HPC enables discovery of new blood pressure drug
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 predicted which molecules would be most likely to enhance the activity of ACE2, rotating them in thousands of different orientations to see how they would bind to certain pockets on the enzyme’s surface.
…After hitting on the “lead” compound, UF researchers then tested it in hypertensive rats that had developed fibrosis of the heart and kidney. The animals received the drug for two weeks. Tissue samples
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InsideTrack: Letter from SGI to LNXI customers
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 certain assets of Linux Networx, Inc.. In conjunction with this transaction SGI has offered employment to a number of Linux Networx employees in the Engineering, Sales and Services areas and acquired LNXI’s spare parts inventory.
And then what it means for LNXI customers (note the honesty):
SGI did not acquire Linux Networx’s service contracts and as such, does not have a service contract in place with you.
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Article: File Systems for HPC Clusters
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 and standard systems.
Read the full article here. [free registration required]
Will SaaS work in HPC?
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 workloads to managed servers. This isn’t grid computing as traditionally known, but rather an application that can be called on-demand to perform a very specific task. I believe that in the future, it may be possible to farm heavy number-crunching from Excel or MATLAB to another company’s server on the fly. I’m just waiting for Microsoft to introduce “Excel Services Live.” You heard it here …
What is the benefit of domain-specific languages?
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 reason, it’s interactive.
But these languages have an added bonus that the HPC community should now take seriously: because they are limited, domain-specific language are easier to optimize. While ACCELLERANT tries to parallelize any and all code, Star-P sticks to just matrix operations. After all, why should a non-programmer bother with stream computing, electronic systems-level design, and partitioned global address spaces when all he …
What is the best way to keep up on HPC news?
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 tutorials for emerging technology. A week here is equivalent to a semester in grad school. A distant second in this category is the International Supercomputer Conference (ISC) held annually in Germany.
Among online sources, the best for original articles is HPCwire, whom I’ve written for. As for news snippets, John E. West’s InsideHPC is a daily source. Coincidentally, John is also a regular …
What is Duff’s Device?
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 pipeline. Programmers who require extreme performance would do well to learn a number of best-practice loop optimizations. Duff’s Device is one of them.
What is Parallel Knoppix?
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 a bootable CD for running MPI applications on a network of workstations. It’s a Linux distribution that executes the common steps for determining hardware and configuring devices. As of this writing, there is no 64-bit version of it, though that may change in the future. The disc image can be downloaded from the project’s website, or may be purchased from LinuxCD.org.
What is Terracotta?
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, Terracotta provides a declarative approach to clustered software. That is, the programmer merely annotates which data members are shared. Likewise, the user may specify which methods contain critical sections, thereby creating a monitor.
The system architecture relies on a central server that stores the state of shared objects. Client nodes (JVMs) receive updates for objects currently in memory; thus, any data transfers occur only at the …
What is CPUShare?
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 profits.
It seems like this system is more aimed for buyers in that they can order CPU time without paying for a cluster. However, the buyer must port his code to CPUShare’s platform. Given the time and money required to use this system, a user may be better served by purchasing an accelerator and porting his software to that, especially since grid computing only works in …
