Bioinformatics
Compilers and Programming Tools
Computational Chemistry
File System
Finite Element Solvers
Graphics
Miscellaneous
Numerical Libraries
Optimization
Parallel Programming Languages and Tools
Queueing and Scheduling Systems
Solid Modeling
Statistics

BLAST

National Center for Biotechnology Information

BLAST is the Basic Local Alignment Search Tool. It is a set of search programs designed to explore all available sequence databases in either protein or DNA. This software has been designed to achieve great speeds while keeping a well-defined statistical interpretation.

BLAST is available on the following HPC machines:

LION-XO

2.2.15

http://gears.aset.psu.edu/hpc/software/bioinf/blast

09-Nov-2006

Versions listed in bold are the default version.

Cister

Martin Frith

Cister predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.

Cister is available on the following HPC machines:

LION-XO

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/cister

09-Nov-2006

Versions listed in bold are the default version.

Intel C++ Compiler

Intel

The Intel C++ Compiler delivers optimal performance on all Intel 32-bit processors, including the Pentium 4 and Intel Xeon, the 64-bit Intel Itanium Processor, the 64-bit x86_64 processor, and the AMD Opteron

ICC is available on the following HPC machines:

LION-XO

9.0

http://gears.aset.psu.edu/hpc/software/comp/icc

31-Jan-2006

Versions listed in bold are the default version.

Intel Fortran Compiler

Intel

The Intel Fortran Compiler delivers optimal performance on all Intel 32-bit processors,including the Pentium 4 and Intel Xeon processors, and the 64-bit Intel Itanium processor.

IFC is available on the following HPC machines:

LION-XO

9.0

http://gears.aset.psu.edu/hpc/software/comp/ifc

31-Jan-2006

Versions listed in bold are the default version.

Lahey/Fujitsu Fortran 95 PRO

Lahey Computer Systems, Inc.

LF95 is an optimizing, ANSI/ISO-standard, Fortran 95 language system and development environment. It offers fast execution speed, quad-precision data types, and full Fortran 95 support.

LF95 is available on the following HPC machines:

LION-XO

8.00a

http://gears.aset.psu.edu/hpc/software/comp/lf95

11-Oct-2007

Versions listed in bold are the default version.

PathScale Compiler Suite

PathScale, Inc.

The PathScale compilers are a set of high-performance C, C++, and Fortran compilers targetted at 64-bit platforms such as AMD's Opteron and Intel's EM64T

pcs is available on the following HPC machines:

LION-XO

2.3

No on-line instructions available

03-Oct-2006

Versions listed in bold are the default version.

Portland PGI Compilers and Tools

The Portland Group

The PGI Compilers and Tools suite offers parallel Fortran, C, and C++ Compilers and tools for Pentium Processor-based workstations.

PGI is available on the following HPC machines:

LION-XO

6.1-1

http://gears.aset.psu.edu/hpc/software/comp/pgi

31-Jan-2006

Versions listed in bold are the default version.

SUN Java2

Sun Microsystems

Java 2 Platform, Standard Edition (J2SE) software is a premier solution for rapidly developing and deploying mission-critical, enterprise applications.

SunJava2 is available on the following HPC machines:

LION-XO

1.4.2_05

http://gears.aset.psu.edu/hpc/software/comp/sunjava2

31-Jan-2006

Versions listed in bold are the default version.

CPMD

CPMD Consortium

The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

CPMD is available on the following HPC machines:

LION-XO

3.9-1

No on-line instructions available

04-Feb-2005

Versions listed in bold are the default version.

Gaussian 03

Gaussian, Inc.

Gaussian 03 is designed to model a broad range of molecular systems under a variety of conditions performing its computations starting from the basic laws of quantum mechanics.

G03 is available on the following HPC machines:

LION-XO

E.01

http://gears.aset.psu.edu/hpc/software/compchem/g03

03-Jan-2008

Versions listed in bold are the default version.

GaussView

Gaussian, Inc.

GaussView makes using Gaussian 03 simple and straightforward: * Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. * Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run. * Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on. We’ll look at many of them in the following pages.

gv is available on the following HPC machines:

LION-XO

4.1

http://gears.aset.psu.edu/hpc/software/compchem/gv

20-Mar-2008

Versions listed in bold are the default version.

Jaguar

Schrödinger, Inc.

Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory.

Jaguar is available on the following HPC machines:

LION-XO

55.011

No on-line instructions available

04-Feb-2005

Versions listed in bold are the default version.

MacroModel

Schrödinger, Inc.

MacroModel is an integrated software system for modeling organic and bioorganic molecules using molecular mechanics.

MModel is available on the following HPC machines:

LION-XO

86.008

No on-line instructions available

04-Feb-2005

Versions listed in bold are the default version.

NWChem

William R. Wiley Environmental Molecular Sciences Laboratory (EMSL)

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 Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.

nwchem is available on the following HPC machines:

LION-XO

5.0

http://

17-Dec-2007

Versions listed in bold are the default version.

ABAQUS

Hibbitt, Karlsson & Sorensen, Inc. (HKS)

ABAQUS is a finite element solver used for stress, heat transfer, and other types of analysis in mechanical, structural, civil, biomedical, and related engineering applications.

Abaqus is available on the following HPC machines:

LION-XO

6.6-1

http://gears.aset.psu.edu/hpc/software/fem/abaqus

20-Feb-2007

Versions listed in bold are the default version.

ANSYS

Ansys, Inc.

ANSYS/Multiphysics is a finite element design and analysis software that allows a user to model problems in structures, thermal/fluid flow and electromagnetics.

Ansys is available on the following HPC machines:

LION-XO

11.0

http://gears.aset.psu.edu/hpc/software/fem/ansys

15-Nov-2007

Versions listed in bold are the default version.

COMSOL Multiphysics

The COMSOL Group

COMSOL Multiphysics is a modeling package for the simulation of any physical process you can describe with partial differential equations (PDEs). It features state-of-the-art solvers that address complex problems quickly and accurately, while its intuitive structure is designed to provide ease of use and flexibility.

comsol is available on the following HPC machines:

LION-XO

3.3

No on-line instructions available

26-Oct-2006

Versions listed in bold are the default version.

FLUENT

Fluent, Inc.

The broad physical modeling capabilities of FLUENT have been applied to industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to glass production, from blood flow to semiconductor manufacturing, from clean room design to wastewater treatment plants. The ability of the software to model in-cylinder engines, aeroacoustics, turbomachinery, and multiphase systems has served to broaden its reach.

fluent is available on the following HPC machines:

LION-XO

6.2.16

No on-line instructions available

31-Mar-2008

Versions listed in bold are the default version.

GAMBIT

Fluent, Inc.

GAMBIT is Fluents geometry and mesh generation software. GAMBITs single interface for geometry creation and meshing brings together most of Fluents preprocessing technologies in one environment. Advanced tools for journaling let you edit and conveniently replay model building sessions for parametric studies. GAMBITs combination of CAD interoperability, geometry cleanup, decomposition and meshing tools results in one of the easiest, fastest, and most straightforward preprocessing paths from CAD to quality CFD meshes.

gambit is available on the following HPC machines:

LION-XO

2.1.2

No on-line instructions available

31-Mar-2008

Versions listed in bold are the default version.

LS-DYNA

Livermore Software Technology Corporation (LSTC)

LS-DYNA is a general-purpose, explicit finite element program used to analyze the nonlinear dynamic response of three-dimensional structures. LS-DYNA can predict how a prototype will respond to real-world events, thus minimizing the time spent in design.

lsdyna is available on the following HPC machines:

LION-XO

9.70-d-6763

No on-line instructions available

07-Apr-2006

Versions listed in bold are the default version.

PyMol

DeLano Scientific, LLC

PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.

pymol is available on the following HPC machines:

LION-XO

20080205-cvs

http://pymol.sourceforge.net/html/

07-Feb-2008

Versions listed in bold are the default version.

AMD Core Math Library (ACML)

AMD

The AMD Core Math Library (ACML) provides developers of scientific and engineering software with a set of linear algebra, fast Fourier transforms and vector math functions optimized for the latest x86_64 processors from AMD. ACML also works with x86_64 Intel processors. ACML contains LAPACK, the basic linear algebra subprograms (BLAS), and the extended BLAS (sparse). In addition, there is a set of fast Fourier transforms in single- and double-precision, real and complex data types.

ACML is available on the following HPC machines:

LION-XO

4.0.1

http://gears.aset.psu.edu/hpc/software/numlib/acml

13-Nov-2007

Versions listed in bold are the default version.

ATLAS

netlib.org

The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.

ATLAS is available on the following HPC machines:

LION-XO

3.6.0

http://gears.aset.psu.edu/hpc/software/numlib/atlas

20-Feb-2007

Versions listed in bold are the default version.

IMSL

Visual Numerics

IMSL is a collection of mathematical and statistical functions that programmers can embed into their applications. The objective of IMSL is to provide high-performance computing and expertise needed to develop and execute sophisticated numerical applications.

IMSL is available on the following HPC machines:

LION-XO

CTT6

http://gears.aset.psu.edu/hpc/software/numlib/imsl

20-Feb-2007

Versions listed in bold are the default version.

Intel Math Kernel Library

Intel

The Intel Math Kernel Library provides developers of scientific and engineering software with a set of linear algebra, fast Fourier transforms and vector math functions optimized for the latest Intel Pentium 4 and Itanium processors, as well as the x86_64 processors from both Intel and AMD. MKL contains LAPACK, the basic linear algebra subprograms (BLAS), and the extended BLAS (sparse). In addition, there is a set of fast Fourier transforms in single- and double-precision, real and complex data types with both Fortran and C interfaces. MKL also includes a set of vectorized transcendental functions in the Vector Math Library (VML), offering both high performance and excellent accuracy compared to the libm functions for most of the processors.

MKL is available on the following HPC machines:

LION-XO

8.01

http://gears.aset.psu.edu/hpc/software/numlib/mkl

20-Feb-2007

Versions listed in bold are the default version.

GAMS

GAMS Development Corporation

No description available.

GAMS is available on the following HPC machines:

LION-XO

22.0

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/BARON

GAMS Development Corporation

No description available.

BARON is available on the following HPC machines:

LION-XO

7.4

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/CONOPT

GAMS Development Corporation

No description available.

CONOPT is available on the following HPC machines:

LION-XO

3

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/CPLEX

GAMS Development Corporation

No description available.

CPLEX is available on the following HPC machines:

LION-XO

9.1

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/DICOPT

GAMS Development Corporation

No description available.

DICOPT is available on the following HPC machines:

LION-XO

2x-C

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/MINOS

GAMS Development Corporation

No description available.

MINOS is available on the following HPC machines:

LION-XO

5.4

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/MPSGE

GAMS Development Corporation

No description available.

MPSGE is available on the following HPC machines:

LION-XO

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/PATH

GAMS Development Corporation

No description available.

PATH is available on the following HPC machines:

LION-XO

4.6

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/SBB

GAMS Development Corporation

No description available.

SBB is available on the following HPC machines:

LION-XO

http://www.gams.com/docs/document.htm

02-Feb-2006

Versions listed in bold are the default version.

GAMS/SNOPT

GAMS Development Corporation

No description available.

SNOPT is available on the following HPC machines:

LION-XO

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG AMPL

ILOG

AMPL is a comprehensive, powerful and flexible algebraic modeling language for the linear, nonlinear and integer programming problems often encountered in optimization.

ampl is available on the following HPC machines:

LION-XO

9.0

No on-line instructions available

31-Jan-2006

LION-XO

9.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG CPLEX

ILOG

ILOG CPLEX delivers high-performance, robust, flexible optimizers for solving linear, mixed-integer and quadratic programming problems in mission-critical resource allocation applications.

cplex is available on the following HPC machines:

LION-XO

9.0

No on-line instructions available

31-Jan-2006

LION-XO

9.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG Scheduler

ILOG

ILOG Scheduler is a software component that supplements ILOG Solver by providing specialized modeling and algorithmic enhancements for solving problems that involve scheduling resources and tasks over a given period of time.

scheduler is available on the following HPC machines:

LION-XO

6.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG SOLVER

ILOG

ILOG Solver is ILOG's constraint-based optimization engine, providing cutting-edge optimization technology that uses logical contraints to power scheduling, sequencing, timetabling, configuration, dispatching and resource-allocation applications.

solver is available on the following HPC machines:

LION-XO

6.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

Infinicon MPI

SilverStorm Technologies (Infinicon)

The Infinicon MPI is a version of the Argonne National Laboratory's MPI implementation, MPICH, with functionality added to enable it to run natively over Infinicon Infiniband, a very high-bandwidth, ultra low-latency network interconnect.

infmpi is available on the following HPC machines:

LION-XO

1.2.5

http://gears.aset.psu.edu/hpc/software/parlib/infinicon

20-Feb-2007

Versions listed in bold are the default version.

MPICH

Argonne National Laboratory Mathematics and Computer Science Divison

MPICH is a freely avaliable, portable implementation of MPI, the standard for message-passing libraries. MPICH runs over fast-ethernet on the machines that it is installed on. It is recommended that if you have code that is communication-intensive that you use one of the MPIs that use a high-speed network.

MPICH is available on the following HPC machines:

LION-XO

1.2.5.2

http://gears.aset.psu.edu/hpc/software/parlib/mpich

31-Jan-2006

Versions listed in bold are the default version.

R

Free Software Foundation

R is a language and environment for statistical computing and graphics. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R is available on the following HPC machines:

LION-XO

2.3.1

http://gears.aset.psu.edu/hpc/software/statistics/r/

09-Nov-2006

Versions listed in bold are the default version.

SAS

SAS

SAS provides tools for mastering data access, management, analysis, and presentation. SAS provides a scalable, integrated software environment specially designed for data access, transformation and reporting. It includes a fourth-generation programming language; ready-to-use programs for data manipulation, information storage and retrieval, descriptive statistics and report writing; and a powerful macro facility that reduces programming time and maintenance headaches.

SAS is available on the following HPC machines:

LION-XO

8.02.02

No on-line instructions available

03-Oct-2006

Versions listed in bold are the default version.