Software at OSC |
Software available on the IBM Opteron ClusterABAQUS - a finite element analysis program ACML - The AMD Core Math Library (ACML) is a set of numerical routines tuned specifically for AMD64 platform processors Altair HyperWorks* - high-performance, comprehensive toolbox of CAE software for engineering design and simulation AMBER - a molecular simulation program ANSYS - an engineering package and support routines for general-purpose, finite-element analysis: statics, mode frequency, stability analysis, heat transfer, magnetostatics, coupled field analysis, and modeling BLAT - a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments ClustalW - a general purpose multiple sequence alignment program for DNA or proteins EMBOSS - a sequence analysis package specially developed for the needs of the molecular biology user community ESPRESSO/PWscf - suite of computer codes for electronic-structure calculations FFTW - a C subroutine library for computing the discrete Fourier transform (DFT) Flow 3D - a general-purpose CFD program Fluent - a general-purpose program for modeling a wide range of fluid-flow and related transport problems Gambit - a software package designed to help analysts and designers build and mesh models for computational fluid dynamics (CFD) and other scientific applications Gaussian 03 - a connected system of programs for performing semiempirical, ab initio, and density functional molecular orbital (MO) calculations GROMACS - a versatile package to perform molecular dynamics HDF5 - a general purpose library and file format for storing scientific data HMMER - used to do sensitive database searching using statistical descriptions of a sequence family's consensus Intel Compilers - an array of software development products from Intel, including C++, FORTRAN compilers, Math Kernel Library(MKL), and Vtune Perf Analyzer LAMMPS - a classical molecular dynamics code designed for high-performance simulation of large molecular systems LSDYNA - an explicit three-dimensional, finite-element code for analyzing the large deformation dynamic response of inelastic solids and structures MacroModel® - molecular modeling software package that allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution Mathematica - From simple calculator operations to large-scale programming and interactive document preparation, Mathematica is the tool of choice at the frontiers of scientific research, in engineering analysis and modeling, in technical education from high school to graduate school, and wherever quantitative methods are used MATLAB - a technical computing environment for high-performance numeric computation and visualization that integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment mpiexec - a replacement program for the script mpirun, which is part of the mpich package. It is used to initialize a parallel job from within a pbs batch or interactive environment. NAG Libraries* - comprehensive collections of routines for the solution of numerical and statistical problems NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems NetCDF (Network Common Data Form) - an interface for array-oriented data access Octave - a high-level language, primarily intended for numerical computations PAUP -- a leading program for performing phylogenetic analysis for bioinformatics sequences PBS - a networked subsystem for submitting, monitoring, and controlling a work load of batch jobs on one or more systems PCBL (Portable Cray Bioinformatics Library) - a low level set of library routines using proprietary Cray hardware to implement some common nucleotide/protein sequence manipulations typical in a bioinformatics context PGI compilers - Parallel Fortran, C, C++ compilers for Intel platforms R - a language and environment for statistical computing and graphics ScaLAPACK - a library of high-performance linear algebra routines for distributed-memory message-passing MIMD computers and networks of workstations supporting PVM and/or MPI sprng & sprng2 - a scalable package for parallel pseudo random number generation Stata - a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics TotalView Technologies Totalview* - debugger for complex code Turbomole - a program package for ab initio electronic structure calculations VASP - the Vienna ab-initio simulation package * Indicates software available through OSC's Statewide Software License Distribution
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