Bioinformatics
Compilers and Programming Tools
Computational Chemistry
Finite Element Solvers
Graphics
Numerical Libraries
Optimization
Parallel Programming Languages and Tools
Solid Modeling
Statistics

Ancestrymap

The Broad Institute

The software estimates the ancestry along the genome of a sample population resulting from recent admixture between two ethnic groups. The program uses data from individuals genotyped at a set of markers, where the markers chosen are preferably the ones that differ significantly in frequency between the two ancestral populations.

ancestrymap is available on the following HPC machines:

Unisys

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

Versions listed in bold are the default version.

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:

Unisys

2.2.11

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

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:

Unisys

9.0

http://rcc.its.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:

Unisys

9.0

http://rcc.its.psu.edu/hpc/software/comp/ifc

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:

Unisys

3.9.1

http://rcc.its.psu.edu/hpc/software/compchem/CPMD

22-Sep-2008

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:

Unisys

6.8-1

http://rcc.its.psu.edu/hpc/software/fem/abaqus

10-Sep-2008

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:

Unisys

11.0

http://rcc.its.psu.edu/hpc/software/fem/ansys

31-Mar-2008

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:

Unisys

6.3.26

No on-line instructions available

14-Oct-2009

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:

Unisys

2.3.16

No on-line instructions available

22-Sep-2008

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:

Unisys

10.0.3.020

http://rcc.its.psu.edu/hpc/software/numlib/mkl

15-Sep-2008

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:

Unisys

10.0

No on-line instructions available

15-Sep-2008

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:

Unisys

11.0

No on-line instructions available

15-Sep-2008

Unisys

9.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG OPL Development Studio

ILOG

ILOG OPL Development Studio's modeling language helps you develop optimization applications quickly, avoiding low-level programming tasks like memory management. You slash the time necessary to deliver high-performance optimization applications.

opl is available on the following HPC machines:

Unisys

3.7.1

No on-line instructions available

16-Sep-2008

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:

Unisys

6.3

No on-line instructions available

15-Sep-2008

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:

Unisys

6.3

No on-line instructions available

15-Sep-2008

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:

Unisys

1.2.7p1

http://rcc.its.psu.edu/hpc/software/parlib/mpich

15-Sep-2008

Versions listed in bold are the default version.

MPIGM

Myricom

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

MPIGM is available on the following HPC machines:

Unisys

1.2.6..14b

http://rcc.its.psu.edu/hpc/software/parlib/mpigm

15-Sep-2008

Versions listed in bold are the default version.

MSC/Patran

MSC Software

MSC/PATRAN provides an open, extensible CAE environment and integrated product set for multi-disciplinary design and analysis which is used to simulate product performance and manufacturing process early in the design cycle. MSC/PATRAN includes a pre- and post-processor with modeling, data integration, simulation, and results evaluation capabilities which are required to simulate product performance.

Patran is available on the following HPC machines:

Unisys

2007a

No on-line instructions available

14-Oct-2009

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:

Unisys

2.7.2

http://rcc.its.psu.edu/hpc/software/statistics/r/

15-Sep-2008

Versions listed in bold are the default version.