Software Packages Available

Abaqus

Abaqus 6.7 from Simulia (a Dassault Systems brand) is available on the Saguaro cluster. Abaqus enables a wide range of linear and nonlinear engineering simulations to be carried out efficiently, accurately, and reliably. The extensive analysis capabilities, superb performance, thorough documentation, high quality, and best-in-class support make Abaqus an effective tool for many engineering analyses. Abaqus is supported within the Abaqus/CAE modeling environment for all common pre- and postprocessing needs. In addition, Abaqus can be accessed from within many common modeling environments that may be appropriate to your needs.

Abaqus/CAE v. 6.7 is a complete solution for finite element modeling, visualization, and process automation. With Abaqus/CAE you can quickly and efficiently create, edit, monitor, diagnose, and visualize advanced Abaqus analyses. The intuitive interface integrates modeling, analysis, job management, and results visualization in a consistent, easy-to-use environment that is simple to learn for new users yet highly productive for experienced users. Abaqus/CAE supports familiar interactive computer aided engineering concepts such as feature-based, parametric modeling, interactive and scripted operation, and GUI customization.

Users can create geometry, import CAD models for meshing, or integrate geometry-based meshes that do not have associated CAD geometry. Interfaces for CATIA V5, Pro/ENGINEER, and SolidWorks enable synchronization of CAD and CAE assemblies and enable rapid model updates with no loss of user-defined analysis features.

The open customization toolset of Abaqus/CAE provides a powerful process automation solution, enabling specialists to deploy proven workflows across the engineering enterprise. Abaqus/CAE also offers comprehensive visualization options which enable users to interpret and communicate the results of any Abaqus analysis.

BLAST

BLAST is a bioinformatics tool that was originally developed at the National Center for Biotechnology Information (NCBI). BLAST quickly finds regions of similarity between protein or nucleotide sequences. It does this by comparing a query sequence with a known sequence from any one of a large number of available databases. BLAST then returns the statistical significance of found matches. This enables researchers to, among other things, scan known genomic or protein sequences for traits characterized in other study organisms.

CHARMM

CHARM++

Cobalt

Cobalt is a parallel, compressible Euler/Navier-Stokes flow solver applicable to to geometries of arbitrary complexity. It is used for providing detailed flow field diagnostics and output into major post processors. Cobalt can divide arbitrary grid into zones, and process each zone on a cluster achieving linear scale up.

Maple

Maple is used to perform everyday mathematical calculations, developing models and creating user-friendly technical applications. Typically used interactively on the cluster.

FLUENT

Fluent (version 6.2.16) is a parallel computational fluid dynamics (CFD) code and simulation environment. It can be used to model fluid environments in high levels of detail including thermodynamic states and turbulence.

Saguaro's installation of Fluent includes GAMBIT, the interactive Fluent preprocessor. GAMBIT may be started interactively using X11. This involves starting a job in the serial queue (which will reserve a CPU exclusively for your use). When entering the qsub command, the scheduler will locate an available processor and you will automatically be logged in to the containing node. This process may take a few seconds. When GAMBIT completes, simply log out of the compute node to end your job. Note that this will require your client machine to support X11 forwarding.

Neuron

NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

Silvaco

Silvaco is installed system wide on the cluster and uses licenses provided by the ASU Fulton School of Engineering. Use of the software is limited to the Engineering department without specific use approval.

Star-P

Star-P (version 2.5.1) from Interactive Supercomputing is a parallel execution platform for MATLAB and Python programs. It provides a data-parallel backend for distributed data storage and task-parallel work sharing facilities. It supports interactive and batch modes of execution for both MATLAB and Python, and supports Python modules including R.

Wien2k

The program package WIEN2k performs electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. In DFT the local (spin) density approximation (LDA) or the improved version of the generalized gradient approximation (GGA) can be used. WIEN2k is an all-electron scheme including relativistic effects and has many features.