Oakley

TotalView Debugger

Introduction

TotalView is a symbolic debugger which supports threads, MPI, OpenMP, C/C++ and Fortran, plus mixed-language codes.  Advanced features include on-demand memory leak detection, heap allocation debugging and the Standard Template Library Viewer (STLView).  Other features like dive, a wide variety of breakpoints, the Message Queue Graph/Visualizer, powerful data analysis and control at the thread level give you the power you need to solve tough problems.  

Gnuplot

Introduction

Gnuplot is a portable command-line driven data and function plotting utility.  It was originally intended to allow scientists and students to visualize mathematical functions and data.  

mpiBLAST

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processors (SMPs).

Python

Python is a high-level, multi-paradigm programming language that is both easy to learn and useful in a wide variety of applications.  Python has a large standard library as well as a large number of third-party extensions, most of which are completely free and open source. We highly recommend using Python 2.7.1, as we have added a lot of Python packages and tuned them to perform well on our systems.

Stata

Stata is a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics. Release 13 32-processor SMP is currently available at OSC.

SPRNG

Computational stochastic approaches (Monte Carlo methods) based on random sampling are becoming extremely important research tools not only in their "traditional" fields such as physics, chemistry or applied mathematics but also in social sciences and, recently, in various branches of industry. An indication of importance is, for example, the fact that Monte Carlo calculations consume about one half of the supercomputer cycles. One of the indispensable and important ingredients for reliable and statistically sound calculations is the source of pseudo random numbers. SPRNG provides a scalable package for parallel pseudo random number generation which will be easy to use on a variety of architectures, especially in large-scale parallel Monte Carlo applications.

SPRNG 1.0 provides the user the various SPRNG random number generators each in its own library. For most users this is acceptable, as one rarely uses more than one type of generator in a single program. However, if the user desires this added flexibility, SPRNG 2.0 provides it. In all other respects, SPRNG 1.0 and SPRNG 2.0 are identical.

ScaLAPACK

ScaLAPACK is a library of high-performance linear algebra routines for clusters supporting MPI. It contains routines for solving systems of linear equations, least squares problems, and eigenvalue problems.

This page documents usage of the ScaLAPACK library installed by OSC from source. An optimized implementation of ScaLAPACK is included in MKL; see the software documentation page for Intel Math Kernel Library for usage information.

R

R is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques, and is highly extensible.

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