This is a continuation of our look at future trends in high performance computing. In part 1 we covered the first five of the top ten trends. In this installment we’ll wrap up with the remaining five.
Future Trends in HPC, part 2
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Category Archives: Science
Future trends in HPC, part 1
As we near the end of 2011, we take a moment to reflect on the past year. It’s been a busy year for IT across virtually all verticals, from mobile and search to enterprise servers and cloud computing. When we attended HPC360 a few weeks ago, we had the pleasure to attend a keynote presentation by Addison Snell, CEO of Intersect Research in which he discussed the most important trends in high performance computing (HPC).
HPC is an exciting and growing industry that ICC has been moving into the past couple years. The traditional HPC space revolved around high-end research facilities particularly in science and engineering. However, with each year technological innovations and tailored systems such as our Supermicro GPU Simcluster have brought the realm of HPC closer to reality for many small/medium-sized business and organizations.
In this 2-part series we will look at the top 10 future trends in HPC from Intersect360′s research, coupled with our own analysis and thoughts. No better way for us computer nerds to close the year right? Let’s get started.
Top 10 HPC Trends for 2012 and Beyond
HPC360 Conference Recap
We just returned from R Systems HPC360, a conference on high performance computing down in Champaign, Illinois which brought together leading industry professionals, academics, scientists, and enthusiasts.
The conference was titled HPC360 “Innovation through Modeling and Simulation”. The event took place at the i Hotel and Conference Center in Champaign, hosted by R Systems and sponsored by a number of companies including Dell, AMD, Intel, and yours truly, ICC!
Advanced Manufacturing Partnership (AMP) to spur innovation
On June 24, President Obama announced the Advanced Manufacturing Partnership (AMP) between the federal government, academia, and businesses to help stimulate the manufacturing sector of the U.S. economy. We have been following the so-called “Missing Middle” of small- to medium-sized manufacturers (SMMs) on this blog, and I’d like to describe some of the recent initiatives to engage this high-potential segment of our economy.
Speaking at Carnegie Mellon University, Obama described that AMP would allocate $500 million of federal money to help make U.S. manufacturing more competitive around the world.
Inspired by a report drafted by the President’s Council of Advisors on Science and Technology (PCAST), which found that there are market failures in the advanced manufacturing space that need to be overcome by government intervention, AMP will focus on five initiatives:
- Manufacturing for national security
- Materials science
- Robotics
- Energy efficiency
- Developing partnerships and consortia between government, universities, and industry Continue reading
The Six Million Dollar Human (adjusted for inflation)
“Gentlemen, we can rebuild him. We have the technology…Better, stronger, faster.”
-from The Six Million Dollar Man
Memresistors and human engineering. Artificial intelligence and supercomputers. Biosynthetic corneal implants and facebook updates. What do these things have in common? The reliance on microprocessors? Hardly.
This technology might soon be packaged into a portable, rugged, ergonomically correct platform. The human skin.
From an article on DiscoveryNews, Hartmut Esslinger, founder and co-CEO of Frog Design, discusses the concept of Dattoos.
The concept of the Dattoo arose in response to current trends towards increasing connectivity and technology as self-expression. To realize a state of constant, seamless connectivity and computability required the convergence of technology and self. The body would need to literally become the interface. Computers and communication devices require physical space, surfaces, and energy. The idea of DNA tattoos (Dattoos) is to use the body itself as hardware and interaction platform, through the use of minimally-invasive, recyclable materials.
Technology is becoming ever more mobile. Moving from the centralized user interface, where platforms are static and require the presence of the individual at a specific location, to the roaming and portable medium we enjoy today. Allowing us to interact with the world, as we traverse it. Incorporating what it has to offer us, as we wish.
Tethering ourselves to devices. Requiring external components to conduct our business imposes layers of abstraction, no matter how small. They remove us, ever so slightly, from experiencing the world as a pure construct.
Storing personal information in a secure medium, easily accessible and capable of interacting with any platform, has huge appeal. The trick is implementing this as yet unproven technology.
Not to mention getting past the sheer macabre implications of getting “hacked”.
GPUs in the news: medical imaging
Next time you feel like bemoaning the state of today’s big thumbed, small minded, video-game generation, think about the social benefit all those gaming man-hours are contributing to medical research.
A team from UC San Diego created an algorithm for CT scan image reconstruction using an NVIDIA GPU, discovering, in the process, the superior effectiveness in creating targeted images of tumor cells. This improvement over traditional medical scans reduces the total radiation cancer patients need to endure. Current technology requires repeated scans in order to produce a detailed enough image for doctors to identify potential tumors. Using GPU’s and gaming hardware, scientists were able to reduce the amount of radiation by a factor of as much as ten.
“In my mind, the most interesting and compelling possibilities of this technique are beyond cancer radiotherapy,” Steve Jiang, senior author of the study and a UCSD associate professor of radiation oncology, said in a statement. “CT dose has become a major concern of the medical community. For each year’s use of today’s scanning technology, the resulting cancers could cause about 14,500 deaths. Our work, when extended from cancer radiotherapy to general diagnostic imaging, may provide a unique solution to solve this problem by reducing the CT dose per scan by a factor of 10 or more.”
CT scanning is widely used and extremely useful in the field of computerized imaging. A scanner snaps a series of X-ray pictures whilst rotating around the subject body. The pictures are assembled to create a cross section of the body. These cross sections are then combined to generate a 3D image. Throw in a large number of Fourier transforms, where data about neighboring points is used to improve information on each individual point, mix in a few b-spline interpolations (I am not making this stuff up)- a mathematical technique that accurately fits smooth curves to data points-and you wind up with the sort of computational dynamic that benefits tremendously from parallel processing.
Where CPU’s perform interpolations one data point at a time, GPU’s can take multiple points and interpolate them in parallel. The high resolution (8000×8000 pixels) of the images and large file sizes make this the sort of computational problem ideally suited to parallel processing. This translates to a 3.6X speedup of segmentation time, compared with CPU-only processing on an Intel quad core Nehalem-class processor. More recent tests point to a speedup of up to 15X. Klaus Mueller at the State University of New York-Stony Brook found that using GPU processing could reduce the time needed for a CT scan reconstruction from 135 seconds to less than seven seconds.
Software has also allowed GPU’s to perform their tasks much more quickly. Solving non-graphics problems on the GPU involved treating non graphic data like vertices or pixel data points and using complicated graphics API’s to process the information. Now, someone with a background in ‘C’ can write a program to get around this issue.
Escaping in to the virtual reality of video games, appeals to a growing segment of the population. Providing them with the best user experience drives sales.
Now it also drives medical innovation.
Platform Computing – innovator in cloud computing software
When Platform Computing began as a company in 1992, computers were used by large organizations much like they had been for several previous decades. If a complex computing job needed to be run, it would be run on one machine, often only during certain times in the day. There was no widespread use of clusters or computing clouds. Computational research that now takes several days or weeks to complete used to take many months or years.
The first commercial project that Platform Computing undertook, according to an interview on HPCintheCloud.com with Platform CEO Songnian Zhou, was to help the engine manufacturer Pratt & Whitney design the engines for the new Boeing 777 airliner. Zhou describes how supercomputers were used back then:
At that time, they were using one Cray supercomputer rather than IBM mainframes to do it — and every night they would run one job. One job! Per night! Using that one Cray they had to explore all the parameters — how big or small, how many blades, and so on — all the design alternatives; that takes dozens and dozens of runs. They had to run half a year, which is of course a big problem for their product cycle to serve the airlines and their customers.
Platform Computing sought to change the way organizations such as Pratt & Whitney used supercomputers. Instead of running one job on one computer at a time, Platform pioneered the use of software to break up complex jobs to be performed on many computers connected together in one computer cluster. The airline and automotive industries, according to Zhou, were the early adopters of this technology and used it to speed up and simplify their design simulations.
Today, cloud computing and clustering have become industry standards, and there are now many companies that offer software and other services to facilitate them. Platform Computing still specializes in private clouds (a network of computers in the same facility most likely owned by the same organization) and community clouds (a network of computers owned and shared exclusively by a few organizations) which means that they cater towards large corporations and organizations that can afford purchasing large clusters.
Public clouds, the type most people think of when they talk about cloud computing, is facilitated mostly by other companies, although Platform has made an effort to reach out to smaller businesses and organizations in 2010.
If you are interested in Platform Computing software for clustering or private clouds, feel free to contact ICC and we can talk to you about the different options they have available to take full advantage of your computing hardware resources.
AMD Fusion processors – from GPU to APU
GPUs (graphics processing units) are a favorite topic on this blog. It is an innovative and powerful computing idea with an almost awkward origin: the graphics card, which has in the past been used to perform calculations necessary for visual rendering, is now used in GPU applications to help the processor perform millions of general computations. In effect, the GPU becomes a specialized processor in the computer.
GPU products have been soaring in popularity recently, especially for scientific uses. But the CPU-GPU arrangement still retains the old CPU-graphics card relationship. That is, the way a CPU and GPU are connected is still the same way that a CPU used to interact with a graphics card, through the PCI-E slot on the motherboard. GPUs are fast, but their speed is limited by this type of connectivity, a remnant from the days when GPUs were just graphics cards. In effect, PCI-E communication between the GPU and motherboard is a bottleneck on performance.
AMD is tackling this problem head-on with their upcoming Fusion line of processors. Instead of connecting a GPU to to the motherboard like an add-on card, AMD proposes to make the GPU part of the same silicon chip as the CPU, eliminating the need for PCI-E communication. They have dubbed this combination of CPU and GPU technology “Accelerated Processing Unit” (APU).
Currently, the AMD Fusion processor is going to be released for the consumer market in desktop and laptop computers. But, while AMD is working on bringing this technology to server boards, many issues (mostly with coding) need to be resolved before this can happen, as John Fruehe of AMD explains in his blog article, “Fusion for Servers”.
Nevertheless, this innovation carries some promise for the future evolution of GPU technology. It has the potential to eliminate the PCI-E bottleneck and make that remnant of GPU’s original function as a graphics card a thing of the past.
But this won’t be easy for AMD. Although it has the advantage of being the only processor manufacturer to also produce graphics cards (AMD bought ATI in 2006) NVIDIA is still the leader in GPU technology. Many commercial battles will still be fought for the future of GPUs between these and other manufacturers, among them the competition between the coding languages of CUDA and OpenCL.
Despite these hurdles, AMD’s plans for using Fusion processors in servers is an nascent idea with a lot of potential to improve the GPU market and make computers – and supercomputers – even faster.
BP oil spill elicits emergency response from HPC
Supercomputers have become an extension of the human mind, “thinking” for us in a short amount of time when our own brains would take countless hours to do the same calculations. In one of the most recent applications of HPC (high-performance computing), scientists have received an emergency grant from the National Science Foundation to model in 3D the future spread of the BP oil spill.
The spill, which occurred on April 20th, has steadily been spreading to the coastal areas of the Gulf of Mexico. Although efforts are underway to stem the expansion of the spilled oil (for instance, today BP started injecting heavy mud around contaminated areas), no one is certain that they will work.
So to prepare for any eventuality, researchers have turned to supercomputers to understand how the the dynamics of the oil. According to the article in Computerworld, 1 million compute hours have been allocated on the supercomputer called “Ranger” at the Texas Advanced Computing Center (one compute hour is one CPU core running for one hour, whereas the Ranger has 63,000 cores).
The model employed to simulate the spill is called Adcirc (Advanced Circulation Model for Oceanic, Coastal and Estuarine Waters). Scientists are currently updating this 2D model to make it 3D. This will allow them to calculate how oil travels underwater when it encounters the various vegetation and other obstructions near the coastal areas.
Another contingency that the researchers are preparing for is the possibility that a summer hurricane will sweep up oil from the Gulf spill and carry it to land, potentially causing contamination in areas where people live. The new 3D model will hope to account for that as well.
As the case of the BP oil spill demonstrates, nations are relying more and more on supercomputers in emergency situations to help scientists and policy makers understand and predict the outcomes of national disasters.
HPC helps combat malaria
Scientific American reports (accessed via HPCwire) that a project partly funded by the Bill and Melinda Gates Foundation will use supercomputing to help stop the spread of malaria, which kills about a million people a year.
The team tasked with working on the malaria project is sharing a 1,104-core HPC (high-performance computing) supercomputer with a nuclear reactor research company. With the help of mathematical modeling, researchers are trying to find patterns in nature that would allow them to predict and control malaria outbreaks. From the Scientific American article:
The software pulls biological data on the behavior and reproductive rates of the Plasmodium parasites and the mosquitoes that carry them, as well as information on infection patterns and immune responses among humans. Other data include where people live and how they travel, environmental factors (temperature, rainfall and elevation) that are important to malaria transmission, and the locations of different species of mosquitoes.
The article also features an interesting discussion about cloud computing compared to local servers. The malaria research team is using local servers and not cloud computing for their simulations, even though the Microsoft software they are using is geared towards the cloud (see our post about the new Microsoft Technical Computing Group).
The team uses local servers for national security reasons – servers in the cloud frequently operate outside of the United States and many government-sponsored research projects can not put their data at risk in such a way. This illustrates that, despite the unifying effects of science and globalization, politics is still a formidable factor in even the noblest of global projects.
The article also notes that cloud computing is still far behind in performance compared to running local servers. As a systems engineer working on the malaria project observes, using local servers is about ten times faster than using the cloud.
While cloud computing technology still has a long way to go to catch up to the performance capabilities of locally-run servers, HPC in all of its forms is nevertheless helping people to battle some of the earth’s deadliest diseases.