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 | 1.9.6 | 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++ | 3.62 | Partial differential equation solver based on the finite element method | |
| Gerris | 1.3.2 | Solver of partial differential equations used in fluid flow. | |
| Git | 2.21.0 | 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 | 3.0.0 | 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 | |
| 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 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 |
| 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 | |
| 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 | 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 | |
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, 7.0.1 | A Front-End for LLVM-Based C Compilers | |
| CUDA | 10.1 | 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 | 4.8.5, 8.2.1 | GNU C, C++, and Fortran Compilers | |
| GNU Octave | 4.4.1 | A high-level language, primarily intended for numerical computations | |
| Intel Compilers | 13.0.1 | Intel C, C++, and Fortran Compilers | |
| Julia | 1.1.0 | Recipe | A High-Performance Numerical Computing Environment and Language |
| LLVM | 6.0.0 & 3.9.1 & 7.0.1 | A Toolkit for Building Compilers | |
| MATLAB | 2018b | 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 | 3.3.8, 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 | |
| gurobi | 8.1.0 | A powerful solver available for LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems | |
| 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 | 1.10.4 | unique technology suite that makes possible the management of large and complex data | |
| Hypre | 2.15.1 | 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 | 4.6.2 & 4.2 & 4.4.4 | libraries for representing scientific data | |
| OpenBLAS | 0.3.5 | A Highly Optimized Linear Algebra Library based on GotoBLAS | |
| OpenCV | 3.2.0 | A Powerful Library for Computer Vision Applications | |
| OpenMPI | 4.0.0 | 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. | |
| TensorFlow | 1.9.0 | A Powerful Deep Learning Library with GPU Support | |
Bioinformatics | |||
| 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 | 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 | 0.11.7 | A quality control tool for high throughput sequence data. | |
| FreeSurfer | 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. | |
| 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 | 963 | Sequence Aligning Software | |
| MAFFT | 7.407 | 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, 4.4.0 | 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 | 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 | |
Materials Science and Computational Chemistry | |||
| 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 | |
| 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 | 2019 | 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 | 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 | 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. | |