Software
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
Applications and Tools
| Package | Vers | Systems | Summary |
|---|---|---|---|
| Autoconf | 2.69 | HPC, Spear | GNU Autoconf is a package to automate the production of software configuration shell scripts |
| bbftp-client | 3.2.1 | HPC | bbftp-client is the client program for bbftp which is designed for transfer of very large files |
| Blender | 2.69 | HPC | Blender is a free and open source 3D animation suite |
| CDO | 1.6.9 | HPC | CDO - Command Line Tools for Climate Model Data Analysis |
| CMake | 3.7.2 | HPC, Spear | A Set of Tools to Simplify Building, Testing and Packaging Software |
| DAQ | 2.0.6 | HPC | The Data Acquisition Library for the Snort IDS |
| ffmpeg | 3.1.7 | HPC, Spear | Audio and Video Generation and Conversion Software |
| freefem++ | 3.53 | HPC | Partial differential equation solver based on the finite element method |
| Gerris | 1.3.2 | HPC | Solver of partial differential equations used in fluid flow. |
| Git | 2.12.0 | HPC, Spear | Git - A Version Control System for Software Development |
| Grace | 5.1.22 | HPC, Spear | A WYSIWYG 2D plotting tool for scientific graphing |
| HADOOP | 1.2.1 (myhadoop-0.30) | HPC | 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. |
| IBM ILOG CPLEX Optimization Studio | 12.5 | HPC, Spear | Mathematical optimization software package |
| IPython | 3.2.1 | HPC | An Interactive Shell for Python with Jupyter Graphical Support |
| JAGS | 4.2.0 | HPC, Spear | A Gibbs Sampler for Bayesian Hierarchical Models with MCMC |
| ParaView | 4.4.0 | HPC, Spear | ParaView is an open-source, multi-platform data analysis and visualization application |
| R (statistical computing) | 3.4.0 / 3.3.2 / 3.2.5 / 3.2.0 / 3.1.3 | HPC, Spear | A popular, full featured, statistical computing package |
| Snort | 2.9.7.3 | HPC | A Powerful Open-Source Network Security Tool |
| Stata | 10.1 | HPC, Spear | Stata is fully featured data analysis and statistical software |
| TAU | 2.23 | HPC | TAU (Tuning and Analysis Utilities) is a software performance analysis tool |
| TotalView | 8.13.0 | HPC | TotalView is a GUI-based parallel and serial debugging tool |
| VisIt | 2.12.2 | HPC, Spear | A software package for visualizing scientific results |
| WGRIB | 1.8.1.2c | HPC, Spear | A Program for Decoding and Working with GRIB Data Files |
Programming Languages and Compilers
| Package | Vers | Systems | Summary |
|---|---|---|---|
| Anaconda | 2.7 | HPC | Python 2.7 with 195 popular packages |
| Chapel | 1.13.0 | HPC | A Modern Parallel Programming Language |
| Cython | 0.25.2 | Spear | A Static Compiler for the Python and Cython Languages |
| GNU Compilers | 4.4.6 | HPC, Spear | GNU C, C++, and Fortran Compilers |
| GNU Octave | 4.2.1 | HPC, Spear | A high-level language, primarily intended for numerical computations |
| Intel Compilers | 13.0.1 | HPC, Spear | Intel C, C++, and Fortran Compilers |
| Julia | 0.5.0 | HPC | A High-Performance Numerical Computing Environment and Language |
| MATLAB | 2017a | HPC, Spear | A high-level language and interactive environment for numerical computation, visualization, and programming |
| NASM | 2.12.02 | HPC | An Assembler for x86 Assembly Code |
| Portland Group Compilers | 12.9.0 64-bit | HPC, Spear | PGI Compilers for C, C++, and Fortran |
| Python | 2.7.5, 3.5.1 | HPC, Spear | Interactive, object-oriented, extensible programming language |
| yasm | 1.3.0 | HPC | A Modular Assembler code for x86 and AMD64 Assembly Code |
Libraries
| Package | Vers | Systems | Summary |
|---|---|---|---|
| ALPS | 2.1 | HPC | Algorithms and Libraries for Physics Simulations |
| ARPACK | 3.1.5 | HPC, Spear | A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems |
| BLAS | 3.2.1 | HPC | Linear Algebra Library |
| Deal.II | 8.4.1 | HPC | C++ software library supporting the creation of finite element codes. |
| FFTW | 3.3.5 & 2.1.5 | HPC | C library to compute the discrete Fourier transforms |
| fonttools | 3.8.0 | HPC | A Python library to Work With Text Font Files |
| h5py | 2.5.0 | HPC | An API for the HDF5 Data Format for Python |
| HDF5 | 1.8.16 | HPC | unique technology suite that makes possible the management of large and complex data |
| Hypre | 2.11.1 | HPC | Library for solving large, sparse linear systems of equations on massively parallel computers |
| LAPACK | 3.6.1 | HPC | Standard software library for linear algebra |
| Model Coupling Toolkit (MCT) | 2.9.0 | HPC | Set of open-source software tools for creating coupled models |
| MPI for Python | 2.0.0 | HPC, Spear | An Implementation of MPI Bindings for Python |
| MVAPICH2 | 2.2 | HPC, Spear | A Highly Scalable MPI Implementation for High-End Computer Systems |
| netCDF | 4.4.1.1 | HPC | libraries for representing scientific data |
| OpenBLAS | 0.2.19 | HPC, Spear | A Highly Optimized Linear Algebra Library based on GotoBLAS |
| OpenMPI | 2.1.0rc3 | HPC, Spear | An MPI Implementation for Parallel Computing |
| SuperLU | 5.2.0 | HPC | Library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
Bioinformatics
| Package | Vers | Systems | Summary |
|---|---|---|---|
| ABySS | 2.0.2 | HPC | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
| BEST | 2.3.1 | HPC, Spear | BEST is a Phylogenetics Program design to estimate Phylogenetic Trees |
| Biopython | 1.68 | HPC | Python library for computational molecular biology. |
| Bowtie | 1.2 | HPC, Spear | Bowtie is an ultrafast, memory-efficient short read aligner |
| Bowtie2 | 2.3.2 | HPC, Spear | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
| BWA | 0.7.15 | HPC, Spear | Software package for mapping low-divergent sequences |
| Clustal W | 2.1 | HPC, Spear | A Program for Alignment of Multiple Genetic or Protein Sequences |
| Clustal X | 2.1 | HPC, Spear | A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W) |
| Cufflinks | 2.1.1 | HPC, Spear | Transcript assembly, differential expression, and differential regulation for RNA Sequencing |
| ELPH | 1.0.1 | HPC, Spear | Motif Finding by Gibbs Sampling in DNA and Protein Sequences |
| FASTQC | 0.11.5 | Spear | A quality control tool for high throughput sequence data. |
| HTSeq | 0.6.1 | Spear | A Python Package for Analysis of High-Throughput Genetic Sequence Data |
| LAST | 833 | HPC, Spear | Sequence Aligning Software |
| MAFFT | 7.309 | HPC, Spear | A Program for Aligning Multiple Sets of Genetic Sequence Data |
| Mauve | 2.4.0 | HPC, Spear | Aligning Multiple Genome Sequences with Large-Scale Evolutionary Events |
| migrate-n | 3.6.11 | HPC | Estimates effective population sizes and past migration rates |
| MrBayes | 3.1.2 & 3.2.1 | HPC, Spear | A Bayesian MCMC Program for Inferring Phylogenetic Models |
| MUMmer | 3.23 | HPC, Spear | An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data |
| RNA-STAR | 2.4.1d | HPC, Spear | Ultrafast universal RNA sequencing aligner |
| SAMtools | 0.1.19 | HPC, Spear | Flexible generic format for storing nucleotide sequence alignment |
| STAR | 2.5.3a | A Program for Ultrafast RNA-seq Sequence Alignments | |
| TopHat | 2.1.1 | HPC, Spear | A spliced read mapper for RNA Sequencing |
| Trimmomatic | 0.36 | Spear | A flexible read trimming tool for Illumina NGS data |
| VMD | 1.9.1 | HPC, Spear | VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software |
Materials Science and Computational Chemistry
| Package | Vers | Systems | Summary |
|---|---|---|---|
| ABINIT | 8.2.2 | HPC | Materials Modeling and Electronic Structure Calculations |
| ADF | 2016.101 | HPC | Amsterdam Density Functional |
| atsas | 2.8.0 | HPC | A program suite for small-angle scattering data analysis from biological macromolecules |
| BigDFT | 1.6.0 | HPC | BigDFT is a DFT program designed to compute Electronic Structures in Parallel |
| Chimera | 1.8.1 | Spear | Molecular modeling system |
| Crystal14 | 1.0.4 | HPC | Software computing electronic wave function and properties of periodic systems |
| Desmond | 3.4.0.2 | HPC | Simulation Software for Molecular Dynamics |
| Gaussian | v09 | HPC, Spear | An application that provides state-of-the-art capabilities for electronic structure modeling |
| GROMACS | 2016.3 | HPC, Spear | GROMACS is a versatile package to perform molecular dynamics |
| GULP | 4.4.0 | HPC | Program for performing a variety of types of simulations on materials |
| LAMMPS | 20160309 | HPC | Large-scale Atomic/Molecular Massively Parallel Simulator |
| moltemplate | 2.1.2 | HPC | A general text-based molecule builder for LAMMPS. |
| NAMD | 2.10 | HPC, Spear | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| nbo6 | 6.0 | HPC | The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions. |
| NWChem | 6.5.26243 | HPC | Application for high performance computational chemistry |
| ORCA | 4.0.0 | HPC | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties |
| PyMOL | 1.6 | Spear | A molecular visualization system on an open-source Python foundation |
| python-ase | 3.13.0 | HPC | ASE is an Atomistic Simulation Environment written in the Python |
| Quantum ESPRESSO | 5.4.0 | HPC | Nanoscale electronic-structure calculations and materials modeling |
| VASP | 5.4.1 | HPC | The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling. |