powerful Deep Learning Library with GPU Support

wannier90 3.0.0

A tool for obtaining maximally-localised Wannier functions

Programming Languages and Compilers
Anaconda 2.7.15, 3.7.3, 3.8.3

Python 2.7, 3.7 and 3.8 with 195 popular packages

Chapel 1.13.0

A Modern Parallel Programming Language

Clang 6.0.0, 7.0.1

A Front-End for LLVM-Based C Compilers

CUDA 11.1

CUDA is a parallel computing platform and programming model for GPUs invented by NVIDIA.

Cython 0.29.12

A Static Compiler for the Python and Cython Languages

GNU Compilers 8.3.1

GNU C, C++, and Fortran Compilers

GNU Octave 4.4.1

A high-level language, primarily intended for numerical computations

Intel Compilers 21, 16, 15

Intel C, C++, and Fortran Compilers

Julia 1.6.1

A High-Performance Numerical Computing Environment and Language

LLVM 6.0.0 & 3.9.1 & 7.0.1

A Toolkit for Building Compilers

MATLAB 2020a

A high-level language and interactive environment for numerical computation, visualization, and programming

NASM 2.15.03

An Assembler for x86 Assembly Code

Portland Group Compilers 21.3.0 64-bit

PGI Compilers for C, C++, and Fortran

Python 3.6.8

Interactive, object-oriented, extensible programming language

yasm 1.3.0

A Modular Assembler code for x86 and AMD64 Assembly Code

Applications and Tools
Apache Spark 2.2.1

Apache Spark is a cluster computing framework for large-scale data processing

Autoconf 2.69

GNU Autoconf is a package to automate the production of software configuration shell scripts

bbftp-client 3.2.1

bbftp-client is the client program for bbftp which is designed for transfer of very large files

Blender 2.69

Blender is a free and open source 3D animation suite

CDO 1.9.6

CDO - Command Line Tools for Climate Model Data Analysis

CMake 3.13.3

A Set of Tools to Simplify Building, Testing and Packaging Software

DCRAW 9.28.0

A Linux Program for Decoding Raw Digital Image Files

ffmpeg 3.1.7

Audio and Video Generation and Conversion Software

freeFem++ 4.7

Partial differential equation solver based on the finite element method

Gerris 1.3.2

Solver of partial differential equations used in fluid flow.

Git 2.32.0.rc2

Git - A Version Control System for Software Development

Grace 5.1.25

A WYSIWYG 2D plotting tool for scientific graphing

GrADS 2.0.2

GrADS - A Data Analysis and Display System for the Earth Sciences

HADOOP 1.2.1 (myhadoop-0.30)

Apache Hadoop is an open-source software framework for distributed storage and distributed processing of very large data sets on computer clusters built from commodity hardware.

HDFView 3.0.0

A GUI Tool for Editing Files for the HDF4 and HDF5 Programs

IPython 7.16.1

An Interactive Shell for Python with Jupyter Graphical Support

JAGS 4.2.0

A Gibbs Sampler for Bayesian Hierarchical Models with MCMC

Jupyter on OpenOnDemand N/A

Detailed instructions on how to set up and use Jupyter on Open OnDemand

Lmod 7.8.9

A Package to Dynamically Manipulate User Environments with Modules

Model Coupling Toolkit (MCT) 2.10.0

Set of open-source software tools for creating coupled models

Ncview 2.1.8

A Visualization Browser for netCDF Data

NEdit 5.7

A graphical UNIX Text Editor

parallel-kmeans 1

A Parallel Implementation of the K-Means Clustering Algorithm

ParaView 5.5.2

ParaView is an open-source, multi-platform data analysis and visualization application

ParMETIS 4.0.3

A Graph and Mesh Partitioning and Sparse Matrix Ordering Program

pkg-config 1.4.2

A powerful and simple tool to find and compiler options for libraries.

R (statistical computing) 4.1.0 / Several Others

A popular, full featured, statistical computing package

SCOTCH 6.0.6

A Scientific Computing Library for Graph Partitioning and Mapping

Snort 2.9.7.3

A Powerful Open-Source Network Security Tool

SPSS 27

SPSS is a powerful GUI statistics program built by IBM

Stata 15

Stata is fully featured data analysis and statistical software

TAU 2.23

TAU (Tuning and Analysis Utilities) is a software performance analysis tool

TotalView 8.13.0, 2018.2.6, 2019.2.12

TotalView is a GUI-based parallel and serial debugging tool

TurboMole 7.4.1

Program Package For Electronic Structure Calculations

VisIt 3.0.0

A software package for visualizing scientific results

WGRIB 1.8.1.2c

A Program for Decoding and Working with GRIB Data Files