General Supercomputing Techniques

The token  indicates that the package is available at CILEA.

Amira	Amira is a software for scientific visualization based on the latest Open Inventor V6.0 from Mercury Computer Systems. The volume rendering techniques provided in Amira allow for interactive high quality lighted volume rendering, slicing with embossing effect and isosurface extraction. Amira is composed by several visualization packages to cover all the fields of scientific visualization. Amira It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 4.1
ATLAS	The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. ATLAS It's available at CILEA Currently is installed on Exadron Intel Xeon Cluster with version 3.6.0
Avizo	Avizo™ software is a powerful, multifaceted tool for visualizing, manipulating, and understanding scientific and industrial data. Wherever three-dimensional datasets need to be processed, in material sciences, geosciences or engineering applications, Avizo offers abundant state-of-the-art features within an intuitive workflow and easy-to-use graphical user interface. Avizo It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 5.0
Basic Linear Algebra Subprograms	BLAS (Basic Linear Algebra Subprograms) is a standardized set of low-level operations often found in computational kernels. This library is divided into three levels: level 1: are routines about vector-scalar operations, level 2: are about matrix-vector operations, level 3: are about matrix-matrix operations.On high performance machines the level 2 and 3 Blas are more efficient than level 1. It has become common use among computer vendors to make an optimized version of the Blas routines for the specific machines. Basic Linear Algebra Subprograms It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster and the Exadron AMD Opteron Cluster and Intel Xeon QuadCore Cluster H.P. with version Intel MKL and PGI
BLACS	The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. BLACS It's available at CILEA Currently is installed on the Exadron Cluster Intel Xeon with version GNU compilers and with version PGI compilers
CMake	CMake is the cross-platform, open-source make system. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. CMake It's available at CILEA Exadron Intel Xeon Cluster with version 2.4.6 and Exadron AMD Opteron Cluster with version 2.4.8
Coin3D	Coin3D is a high-level 3D graphics toolkit for developing cross-platform real-time 3D visualization and visual simulation software. Coin3D is built on OpenGL and uses scene graph data structures to render 3D graphics in real-time. Basic import, rendering, and interaction with a 3D object can be implemented in just a few lines of code, and programmer efficiency is greatly increased compared with programming directly with OpenGL. Coin3D It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 2.5.0
Cross-Platform Rich Client Development Framework	Qt is a comprehensive development framework that includes an extensive array of features, capabilities and tools that enable development of high-performance, cross-platform rich-client and server-side applications. Cross-Platform Rich Client Development Framework It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 4.3.3
FFTW	FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. FFT It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster and the Exadron AMD Opteron Cluster and Intel Xeon QuadCore Cluster H.P. with version 3.01 Intel and 3.1.2 gcc and 3.01 PGI
GNU Scientific Library	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. GNU Scientific Library It's available at CILEA Exadron Intel Xeon Cluster with version 1.7 and 1.6, Exadron AMD Opteron Cluster with version 1.6
HDF5	FHDF5 is a general purpose library and file format for storing scientific data. It allows creating and storing any kind of scientific data structure, such as images, arrays of vectors, structured and unstructured grids. HDF5 It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster with version 1.6.4 (GNU) 1.6.5 (Intel - PGI) and on the Exadron AMD Opteron Cluster 1.6.5 (Intel).
HPF	High Performance Fortran is a set of extensions to Fortran for the implementation on parallel architectures, particularly for data-parallel computation. It is architecture independent: can be implemented across distributed and shared memory. HPF. It's available at CILEA Currently is installed on the HP servers with the version 3.0.
HSL	HSL: is a set of Fortran codes for many mathematical problems, it is composed in two part: one more update, that is HSL2002, and the other, HSL archive, containings the an old package of previous releases.The routines regard those areas:Differential equations, Eigenvalues and eigenvectors, Mathematical functions, Geometrical problems, Integer valued functions, Sorting Linear programming, Matrices and linear algebra, Nonlinear equations, Input and output aids, Polynomial and rational functions, Numerical integration, Statistics, Interpolation and approximation, Optimization and nonlinear data fitting, Test program generators. Harwell Subroutine Library. It's available at CILEA Currently is installed on the HP servers. with the version 12.0.
IMSL	"IMSL is a collection of mathematical and statistical functions suited for  high-performance computing and for solving sophisticated numerical alghoritms: it has a  version for C (CNL), for Java  (JMSL), and both for  Fortran 77 (FNL) and Fotrtran 90(F90 MP:it uses MPI for computing on distributed memory systems;it includes the whole FNL library). Mathematical routines concern:Linear Systems, Eigensystem Analysis,Interpolation and Approximation, Integration and Differentiation, Differential Equations, Transforms, Nonlinear Equations. Optimizations Statistical routines concern: Basic Statistics, Regression, Correlation and Covariance,Analysis of Variance, Categorical and Discrete Data Analysis, Non parametric Statistics, Tests of Goodness-of-Fit,Time Series and Forecasting, Multivariate Analysis, Survival Analysis, Probability Distribution Functions and Inverses, Random Number Generator." IMSL. It's available at CILEA Currently is installed on the HP servers. with the version 10.4.
Intel® Cluster Toolkit	The Intel® Cluster Toolkit Compiler Edition 3.2 provides the high performance computing (HPC) user with cluster-computing software tools bundled into a single integrated package: Intel® MPI Library, Intel® Math Kernel Library, Intel® Trace Analyzer and Collector, Intel® MPI Benchmarks, Intel Fortran and Intel C/C++ 11.1 compilers. Intel® Cluster Toolkit It's available at CILEA Currently is installed on Exadron Intel Xeon Cluster and Exadron AMD Opteron Cluster and Intel Xeon QuadCore H.P. with version 3.2
KOJAK	KOJAK is a performance-analysis tool for parallel applications supporting the programming models MPI, OpenMP, SHMEM, and combinations thereof. Its functionality addresses the entire analysis process including instrumentation, post-processing of performance data, and result presentation. KOJAK It's available at CILEA Currently is installed on Exadron Intel Xeon Cluster with the version 2.2
LAM/MPI	LAM/MPI is a high-quality open-source implementation of the Message Passing Interface specification, including all of MPI-1.2 and much of MPI-2. Intended for production as well as research use, LAM/MPI includes a rich set of features for system administrators, parallel programmers, application users, and parallel computing researchers. LAM/MPI It's available at CILEA Exadron AMD Opteron Cluster with version 7.1.4 Intel and with version 7.1.4 PGI and with version 7.1.4 GCC
Linear Algebra PACKage	LAPACK is written in Fortran77 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex matrices, in both single and double precision. Linear Algebra PACKage It's available at CILEA Currently is installed on the Currently is installed on Exadron Intel Xeon Cluster and Exadron AMD Opteron Cluster and Intel Xeon QuadCore H.P. with version Intel compilers and with version PGI compilers
MLIB	MLIB is an high performance numerical package optimized for the architecture of HP machines: it consists of  two distinct libraries: 1.LAPACK 2.VECLIB. VECLIB is a collection of subprograms optimized for Hewlett-Packard servers, providing mathematical software, such as sparse linear equation solvers and sparse eigensolvers, and computational kernels,such as the Basic Linear Algebra Subprograms and fast Fourier transforms, for engineering and scientific application programs. MLIB. It's available at CILEA Currently is installed on the HP servers. with the version 8.1.1.
MPI	MPI is a library for message-passing communications designed for high performance parallelism on a wide variety of computing platforms, from massively parallel machines to workstation clusters. MPI It's available at CILEA Currently is installed on the Exadron Cluster Intel Xeon and HP Cluster Intel Xeon QuadCore and Exadron Cluster AMD Opteron with the versions Ethernet MPI-CH 1.2.7, with version Myrinet MPI-CH 1.1.2
NAG parallel Fortran library	The NAG library includes functions for the solution of linear equations, eigenvalue problems, minimization of least squares and general nonlinear problems, together with many other mathematical and statistical algorithms. The NAG Fortran parallel library has been specifically developed to easily enable applications to take advantage of distributed memory parallel computers. NAG parallel Fortran library It's available at CILEA Currently is installed on: Exadron Cluster Intel Xeon and Exadron Cluster AMD Opteron with version Fortran parallel library
NCAR Graphics	NCAR Graphics is a Fortran and C based software package for scientific visualization. NCAR Graphics It's available at CILEA Currently is installed on Exadron Intel Xeon Cluster and Exadron AMD Opteron Cluster and Intel Xeon QuadCore H.P. with version 4.4.1 (Intel and PGI)
Network Common Data Form	NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. Network Common Data Form It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster and on the Exadron AMD Opteron and Intel Xeon QuadCore Cluster H.P. with version 3.6.2
Open Babel	Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Open Babel It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 2.1.1
OpenMOIV	OpenMOIV is an object-oriented 3D multi-platform toolkit that facilitates the rendering and interaction of chemical systems. OpenMOIV is a derived product of Molecular Inventor™, and it is partially compatible with applications developed using Molecular Inventor™. Opposing to the original library, OpenMOIV is multi-platform (you can use in any platform that has a version of the Open Inventor toolkit) and independent of the windowing system. It includes a new set of functionalities to work with protein structures and rendering them with a lot of new display styles. OpenMOIV It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster with version 1.0.3
OpenMP	It is an application programming interface for writing shared memory parallel program. It is a set of directives that extend the Fortran, C and C++ sequential programming model, with single-program multiple data (SPMD) constructs, work-sharing  and synchronization constructs, and provide support for sharing and privatization of data. OpenMP is portable, scalable and gives  a simple and flexible interface for developing parallel applications but it can be used only in shared memory architecture. OpenMP. It's available at CILEA Currently is installed on the AVOGADRO and HP servers. with the version 1.0
OpenMPI	OpenMPI is a library for message-passing communications designed for high performance parallelism on a wide variety of computing platforms, from massively parallel machines to workstation clusters. OpenMPI It's available at CILEA Currently is installed on the Exadron Cluster AMD Opteron with version Infiniband Open MPI March 2006 HP Cluster Intel Xeon QuadCore with version Infiniband Open MPI with version 1.2.5, 1.3.3
PGI® CDK	The PGI CDK Cluster Development Kit® contains all the software development and cluster management tools you need to get a Linux cluster running production applications. It allows a user to compile, debug, and profile the developing code. PGI® CDK It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster and the Exadron AMD Opteron and HP Cluster Intel Xeon QuadCore with version 9.0-2
PVM	Parallel Virtual Machine  is an old message-passing library, as MPI it is very portable and can be used  both in shared and distributed memory machine, but it is more obsolete and less efficient than MPI. PVM. It's available at CILEA Currently is installed on the HP servers with the version 3.3.111.
Scalable Modeling System	The SMS is a directive-based parallelization tool that translates Fortran code into a parallel version that runs efficiently on both shared and distributed memory systems. This software has been used successfully to parallelize and run many oceanic and atmospheric models. Scalable Modeling System It's available at CILEA Currently is installed on Exadron Intel Xeon Cluster with version 2.9.0
The Visualization ToolKit	The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. The Visualization ToolKit It's available at CILEA Currently is installed on Exadron AMD Opteron Cluster .
Zlib	Zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms. Zlib It's available at CILEA Currently is installed on the Exadron Intel Xeon Cluster with version 1.1.4 and on the Exadron AMD Opteron Cluster 1.2.3.

Edited by: Paride Dagna
Modified: 2009-09-04 12:35:27