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 |
|---|---|---|---|
| ADF | 2016.101 | HPC | Amsterdam Density Functional |
| atsas | 2.6.1 | HPC | A program suite for small-angle scattering data analysis from biological macromolecules |
| Blender | 2.69 | HPC | Blender is a free and open source 3D animation suite |
| 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 |
| freefem++ | 3.31-2 | HPC | Partial differential equation solver based on the finite element method |
| Gaussian | v09 | HPC, Spear | An application that provides state-of-the-art capabilities for electronic structure modeling |
| Gerris | 1.3.2 | HPC | Solver of partial differential equations used in fluid flow. |
| Grace | 5.1.22 | HPC, Spear | A WYSIWYG 2D plotting tool for scientific graphing |
| GROMACS | 4.5.7 | 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 |
| IBM ILOG CPLEX Optimization Studio | 12.5 | HPC, Spear | Mathematical optimization software package |
| LAMMPS | 20150316 | HPC | Large-scale Atomic/Molecular Massively Parallel Simulator |
| MATLAB | 2015b | HPC, Spear | A high-level language and interactive environment for numerical computation, visualization, and programming |
| moltemplate | 1.34 | HPC | A general text-based molecule builder for LAMMPS. |
| NWChem | 6.3.2 | HPC | Application for high performance computational chemistry |
| ORCA | 3.0.0 | HPC | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties |
| ParaView | 4.4.0 | HPC | ParaView is an open-source, multi-platform data analysis and visualization application |
| PyMOL | 1.6 | Spear | A molecular visualization system on an open-source Python foundation |
| python-ase | 3.9.1.4567 | HPC | ASE is an Atomistic Simulation Environment written in the Python |
| Quantum ESPRESSO | 5.3.0 | HPC | Nanoscale electronic-structure calculations and materials modeling |
| R (statistical computing) | 3.1.3 / 3.2.0 | HPC, Spear | A popular, full featured, statistical computing package |
| 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 | 2.6.3 | HPC, Spear | A software package for visualizing scientific results |
Programming Languages and Compilers
| Package | Vers | Systems | Summary |
|---|---|---|---|
| Anaconda | 2.7 | HPC | Python 2.7 with 195 popular packages |
| GNU Compilers | 4.4.6 | HPC, Spear | GNU C, C++, and Fortran Compilers |
| GNU Octave | 3.4.2 | HPC, Spear | A high-level language, primarily intended for numerical computations |
| HDF5 | 1.8.12 | HPC | unique technology suite that makes possible the management of large and complex data |
| Hypre | 2.8.0b | HPC | Library for solving large, sparse linear systems of equations on massively parallel computers |
| 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 |
| Python | 2.7.5, 3.5.1 | HPC, Spear | Interactive, object-oriented, extensible programming language |
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 | 8.2.1 | HPC | C++ software library supporting the creation of finite element codes. |
| FFTW | 3.3.4 | HPC | C library to compute the discrete Fourier transforms |
| LAPACK | 3.8.4 | HPC | Standard software library for linear algebra |
| Model Coupling Toolkit (MCT) | 2.8.3 | HPC | Set of open-source software tools for creating coupled models |
| NAMD | 2.10 | HPC, Spear | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
| netCDF | 4.3.3.1 | HPC | libraries for representing scientific data |
| SuperLU | 4.3 | HPC | Library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
Bioinformatics
| Package | Vers | Systems | Summary |
|---|---|---|---|
| ABySS | 1.3.6 | HPC | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
| Biopython | 1.58 | HPC | Python library for computational molecular biology. |
| Bowtie | 1.0.0 | HPC, Spear | Bowtie is an ultrafast, memory-efficient short read aligner |
| Bowtie2 | 2.1.0 | HPC, Spear | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
| BWA | 0.7.5a | HPC, Spear | Software package for mapping low-divergent sequences |
| Cufflinks | 2.2.1 | HPC, Spear | Transcript assembly, differential expression, and differential regulation for RNA Sequencing |
| FASTQC | 0.11.3 | Spear | A quality control tool for high throughput sequence data. |
| LAST | 4.11 | HPC, Spear | Finds similar regions between sequences, and aligns them. |
| 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 |
| TopHat | 2.0.14 | HPC, Spear | A spliced read mapper for RNA Sequencing |
| Trimmomatic | 0.33 | Spear | A flexible read trimming tool for Illumina NGS data |