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
| 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. |
| 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 |
| 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 |
| 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 |
| 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 |