insideHPC.com

Also at the new HPCwire today, news that U of Florida researchers used HPC to find a new drug that lowers blood pressure and prevents heart and kidney damage, at least in rats. More research in humans coming.

Researchers used one of the world’s most powerful supercomputers to process 140,000 prospective drug compounds in a matter of weeks. The computer

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The letter linked below was sent from SGI to Linux Networx customers, and the InsideTrack secured a copy through its vast network of industry insiders.

The letter, from SGI Global Services VP Bob Pette, outlines what LNXI customers can expect. A few highlights of interest.

First, SGI’s take on what happened

Today SGI announced the purchase of

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Jeffrey B. Layton has written yet another interesting article for Linux Magazine.  This time, he’s put together an overview for those interested in implementing a parallel file system on a cluster.

If you have an interest in pulling together your own cluster, or maybe you just want to understand more about cluster technology, it’s necessary to grok the differences between clusters

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Software-as-a-Service is useful for products that require network connectivity, such as email and instant messaging; just witness the popularity of Gmail and Meebo. Among enterprise customers, ERP/CRM applications hold some degree of promise, like Salesforce.com. So then the question is whether technical computing customers could use SaaS.

The best example I can think of is in offloading hefty …

For starters, domain-specific languages make users more productive than general-purpose languages and give them more flexibility than a simple GUI. Consider what SQL gives to database managers, or Excel to finance professionals. And while C++ has features like polymorphism and operator overloading that allow for “syntactic sugar” in mathematics libraries, most engineers will prefer MATLAB because, if for no other …

Staying informed in this market can be difficult given our niche position. However, there are a few sources that anyone in this field should most definitely be familiar with.

First and foremost are the conferences, namely Supercomputing (SC). Held annually in the US, this monster get-together showcases all of the latest in research and development, plus offers a number of …

Duff’s Device is a loop-optimization technique for C code that relies on macros to unroll a repetitive task. The primary benefit of loop unrolling is reduce branching, which is one of the single most expensive operations in computing. While some branching is necessary for the cache, too much branching will actually break the memory hierarchy, in addition to the …

Have you ever been in a position where you needed to run an MPI application a few times, but not enough times to justify buying your own cluster? Do you have access to a few PCs, but can’t or don’t want to install any software such as Condor on them? Then maybe you could use Parallel Knoppix.

Parallel Knoppix is …

Terracotta is an open source distributed shared object facility for Java, which allows multithreaded applications to run on clusters with minimal changes. It works with existing application servers and other web platforms, which makes distributing application loads across multiple nodes (JVMs) straightforward. It performs thread synchronization and even thread migration transparently for the user.

In addition to the runtime facilities, …

CPUShare is a grid computing initiative that pays its participants for providing idle processing time. Unlike BOINC, the provider is selling his time rather than donating it. While there is no word on the actual revenue a seller could reasonably expect to earn, anyone considering this program should consider the cost of electricity for running the software before picturing …

I received this question in reference to an article from a few months ago. My paper was about functionality instead of mere performance, though my comments regarding RDMA-based overhead should hint at how poor InfiniBand is for some applications. Many of the benchmarks out there assume that the memory region is being reused and that the protection tags can …

AMD has announced a Stream Processor that comes from its recent acquisition of ATI. The processor is currently available on a PCI Express board and is provided with one gigabyte of dedicated memory. It also comes with the Close to Metal (CTM) interface for software developers. CTM is the target of stream programming platforms such as PeakStream …

CUDA (compute unified device architecture) is NVIDIA’s GPU architecture featured in the GeForce 8800. Positioning itself as a new means for general purpose computing with GPUs, CUDA provides 128 cooperating cores. Because the cores can communicate with each other, the GPU can run multithreaded applications without the need for stream computing. Along with this innovation, NVIDIA has released …

Multi-core systems, in combination with specialized co-processors for hefty tasks, are hailed as the future of high-performance computing. In a bus-based architecture, the environment is an SMP in which all of the memory is accessible by all of the processors in the same amount of time. This setup works well for a few cores, but has tremendous trouble for the …

As mentioned previously, the greatest hurdle to FPGA adoption is the developer’s perception of usability. Usually a computer engineer must design the hardware via a description language such as Verilog or VHDL. This process involves defining the transfer of data between registers, which is a distinct departure in the practices most software engineers use. A newer approach is to …