OnDemand is our "one stop shop" for access to our High Performance Computing resources. With OnDemand, you can upload and download files, create, edit, submit, and monitor jobs, run GUI applications, and connect via SSH, all via a web broswer, with no client software to install and configure.
SuperLU is a library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. It comes in two different flavors: SuperLU_MT (multithreaded) for shared memory parallel machines and SuperLU_DIST for distributed memory parallel machines.
TurboVNC is an implementation of VNC optimized for 3D graphics rendering. Like other VNC software, TurboVNC can be used to create a virtual desktop on a remote machine, which can be useful for visualizing CPU-intensive graphics produced remotely.
JasPer is an extensible open source utility designed for the manipulation, conversion, compression and decompression of digital images. Currently supported image formats include bmp, jp2, jpc, jpg, pgx, mif and ras.
Version 1.900.1 is available on the Oakley cluster.
In order to use the JasPer library, you must load the JasPer module into your environment. To load the JasPer module, type the following command:
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 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.
"RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments."
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 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 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.