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

Package Version   Summary

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 1.6.9 CDO - Command Line Tools for Climate Model Data Analysis
CMake 3.11.1 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++ 3.53 Partial differential equation solver based on the finite element method
Gerris 1.3.2 Solver of partial differential equations used in fluid flow.
Git 2.12.0 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 2.11.0 A GUI Tool for Editing Files for the HDF4 and HDF5 Programs
IBM ILOG CPLEX Optimization Studio 12.5 Mathematical optimization software package
IPython 3.2.1 An Interactive Shell for Python with Jupyter Graphical Support
JAGS 4.2.0 A Gibbs Sampler for Bayesian Hierarchical Models with MCMC
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 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
R (statistical computing) 3.5.1 / 3.3.2 / 3.2.5 / 3.2.0 / 3.1.3 Recipe A popular, full featured, statistical computing package
Snort 2.9.11.1 A Powerful Open-Source Network Security Tool
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 TotalView is a GUI-based parallel and serial debugging tool
VisIt 2.12.2 A software package for visualizing scientific results
WGRIB 1.8.1.2c A Program for Decoding and Working with GRIB Data Files

Programming Languages and Compilers

Anaconda 2.7.15, 3.4.8 Python 2.7 and 3.4 with 195 popular packages
Chapel 1.13.0 A Modern Parallel Programming Language
Clang 6.0.0 A Front-End for LLVM-Based C Compilers
CUDA 9.0 CUDA is a parallel computing platform and programming model for GPUs invented by NVIDIA.
Cython 0.25.2 A Static Compiler for the Python and Cython Languages
GNU Compilers 7.3.1 GNU C, C++, and Fortran Compilers
GNU Octave 4.2.2 A high-level language, primarily intended for numerical computations
Intel Compilers 13.0.1 Intel C, C++, and Fortran Compilers
Julia 0.6.3 Recipe A High-Performance Numerical Computing Environment and Language
MATLAB 2018b, 2017a Recipe A high-level language and interactive environment for numerical computation, visualization, and programming
NASM 2.13.03 An Assembler for x86 Assembly Code
Portland Group Compilers 12.9.0 64-bit PGI Compilers for C, C++, and Fortran
Python 2.7.5, 3.7.0 Interactive, object-oriented, extensible programming language
yasm 1.3.0 A Modular Assembler code for x86 and AMD64 Assembly Code

Libraries

ALPS 2.1 Algorithms and Libraries for Physics Simulations
ARPACK 3.5.0 A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
BLAS 3.2.1 Linear Algebra Library
Boost 1.66.0 Boost - A Powerful, Multipurpose library of C++ Tools
DAQ 2.0.6 The Data Acquisition Library for the Snort IDS
Deal.II 8.4.1 C++ software library supporting the creation of finite element codes.
FFTW 3.3.5, 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
h5py 2.8.0 An API for the HDF5 Data Format for Python
HDF4 4.2.13 Tools and File Structures for Storing and Analyzing Scientific Data
HDF5 1.10.2 unique technology suite that makes possible the management of large and complex data
Hypre 2.14.0, 2.8.0b 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 2.0.0 An Implementation of MPI Bindings for Python
MVAPICH2 2.3rc2 A Highly Scalable MPI Implementation for High-End Computer Systems
netCDF 4.6.1, 4.4.4, 4.3.0, 4.2 libraries for representing scientific data
OpenBLAS 0.3.2, 0.2.14 A Highly Optimized Linear Algebra Library based on GotoBLAS
OpenMPI 3.1.0 An MPI Implementation for Parallel Computing
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.

Bioinformatics

ABySS 2.1.0 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 1.10.0 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 0.7.15 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 1.0.1 Motif Finding by Gibbs Sampling in DNA and Protein Sequences
FASTA 36.3.8e Searching Biological Sequence Data for Regions of Similarity
FASTQC 0.11.5 A quality control tool for high throughput sequence data.
Glimmer 3.02b An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes
HMMER 3.1b2 An HMM-based Algorithm for Sequence Alignment and Homolog Finding
HTSeq 0.6.1 A Python Package for Analysis of High-Throughput Genetic Sequence Data
LAST 833 Sequence Aligning Software
MAFFT 7.309 Recipe 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 Estimates effective population sizes and past migration rates
MIRA 4.0.2 A Genome Assembly and Mapping Program
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 2.0.1 RNA-Seq Transcript Assembly using the ABySS Algorithm
Trimmomatic 0.38 A flexible read trimming tool for Illumina NGS data
VMD 1.9.3 VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software

Materials Science and Computational Chemistry

ABINIT 8.8.3 Materials Modeling and Electronic Structure Calculations
ADF 2016.101 Amsterdam Density Functional
atsas 2.8.0 A program suite for small-angle scattering data analysis from biological macromolecules
BigDFT 1.6.0 BigDFT is a DFT program designed to compute Electronic Structures in Parallel
Charmm 41 Recipe 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 Recipe An application that provides state-of-the-art capabilities for electronic structure modeling
GROMACS 2018.2 GROMACS is a versatile package to perform molecular dynamics
GULP 4.4.0 Program for performing a variety of types of simulations on materials
LAMMPS 20180822 Large-scale Atomic/Molecular Massively Parallel Simulator
libxc 3.0.0 A DFT Exchange and Correlation Functionals Library
moltemplate 2.1.2 A general text-based molecule builder for LAMMPS.
NAMD 2.10 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 6.5.26243 Application for high performance computational chemistry
ORCA 4.0.0.2 Recipe 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 3.16.2 ASE is an Atomistic Simulation Environment written in Python
Quantum ESPRESSO 5.4.0 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.