Mac OS X at UC Davis

High Performance Computing

UCLA Plasma Physics Group's New Cluster

To advance physics research, the UCLA Plasma Physics Group recently acquired a new cluster of 128 DP Xserve G5s. We were able to achieve over a TeraFlop with the new "Dawson" Cluster. You're welcome to read more about it at today's announcement:
http://daugerresearch.com/pr/DawsonXserveG5Cluster.html
For technical details:
http://daugerresearch.com/fractaldemos/DawsonCluster/DawsonCluster128Benchmark.html

New ADC Web Page: High Performance Computing

This new page describes resources for High Performance Computing on the Macintosh platform. It provides links to Apple and third-party resources of relevance to the HPC space. http://developer.apple.com/hardwaredrivers/hpc/index.html

Virginia Tech Terascale Cluster

The VT Cluster is ranked No. 3 in the world.

Here is an October 30 article on the Virginia Tech G5 Cluster.

Combining the power of 1,100 Apple computers, the Terascale Cluster project is bringing Virginia Tech to the forefront in the supercomputing arena. This article is an interview on Macslash with Dr. Srinidhi Varadarajan the director of the Terascale Computing Facility at Virginia Tech.

Cluster Computing Resources

http://www.apple.com/server/clustering.html

Here's more information on the Apple bioinformatics cluster and its use.
http://education.apple.com/webcast/workgroupcluster/

G5 Performance Benchmarks

This paper (PDF) describes testing conducted by NASA Langley Research Center during an evaluation of a PowerMac G5 system for computational fluid dynamics (CFD) simulation.
PDFs require the free Adobe Reader.

A recent post on the Apple SciTech listserve presents some benchmark results for Matlab running on the new G5 processor.

This .edu site has a wealth of information regarding High Performance Computing Website on the Macintosh platform.

2004 Supercomputing Conference

Next year's Supercomputing Conference will be held in Pittsburgh, PA, November 6-12. Check out the website for more information and conference details.

Scientific Computing by Apple

A good resource for scientists using the Macintosh platform is the Scitech Listproc hosted by Apple. Discussions involving CPU performance issues and source code compatibility can be found there.

Matlab Support

Jaguar Installation

Running Matlab on OS X 10.2 (Jaguar) is discussed by The Mathworks. There are installation issues and some workarounds for installing Matlab 6.5.

Further Troubleshooting may also be available at:
http://www.mathworks.com/support/tech-notes/1300/1317.shtml

You can delete everything you downloaded, after the install.

Hardware

There is a "rudimentary" driver for PCI-GPIB cards. It is probably not a speed demon for large data transfers, but it works for instrumentation.

Data acquisition solutions are currently available from National Instruments and PowerLab. Other hardware includes a USB I/O device. The Labjack is a neat USB interface that is currently being worked on to get the software right for OS X. Check the Forum for the latest developments on the interface softare.

Mathematical

For 2D or 3D PDE problems like: heat flow, stress analysis, fluid mechanics, chemical reactions, electromagnetics, and diffusion, FlexPDE from takes you from mathematical model to numerical solution to graphical display.

The GETFEM++ project is centred around the development of a generic and efficient C++ library for finite element methods elementary computations.

Satimage offers SmileLab, for users of Mac OS X who process numerical data. Additionally, there is a great collection of links maintained for users of the Macintosh in Chemistry.

From simple calculator operations to large-scale programming and interactive document preparation, Mathematica is the tool of choice at the frontiers of scientific research.

Modeling

PyMOL - open source molecular modeling program

Spartan - commercial molecular modeling program

Modeller - a protein structure modeling program

SysQuake - powerful and flexible software for the design and simulation of dynamic systems

TetrUSS - computational fluid dynamics (CFD) software

Programming

f95 - NAGware Fortran 95 compiler

Ch - an embeddable C/C++ interpreter for cross-platform scripting, shell programming, 2D/3D plotting and numerical computing.

Lingon - Lingon is a graphical interface for creating launchd configuration files and controlling them through launchctl for Mac OS X Tiger. (launchd is a system daemon that is used to run scripts/programs automatically, repeatedly or at certain times.) You get all your launchd configuration files listed in a table so you easily can see which are loaded and what they do, and you can also load and unload any easily. If you want to create or edit a launchd configuration file you can do that in Lingon through an assistant or in an easy graphical way (or through an built-in text editor, should you want to).

Organization

Daylight - Chemical information system

KaleidaGraph - graphing application

Chemaxon - Java tools for chemical structure and reactions

Announcements

Free Linda System now available for Mac OS X

To celebrate our 25th anniversary, Scientific Computing Associates, Inc. (SCAI) has made a four-processor TCP Linda system (for C programs) available at no charge for Apple users running Mac OS X. Programmers can use TCP Linda to develop and run parallel applications easily on clusters or networks of Apple computers running OS X. This is a perpetual license for TCP Linda, providing a fully functional system available by download at http://www.lindaspaces.com.

TCP Linda is a proven industry standard for parallel programming, and well-known for its ease of use, reliability, and efficiency. Linda, introduced in the mid-1980s, was the first commercial product to implement virtual shared memory (VSM) for supercomputers and large workstation clusters. TCP Linda is content-addressable, not address-based, making it much easier to build applications and fully utilize hardware capacity. Benchmarks demonstrate excellent performance and scalability.

TCP Linda provides a simple, yet complete command set that can be added to programs to enable process creation, synchronization and communication. Every Linda software system employs a powerful Linda optimizing (pre)compiler and a carefully tuned, architecture-specific run-time system. With the free four-processor TCP Linda system, users can parallelize any program written in C using just four simple TCP Linda operations.

The Linda manual, FAQs, and whitepapers are also available at http://www.lindaspaces.com/support/.

In addition, the classic text, “How to Write Parallel Programs,” by Nicholas Carriero and David Gelernter is available in PDF format at http://www.lindaspaces.com/book/index.html.

TetrUSS Computational Fluid Dynamics software

NASA Langley Research Center is announcing the immediate availability of its "TetrUSS" computational fluid dynamics (CFD) software for Mac OS X. TetrUSS is a suite of computer programs used for fluid dynamics and aerodynamics analysis. For more details, see: http://aaac.larc.nasa.gov/tsab/tetruss/mac/

AutoCAD for OS X

Autodesk requests AutoCAD for OS X feedback

While no solid information suggests that an OS X version of AutoCAD is being developed, Autodesk is open to the possibility, and is exploring its options.

"At Autodesk, we are always interested in the latest complementary hardware technology our customers are investing in," said a spokesperson. "While we are not currently pursuing a port of AutoCAD to the Apple OS X operating system, the AutoCAD Product Manager is interested in hearing from customers who are requesting this."

The company spokesperson said that readers can e-mail Eric Stover, AutoCAD's product manager, at eric.stover@autodesk.com with the subject "AutoCAD for OS X".

Remember folks, this is NOT a call for spam. If you don't have a real interest in the software don't bother.

Fovea Pro 3

Reindeer Graphics, Inc. announces the immediate availability of the newest release of its flagship image processing, analysis and measurement package, Fovea Pro. Fovea Pro 3 provides Mac OS X native functionality under Photoshop 7.x and many new features , including the all-new Interactive Deconvolution, a plug-in that provides a user-adjustable point spread function generator for deconvolving both defocus and motion blurs. Fovea Pro 3 also features condensed and reorganized menus, providing users with more intuitive access to the 150+ functions that Fovea Pro contains. Fovea Pro 3 works with Photoshop 5.x, 6, and 7 on Mac OS X 10.2, Mac OS 9.2, and Windows 98 or better.

Scientific Computing Using Mac OS X