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
Apache Spark 2.2.1 HPC Apache Spark is a cluster computing framework for large-scale data processing
WGRIB 1.8.1.2c HPC, Spear A Program for Decoding and Working with GRIB Data Files
Ncview 2.1.8 HPC, Spear A Visualization Browser for netCDF Data
IPython 3.2.1 HPC An Interactive Shell for Python with Jupyter Graphical Support
Snort 2.9.7.3 HPC A Powerful Open-Source Network Security Tool
parallel-kmeans 1 HPC A Parallel Implementation of the K-Means Clustering Algorithm
NEdit 5.7 HPC, Spear A UNIX Text Editor
JAGS 4.2.0 HPC, Spear A Gibbs Sampler for Bayesian Hierarchical Models with MCMC
ParMETIS 4.0.3 HPC, Spear A Graph and Mesh Partitioning and Sparse Matrix Ordering Program
HDFView 2.11.0 HPC, Spear A GUI Tool for Editing Files for the HDF4 and HDF5 Programs
Git 2.12.0 HPC, Spear Git - A Version Control System for Software Development
ffmpeg 3.1.7 HPC, Spear Audio and Video Generation and Conversion Software
CMake 3.11.1 HPC, Spear A Set of Tools to Simplify Building, Testing and Packaging Software
CDO 1.6.9 HPC CDO - Command Line Tools for Climate Model Data Analysis
bbftp-client 3.2.1 HPC bbftp-client is the client program for bbftp which is designed for transfer of very large files
Autoconf 2.69 HPC, Spear GNU Autoconf is a package to automate the production of software configuration shell scripts
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.
ParaView 4.4.0 HPC, Spear ParaView is an open-source, multi-platform data analysis and visualization application
freefem++ 3.53 HPC Partial differential equation solver based on the finite element method
TotalView 8.13.0 HPC TotalView is a GUI-based parallel and serial debugging tool
TAU 2.23 HPC TAU (Tuning and Analysis Utilities) is a software performance analysis tool
Gerris 1.3.2 HPC Solver of partial differential equations used in fluid flow.
Blender 2.69 HPC Blender is a free and open source 3D animation suite
Model Coupling Toolkit (MCT) 2.9.0 HPC Set of open-source software tools for creating coupled models
IBM ILOG CPLEX Optimization Studio 12.5 HPC, Spear Mathematical optimization software package
Stata 15 HPC, Spear Stata is fully featured data analysis and statistical software
R (statistical computing) 3.5.1 / 3.3.2 / 3.2.5 / 3.2.0 / 3.1.3 HPC, Spear A popular, full featured, statistical computing package
Grace 5.1.22 HPC, Spear A WYSIWYG 2D plotting tool for scientific graphing
VisIt 2.12.2 HPC, Spear A software package for visualizing scientific results

Programming Languages and Compilers

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

Libraries

Package Vers Systems Summary
OpenBLAS 0.2.19 HPC, Spear A Highly Optimized Linear Algebra Library based on GotoBLAS
h5py 2.8.0 HPC An API for the HDF5 Data Format for Python
DAQ 2.0.6 HPC The Data Acquisition Library for the Snort IDS
MVAPICH2 2.3rc2 HPC, Spear A Highly Scalable MPI Implementation for High-End Computer Systems
MPI for Python 2.0.0 HPC, Spear An Implementation of MPI Bindings for Python
OpenMPI 3.1.0 HPC, Spear An MPI Implementation for Parallel Computing
fonttools 3.8.0 HPC A Python library to Work With Text Font Files
FIAT 1.6.0.dev0 HPC, Spear An Automatic Basis Function Tabulator for the Finite Element Package FEniCS
Hypre 2.11.1 HPC Library for solving large, sparse linear systems of equations on massively parallel computers
HDF5 1.10.2 HPC unique technology suite that makes possible the management of large and complex data
FFTW 3.3.5 & 2.1.5 HPC C library to compute the discrete Fourier transforms
netCDF 4.6.1 HPC libraries for representing scientific data
LAPACK 3.8.0 HPC Standard software library for linear algebra
BLAS 3.2.1 HPC Linear Algebra Library
ARPACK 3.5.0 HPC, Spear A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
SuperLU 5.2.0 HPC Library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
Deal.II 8.4.1 HPC C++ software library supporting the creation of finite element codes.
ALPS 2.1 HPC Algorithms and Libraries for Physics Simulations

Bioinformatics

Package Vers Systems Summary
Trans-ABySS 1.5.5 HPC, Spear RNA-Seq Transcript Assembly using the ABySS Algorithm
STAR 2.5.3a A Program for Ultrafast RNA-seq Sequence Alignments
BLAT 34 HPC, Spear A Low-Memory Footprint Genetic Sequence Alignment Tool
MUMmer 3.23 HPC, Spear An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data
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
HTSeq 0.6.1 Spear A Python Package for Analysis of High-Throughput Genetic Sequence Data
MIRA 4.0.2 HPC A Genome Assembly and Mapping Program
MrBayes 3.2.1 HPC, Spear A Bayesian MCMC Program for Inferring Phylogenetic Models
Glimmer 3.02b HPC, Spear An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes
FASTA 36.3.8e HPC, Spear Searching Biological Sequence Data for Regions of Similarity
ELPH 1.0.1 HPC, Spear Motif Finding by Gibbs Sampling in DNA and Protein Sequences
Clustal X 2.1 HPC, Spear A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W)
Clustal W 2.1 HPC, Spear A Program for Alignment of Multiple Genetic or Protein Sequences
BEST 2.3.1 HPC, Spear BEST is a Phylogenetics Program design to estimate Phylogenetic Trees
BEAST 1.8.4 HPC, Spear BEAST is a Bayesian Analysis program for Building and Analyzing Phylogenetic Trees
VMD 1.9.3 HPC, Spear VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software
migrate-n 3.6.11 HPC Estimates effective population sizes and past migration rates
Trimmomatic 0.38 Spear A flexible read trimming tool for Illumina NGS data
FASTQC 0.11.5 Spear A quality control tool for high throughput sequence data.
RNA-STAR 2.4.1d HPC, Spear Ultrafast universal RNA sequencing aligner
TopHat 2.1.1 HPC, Spear A spliced read mapper for RNA Sequencing
Cufflinks 2.1.1 HPC, Spear Transcript assembly, differential expression, and differential regulation for RNA Sequencing
LAST 833 HPC, Spear Sequence Aligning Software
SAMtools 0.1.19 HPC, Spear Flexible generic format for storing nucleotide sequence alignment
BWA 0.7.15 HPC, Spear Software package for mapping low-divergent sequences
Biopython 1.68 HPC Python library for computational molecular biology.
Bowtie2 2.3.2 HPC, Spear Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
Bowtie 1.2 HPC, Spear Bowtie is an ultrafast, memory-efficient short read aligner
ABySS 2.0.2 HPC Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Materials Science and Computational Chemistry

Package Vers Systems Summary
FPLO14.00 49 HPC A Solver for the Kohn-Sham Equations on Regular Lattices
Charmm 41 HPC A Computational Chemistry program for Molecular Modeling and Simulation
BigDFT 1.6.0 HPC BigDFT is a DFT program designed to compute Electronic Structures in Parallel
ABINIT 8.2.2 HPC Materials Modeling and Electronic Structure Calculations
VASP 5.4.1 HPC The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling.
nbo6 6.0 HPC The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions.
GULP 4.4.0 HPC Program for performing a variety of types of simulations on materials
Quantum ESPRESSO 5.4.0 HPC Nanoscale electronic-structure calculations and materials modeling
python-ase 3.16.2 HPC ASE is an Atomistic Simulation Environment written in the Python
moltemplate 2.1.2 HPC A general text-based molecule builder for LAMMPS.
atsas 2.8.0 HPC A program suite for small-angle scattering data analysis from biological macromolecules
Crystal17 Crystal17/1.0.1 HPC Software computing electronic wave function and properties of periodic systems
ADF 2016.101 HPC Amsterdam Density Functional
LAMMPS 20171023 HPC Large-scale Atomic/Molecular Massively Parallel Simulator
NWChem 6.5.26243 HPC Application for high performance computational chemistry
GROMACS 2018.2 HPC, Spear GROMACS is a versatile package to perform molecular dynamics
Desmond 3.4.0.2 HPC Simulation Software for Molecular Dynamics
Chimera 1.8.1 Spear Molecular modeling system
PyMOL 1.6 Spear A molecular visualization system on an open-source Python foundation
NAMD 2.10 HPC, Spear A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Gaussian v09 HPC, Spear An application that provides state-of-the-art capabilities for electronic structure modeling
ORCA 4.0.0.2 HPC ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties