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 15 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
Crystal17 Crystal17/1.0.1 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.