Software on Quest
Below is a list of key software programs installed on Quest for general use.
This list is subject to change, and additional software not listed here may be available. For the complete list, run the command, module available. Except where noted, Modules Software Environment Manager must be used to set up your environment to use the Quest software.
- ATLAS - Automatically Tuned Linear Algebra System, compiled for non-hyperthreading and tested.
- Boost C++ Libraries - Portable C++ source libraries that work well with the C++ Standard Library.
- Charm++ - Object oriented programming language based on C++ for parallel programming.
- Cmake - A cross platform make needed by a few environments in order to build their software.
- CP2K – Open source molecular dynamics program written in Fortran 95.
- Eclipse – A multi-language integrated development environment (IDE).
- Espresso – A web editor for Mac users.
- FFTW – A software library for computing discrete Fourier transforms (DFTs).
- Firefox - Web browser.
- git - A collaborative source code versioning system.
- gnuplot - An open source plotting program. RHEL's version doesn't contain some of the label manipulation routines that later versions have.
- Grace – A 2D plotting tool for X11 system and M*tif, designed for use on Unix.
- gsl - Gnu Scientific Library.
- HDF5 – A data model, library, and file format for storing and managing large data sets.
- KNITRO - A solver for nonlinear optimization. Programming interfaces for MATLAB, C/C++, Fortran and Java.
- LAMMPS – A classical molecular dynamics code for soft and solid-state materials.
- Lumerical Solutions FDTD – A 3D Maxwell solver for analyzing interactions of UV, visible, and IR radiation.
- A high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation. See Using MATLAB on Quest for more information.
- Meep – A finite-difference time-domain (FDTD) simulation software package.
- Metis – A set of serial programs for partitional graphs, finite element meshes, and producing fill reducing orderings for sparse matrices.
- NWChem – An ab initio computational chemistry software, also including quantum chemical and molecular dynamics functionality.
- Octave – A high-level programming language used for numerical computations.
- ParaView - Data Analysis and Visualization for extremely large datasets using distributed memory resources.
- pdflib-lite - Libraries used in the creation of PDF documents.
- Perl - The ActivePerl distribution of Perl 5.14, a family of high-level, general-purpose, interpreted, dynamic programming languages.
– Several versions of the Anaconda distribution of Python are available. The default module, python/anaconda is for Python 2.7. python/anaconda3 is Python 3.4, while python/anaconda3.6 is Python 3.6. Other Python modules not using the Anaconda distribution are also available on Quest, but their use is highly discouraged and the modules may be removed in the future. If you use python without loading a module, you will be using the default Python installation available from the operating system; again, this is highly discouraged.
- Q-Chem – A comprehensive ab initio quantum chemistry package.
- Qt – A cross-platform application and UI framework for C++ or QML.
- R - Software environment for statistical computing and graphics. Both the command line R progam (R) and RStudio Desktop (rstudio) options are available after loading R modules for versions 3.2.2 and newer. See Using R on Quest for more information.
- ROOT – A set of object-oriented frameworks to store and analyze large data sets.
- Ruby – A dynamic, reflective, object-oriented, general-purpose programming language.
- SAS - SAS is available with modules from the Education Analytical Suite.
- Stata - Stata is available after loading the stata/14 module (module load stata/14). For batch jobs, use stata-se or stata-mp; stata alone starts Stata IC. For interactive jobs where the GUI is desired, use xstata-mp or xstata-se. Stata MP is only licensed for 4 cores per instance. Please do not request more than 4 cores when using Stata MP, as the resources will be wasted.
- SQL database clients – psql, sqlite3, and mysql command line client programs are available without loading any modules.
- TeX Live - the TeX document production system.
- utilities - scripts to help manage projects, and a variety of utility programs (use module help utilities to get a list)
- Wolfram Mathematica - Symbolic computation, high-precision numerical work, graphics and visualization.
- VASP – A package for an initio quantum mechanical molecular dynamics.
- VisIt – A tool for parallel visualization and graphical analysis on Unix and Windows.
- XZ Utils - A general-purpose data compression software.
- Hypre – A library for solving large, sparse linear systems of equations.
- NetCDF – A set of software libraries and self-describing, machine-dependent data formats, supporting creation, access, and sharing of array-oriented scientific data.
- PCRE – Perl Compatible Regular Expressions library is a set of functions that implement regular expression pattern matching using the syntax and semantics as Perl 5.
- ScaLAPACK – A library of high-performance linear algebra routines for parallel distributed memory.
For information on compilers, MPI libraries, and debugging tools, see Compiling Code on Quest.