Research Software
IS&T currently provides research computing support for the following applications:
Abinit
Abinit is a computing program that allows users to calculate properties of systems made of electrons and nuclei, including total energy, charge density, and electronic structure. Using various molecular theories, Abinit can also perform molecular dynamics simulations, generate dynamical matrices, compute excited states, and more. Abinit is a collaboration focused tool, and allows for the modification of coding and programing to suit your needs and the needs of your project.
Abinit is available on the following HPC resources: Vela
Get additional information on Abinit.
Gromacs
Gromacs is a high performance program used to compute molecular dynamics. Gromacs focuses on calculating biochemical molecules like proteins, lipids, and nucleic acids that contain complicated bonded interactions. However, Gromacs’ efficient and speedy calculations also lend well to non-biochemical molecules.
Gromacs is available on the following HPC resources: Vela
Get additional information on Gromacs.
EnginFrame
EnginFrame is the most advanced, commercially supported Grid Portal in the industry, and has a proven track record of successful production deployments within corporate networks and research Grids. EnginFrame enables efficient Inter-/Intranet access to Grid-enabled infrastructures. HPC clusters, data, licenses, batch & interactive applications can be accessed by any client using a standard browser.
Software used on the following HPC resources: CARINA (Version 5)
Get additional information on EnginFrame .
LoadLeveler
Tivoli Workload Scheduler LoadLeveler is a parallel job scheduling system that allows users to run more jobs in less time by matching each job’s processing needs and priority with the available resources, thereby maximizing resource utilization. LoadLeveler also provides a single point of control for effective workload management and supports high availability configurations. In addition, it offers detailed accounting of system utilization for tracking or chargeback.
Software used on the following HPC resources: CARINA (Version 4.1.0.8)
Get additional information on LoadLeveler.
Load Sharing Facility (LSF)
Platform LSF is the most powerful workload manager for demanding, distributed and mission-critical high performance computing environments. It provides a complete set of workload management capabilities; all designed to work together to address your high performance computing needs.
Software used on the following HPC resources: OCTANS (Version 7 Update 6)
Get additional information on Load Sharing.
Gaussian
Gaussian is an electronic structure program, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).
Software used on the following HPC resources: CARINA (G03) and OCTANS (G03)
Get additional information on Gaussian.
MATLAB
Application for technical computing and model-based design. Core products are MATLAB® for mathematical calculations, analyzing and visualizing data, and writing applications; and Simulink® for modeling and simulating complex dynamic systems.
Georgia State has negotiated with The MathWorks, Inc. for a Total Academic Headcount (TAH) Campus License Agreement. The TAH Campus License provides access to MATLAB standard configurations and a set of additional products available to any faculty, staff and student of Georgia State. More information on how to start using the campus-wide MATLAB license.
Matlab on Linux high-performance research cluster, MATLAB and MATLAB Distributed Computing Server
Software used on the following HPC resources: OCTANS (Matlab Distributed Computing Server 2012a)
Get additional information on MATLAB.
AMMP
AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP.
Software used on the following HPC resources: OCTANS (Custom Installation)
Get additional information on AMMP.
Amber
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.
Software used on the following HPC resources: CARINA (Version 8)
Get additional information on Amber.
SAS
SAS helps solve next-generation business problems with market-leading business analytics solutions. Through advancements in high-performance computing, improvements in environment management, enhancements in data management, and expanded analytics capabilities to better manage and process “big data,” SAS software’s “big analytics” technologies are embedded in a framework that supports the entire decision-making process.
Software can be found on the following HPC resources: CARINA (Version 9.2)
Get additional information on SAS.
NAMD
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
Software can be found on the following HPC resources: CARINA (Versions 2.7 and 2.8)
Get additional information on NAMD.
The R Project for Statistical Computing
R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, etc.) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.
Software used on the following HPC resources: OCTANS (Version 2.13.2)
Get additional information on the R Project .
NWChem
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
NWChem software can handle:
Biomolecules, nanostructures, and solid-state
From quantum to classical, and all combinations
Gaussian basis functions or plane-waves
Scaling from one to thousands of processors
Properties and relativity
Software used on the following HPC resources: OCTANS (Version 6.0)
Get additional information on NWCHemat.
Mathematica
Almost any workflow involves computing results, and that’s what Mathematica does—from building a hedge fund trading website or publishing interactive engineering textbooks to developing embedded image recognition algorithms or teaching calculus.
Mathematica is renowned as the world’s ultimate application for computations. But it’s much more—it’s the only development platform fully integrating computation into complete workflows, moving you seamlessly from initial ideas all the way to deployed individual or enterprise solutions.
Software used on the following HPC resources: OCTANS (Version 8.0)
Get additional information on Mathematica.
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