Software Package:

Gaussian 03

Version:

Revision C.02

Location:

/opt/g03

Description:

Gaussian is a computational chemistry package that has become the standard code for fast electronic structure calculations. It is able to utilize shared-memory multi-processor architectures. Gaussian has been developed over the course of several decades by a host of people, and is now distributed by Gaussian, Inc., Pittsburgh PA.

Related links:

For local usage look at HPCVL Gaussian FAQ.

For more information go to Gaussian web site:
http://www.gaussian.com/

See Also:

Gamess, NWChem, Crystal, Namd2, Amber

Previous Version:

Gaussian 98

Version:

Revision A.11

Location:

/opt/g98

Description:

(see Gaussian 03 above)

Related links:

(see Gaussian 03 above)

Software Package:

ADF and BAND

Version:

2005.1b

Location:

/opt/adf

Description:

ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution). A separate program for calculation on periodic systems (polymers, surfaces and solids) is called BAND. The underlying theory is Density Functional Theory, specifically the solution of the Kohn-Sham equations. ADF is arguably the best available ab-initio code for transition metals and other heavy elements. It is unique in its usage of Slater (exponential) type basis sets, which provides higher accuracy with smaller size. ADF and Band are trademarks of SCM.

Related links:

For local usage look at HPCVL ADF/Band FAQ.

For more information go to the SCM:ADF web site

See Also:

Gaussian, Gamess, NWChem, Crystal, Namd2, Amber

Software Package:

Gamess (US)

Version:

22 FEB 2006 R2

Location:

/opt/gamess

Description:

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. It is particularly suitable for controlled limited or full CI calculations. GAMESS is able to utilize multiple processors. It is maintained by the members of the Gordon research group at Iowa State University.

Related links:

For local usage look at HPCVL Gamess FAQ

For more information go to Gamess website:
http://www.msg.ameslab.gov/GAMESS/GAMESS.html

See Also:

Gaussian, NWChem, Crystal, Namd2, Amber

Software Package:

Northwest Computational Chemistry Package (NWChem)

Version:

5.0 (MPI)

Location:

/opt/nwchem

Description:

NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the High-performance Computational Chemistry group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL).

Related links:

For local usage look at HPCVL NWChem FAQ

For more information go to the NWChem website:

See Also:

Gaussian, Gamess, Crystal, Namd2, Amber

Software Package:

Crystal 98

Version:

1.0b

Location:

/opt/crystal98

Description:

The CRYSTAL package performs ab-initio calculations on the ground-state energy, electronic wave function and properties of periodic systems. Hartree-Fock and Kohn-Sham Hamiltonians (DFT) can be used. Systems may be periodic in 0 (molecules), 1 (polymers), 2 (slabs) or 3 dimensions (crystals). Single-particle wave functions are expressed in terms of linear combinations of so-called Bloch orbitals. The program was designed by V. R. Saunders, R. Dovesi, C. Roetti, M. Causa, N. M. Harrison, and C. M. Zicovich-Wilson. It is the only available solid-state code that is able to perform Hartree-Fock type calculations in a tight-binding model.

Related links:

For local usage look at HPCVL Crystal FAQ

For more information go to the Crystal website

See Also:

Gaussian, Gamess, NWChem, Namd2, Amber

Software Package:

NAMD

Version:

NAMD 2.5b1 (Apr. 2002)

Location:

/opt/namd

Description:

NAMD is a parallel code for molecular dynamics simulation of large biomolecular systems, developed by the Theoretical Biophysics Group ("TBG") in the Beckman Institute of the University of Illinois

Related links:

For local usage look at HPCVL NAMD2 FAQ

For more information go to the NAMD2 website.

See Also:

Gaussian, Gamess, NWChem, Crystal, Amber

Software Package:

Amber

Version:

7

Location:

/opt/amber7

Description:

AMBER is a set of molecular mechanical force fields for the simulation of biomolecules; and a package of molecular simulation programs which includes source code and demos.

Related links:

HPCVL Amber FAQ

For more information go to the Amber website

See Also:

Gaussian, Gamess, NWChem, Crystal, Namd2

Software Package:

Sun HPC ClusterTools

Version:

6.0

Location:

/opt/SUNWhpc

Description:

Sun HPC ClusterTools software provides the tools for developing distributed memory parallel applications and for managing distributed resources in the execution of these applications. The suite consists in Sun MPI Library, Sun Parallel File System, and the Sun Cluster Runtime Environment (CRE) .

Related links:

For local usage look at HPCVL Parallel Programming FAQ

For more information go to SUN HPC website:
http://www.sun.com/solutions/hpc/

See Also:

Sun MPI

Software Package:

Sun Cluster Runtime Environment

Version:

3.0

Location:

/opt/SUNWhpc

Description:

Sun Cluster Runtime Environment (CRE) is the Sun HPC ClusterTools component that serves as the runtime resource manager for message-passing programs. It supports interactive execution of Sun HPC applications on single SMPs or on cluster of SMPs, and gives also information about job activity and cluster resources.

Related links:

For local usage look at HPCVL Parallel Programming FAQ

For more information go to SUN website:
http://www.sun.com/solutions/hpc/

See Also:

SUN HPC ClusterTools, Sun MPI

Software Package:

SUN MPI

Version:

6.0

Location:

/opt/SUNWhpc

Description:

Sun MPI is the Sun's optimized version of the Message Passing Interface (MPI) communications Library. MPI is the standard for writing message-passing programs and, was designed for high performance programming on both massively parallel machines and on workstation clusters.

Related links:

For local usage look at HPCVL Parallel Programming FAQ

For more information go to SUN website:
http://www.sun.com/solutions/hpc/

See Also:

SUN HPC ClusterTools, SUN CRE

Software Package:

PVM (Parallel Virtual Machine)

Version:

3.4

Location:

/usr/local/pvm3

Description:

PVM (Parallel Virtual Machine) is a message passing programming system, designed to link separate host machines to form a ``virtual machine'' which is a single, manageable computing resource. The PVM system is portable to a wide variety of architectures including workstations, multiprocessors and supercomputers.

Related links:

For local usage look at HPCVL PVM FAQ

For more information go to PVM website:
http://www.netlib.org/pvm3/index.html

See Also:

SUN HPC ClusterTools, Sun MPI

Software Package:

HWT (HPCVL Working Template)

Version:

5.3

Location:

/opt/hwt

Description:

The HPCVL Working Template (HWT) is a toolset that facilitates program development, especially in a parallel environment. It contains facilities for the maintanance of multiple program versions from a single source, for automatic relative debugging, and for simple timing of code computer code. The HWT supports the Fortran, C, and C++ programming languages, as well as MPI for distributed-memory, and OpenMP for shared-memory parallel programming.

Related links:

For a short introduction look at the HPCVL HWT FAQ. The HWT manual is also downloadable from our website.

See Also:

Sun MPI, gdb debugger, Sun Studio Programming Environment

Software Package:

Numerical Algorithms Group (NAG)

Version:

Fortran Libraries Mark 21,
C Libraries Mark 8,
fl90 Libraries Release 4,
SMP Libraries Release 2,
Parallel Libraries Release 3,
Iris Explorer Release 5.0

Location:

/opt/nag

Description:

The NAG libraries and supporting software are a large collection of numerical routines ranging from simple implementations of special functions to complex optimization techniques. The libraries include:

Fortran Library (original NAG library routines)
C-Library
fl95 Library
SMP and Parallel Libraries (for parallel execution).

The software comes with a Fortran compiler, and a powerful data visualization tool called "Iris Explorer".

Related links:

For local usage look at our HPCVL NAG FAQ

For more information go to NAG Home page.

See Also:

PETSc

Software Package:

PETSc

Version:

2.1.3

Location:

/usr/local/petsc-2.1.3

Description:

PETSc, the Portable Extensible Toolkit for Scientific computation, is a suite of data structures and routines for the parallel (and serial) implementation of large scale application codes. PETSc uses the MPI (e.g. Sun MPI) library for its message-passing communications.

Related links:

For local usage look at HPCVL Parallel Programming FAQ

For more information go to the
PETSc website

See Also:

NAG

Software Package:

FFTW

Version:

3.1.2

Location:

/opt/fftw

Description:

FFTW is allegedly the Fastest Fourier Transform in the West. The package was developed by Matteo Frigo and Steven G. Johnson at MIT and is free software. It consists of C-routines that are accessible via a library archive, and may be used from both C and Fortran programs. The routines have the ability to adopt their algorithm to size and type of the required Fourier transform, as well as to the type of machine on which they are executed. Additionally FFTW provides shared-memory parallelism via multithreading.

Related links:

For more information go to FFTW website:
http://www.fftw.org/

See Also:

NAG

Software Package:

FLUENT

Version:

6.2

Location:

/opt/fluent/Fluent.Inc

Description:

FLUENT is a state-of-the-art computer program for modeling fluid flow and heat transfer in complex geometries. It provides adaptive mesh capabilities and may be run in parallel. It is written in C and uses a client/server architecture. It provides a graphical user interface as well as a batch language. FLUENT is a registered trademark of Fluent Inc, Lebanon NH.

Related links:

For local usage look at our HPCVL Fluent FAQ

For more information go to Fluent website: http://www.fluent.com/

See Also:

Abaqus, PETSc

Software Package:

FIDAP

Version:

8.7

Location:

/opt/fluent/Fluent.Inc

Description:

FIDAP is a finite-element based fluid dynamics analysis package. It allows the modeling of fluid flow, heat transfer and related phenomena in complex geometries. Problems can be solved on unstructure meshes that may be created with ease. The package consists of several modules which may be accessed from a graphical user interface, or called seperately. It supports multiple processor machines for high-performance execution of the finite-element solver. FIDAP is a registered trademark of Fluent Inc, Lebanon NH.

Related links:

For local usage look at our upcoming FIDAP FAQ

For more information go to the FIDAP website

See Also:

Fluent, Abaqus, PETSc

Software Package:

Abaqus

Version:

6.5

Location:

/opt/abaqus

Description:

The ABAQUS suite of software for finite element analysis (FEA) consists of three core products - ABAQUS/Standard, ABAQUS/Explicit and ABAQUS/CAE. ABAQUS/Standard is used to solve traditional implicit finite element analyses, such as static, dynamics, thermal with a wide range of contact and nonlinear material options. ABAQUS/Explicit is focused on transient dynamics and quasi-static analyses using an explicit approach appropriate in many applications such as drop test, crushing and many manufacturing processes. ABAQUS/CAE, is a modeling and visualization environment for ABAQUS analysis products. It offers direct access to CAD models, advanced meshing and visualization, and an exclusive view towards ABAQUS analysis.

Related links:

Please see our Abaqus FAQ for more information

For more information go to the Abaqus website

See Also:

Fluent, Fidap, Adina

Software Package:

Adina

Version:

8.3

Location:

/opt/adina

Description:

Adina is a comprehensive finite-element system that may be used for structural analysis, simulation of fluids, and computations on the interaction of fluids with structures. It is designed with ease of use and broad applicapility in mind. It provides a grahical user interface and can be used on multi-processor machines. Adina is a trademark of ADINA R & D, Inc.

Related links:

For local usage watch out for our upcoming Adina FAQ

For more information go to the Adina website.

See Also:

Abaqus, Fluent, Fidap

Software Package:

AutoDock

Version:

3.05

Location:

/opt/autodock

Description:

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock has been widely used and there are many examples of its successful application in the literature. It is very fast, provides high quality predictions of ligand conformations, and good correlations between predicted inhibition constants and experimental ones. Usage of AutoDock on HPCVL machines is restricted to non-commercial academic research.

Related links:

For local usage look at HPCVL AutoDock FAQ. For more information go to the AutoDock website

Software Package:

NAG Iris Explorer

Version:

5.0

Location:

/opt/nag/explorer

Description:

The Iris Explorer is a very powerful visualization tool. It is designed in a modular manner to offer maximum flexibility and feartures an intuitive point-and click interface. Visualizations ranging from simple bar graphs to complex color-coded contour graphics on 3D objects are possible. In addition, users can develop and program their own modules with the help of a library of visualization functions. The Iris Explorer is provided and licensed by the Numerical Algorithms Group (NAG).

Related links:

For local usage look at HPCVL Iris Explorer FAQ. For more information go to the Iris Explorer Online Documentation at the NAG Website.

Software Package:

Grid Engine

Version:

6.0 Upgrade 8

Location:

/opt/n1ge6

Description:

Sun Grid Engine is a load management tool for heterogeneous, distributed computing environments. Grid Engine provides an effective method for distributing the batch workload among multiple computational servers. In doing so, it increases the productivity of all of the machines and simultaneously increases the number of jobs that can be completed in a given time period. Also, the need for outside computational resources is reduced. All production jobs on the Sun Fire Cluster have to be submitted to Grid Engine.

Related links:

For local usage look at HPCVL Grid Engine FAQ

For more information go to SUN Grid Engine website: http://wwws.sun.com/software/gridware/

See Also:

SUN HPC ClusterTools, SUN CRE

Software Package:

gdb

Version:

6.1

Location:

/opt/csw/bin

Description:

The GNU debugger (gdb) is a standard tool for debugging C and (to a lesser extent) Pascal code. It is largely line-based and uses a standard set of commands, such as "print", "stop at" or "stop in". The main reason for its installation on the SunFire cluster is its use in combination with the Gnu Pascal compiler gpc. This debugger is public domain and very portable. Note that for Fortran and C/C++ programs, the use of Sun Studio is recommended.

Related links:

For more information go to GNU gdb website: http://www.gnu.org/software/gdb/gdb.html

See Also:

gpc

Software Package:

Sun Studio

Version:

11

Location:

/opt/SUNWspro

Description:

Sun Studio is an extensive developer's programming package that includes compilers (Fortran 77, 90 and 95, C, C++), a debugger, and various profiling tools. It features, a graphical user interface, interfaces with a variety of editors, as well as a makefile facility. It lets you develop and modify programs and keep track of your work in the form of "projects".

Related links:

For local usage look at HPCVL Setup FAQ

For more information go to the
SUN website

See Also:

FORTRAN, C/C++, gpc

Software Package:

Sun C/C++ compiler

Version:

5.8

Location:

/opt/SUNWspro

Description:

The Sun C/C++ compiler is a compiler that offers a large number of options and is designed to produce highly optimized object code on our Sun UltraSparc computers. The C compiler is able to "loop parallelize" code for execution on a multi-processor shared memory system, as well as to interface with the C bindings of the MPI parallel message-passing system. The compiler can handle code that is written in C and C++. It is part of the Studio developer's package.

Related links:

For local usage look at HPCVL Setup FAQ

For more information go to SUN website:
http://developers.sun.com/sunstudio

See Also:

FORTRAN, gpc

Software Package:

Sun Fortran (f95) compiler

Version:

8.2 (f77, f90, f95)

Location:

/opt/SUNWspro

Description:

The Sun Fortran compiler is a compiler that offers a large number of options and is designed to produce highly optimized object code on our Sun UltraSparc computers. It is able to "loop parallelize" code for execution on a multi-processor shared memory system, as well as to interface with the Fortran bindings of the MPI parallel message-passing system. The compiler can handle code that is written in Fortran 77 (f77), Fortran 90, and Fortran 95 (f90, f95). It is part of the Sun Studio developer's package.

Related links:

For local usage look at HPCVL Setup FAQ

For more information go to SUN website: http://developers.sun.com/sunstudio

See Also:

C/C++, gpc

Software Package:

gpc (Gnu Pascal Compiler)

Version:

2.1

Location:

/usr/local/bin

Description:

The GNU Pascal compiler is a public-domain compiler that has a great deal of extensions and compatibility features built into it, and is designed to be very portable. It supports ISO-7185 Standard Pascal and ISO-10206 Extended Pascal, as well as Borland Pascal 7.0 and parts of Pascal-SC. It makes use of some features of the Gnu C Compiler (GCC) and is able to use the GNU debugger (gdb).

Related links:

For local usage look at HPCVL Pascal FAQ

For more information go to Gnu Pascal Compiler website:
http://www.gnu-pascal.de/

See Also:

FORTRAN, C/C++, gdb

Software Package:

emacs/xemacs

Version:

Location:

/opt/csw/bin/ (emacs) and /opt/SUNWspro/bin/xemacs (xemacs)

Description:

Emacs. is a powerful editing written originally by Richard Stallman and is common to most Unix systems. There exists a wealth of information of the use of Emacs. Emacs can be started either at the command line or using the Emacs graphical interface.
Xemacs is the version that comes with Sun Studio. It is very useful when you run or debug your code.

Related links:

Refer to the Emacs man page for more information on the details of usage or go to the following Emacs FAQ

See Also:

vi, Emacs Reference Card

Software Package:

vi

Version:

Location:

/usr/bin

Description:

vi is a text editor which was originally written by Bill Joy in 1976 and is loosely based on a combination of ed and ex. vi comes standard with most Unix environments. It is not graphically driven, hence there is no overhead associated with exporting graphics across a network. The new user to vi may find it somewhat cumbersome at first, but with experience many choose to solely use vi as it provides a portable and dynamic editing environment from which to work. There exists a wealth of documentation and tutorials on the use of vi.

Related links:

For a quick reference guide to common vi commands please refer to
VI Editor Command Reference.

See Also:

emacs/xemacs.