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