We are drowning in the genome data that our high-throughput sequencing machines create every day,” said Dr. Bingqiang Wang, head of high performance computing from BGI. “GPU acceleration of our genome analysis applications enables our scientists to crunch through data and gain insights into bacteria, plants and humans faster than was ever possible. It offers the potential for researchers and healthcare professionals to identify highly effective and affordable individualized medicines and treatments.”

Speedups like this are considered critically important in determining chemical building blocks that make up a DNA molecule. With a goal of $1,000 genome, the genomics industry aims to make DNA clinical diagnostic tests as a practical component of patient care.

Read the Full Story.

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The post The Dawn of Personal Genomics – BGI Tackles DNA Big Data Using Nvidia GPUs appeared first on insideHPC.

Peg Williams was recently named to the position of Senior Vice President, HPC Systems at Cray.  In her new role, Williams is responsible for the company’s R&D efforts along with the product and business line management.  With more than 20 years experience in HPC, she has a keen understanding of the increasing complexity of high-end HPC systems, and she evangelizes the critical role of software for this next generation of systems.

The Exascale Report: With the recent announcement of Titan, we can expect to see more discussion around accelerators, so let’s talk about the software component of exascale systems. Why do you feel software has become a critical discussion for all parties when talking about exascale?

WILLIAMS: I think there are several key roles that software plays in the discussion of exascale. One is in the area of reliability – what can you do on the software side to impact reliability, isolating the user from machine failures and allowing the system to continue to run.

There’s also work that needs to be done on the software side relative to programming models. One of the big issues application developers have going forward is dealing with the complexity of these very large systems.  For example, at the application level, it’s not only how do we find the parallelism, but once we do, how do we explain where it is?  How can they express all of that parallelism in a way that a compiler or certain tools can actually map all of that to the machine?

These are some of the big challenges on the software side. I think software has to help in the reliability piece of this and it certainly has to help in terms of making sure that there is a way to express the parallelism, and then once it’s expressed to take it and do something with it in mapping it to the architectures.

TER:  And you’re really talking about the programming models at this point?

WILLIAMS: Mostly the programming environments that the vendors create around the community-adopted programming models.  In our programming environment we have compilers and tools and libraries and all kinds of things that work together, but yes, I’m mostly talking about that marriage between what the application developer needs to do and how they need to hand it over to someone who might be building a compiler or tool set or library set to get the job done

TER: And this is only complicated I’m guessing when we add accelerators into the equation?

WILLIAMS: Yes – the fact that accelerators are there forces you to have to find the parallelism to use them.  If you have an accelerator but there’s not enough parallelism, or you can’t tell me about the parallelism in your application to allow me to map it to the accelerator – it won’t do you any good.

This is an area actually where I think that Cray has an advantage, especially if you look at a GPU-like architecture, and I actually think the Many-core space is like this too, but if you think of a GPU, at its highest level, a GPU is like a vector.  It’s going to compute like a vector computes.  There’s no company that understands vector processing better than Cray.

So we’ve got a history of being able to find parallelism in code and map that parallelism on to vector-like architectures.  There’s a rich history of skills here that I believe we can bring to bear in this accelerator space.  It’s the human capital that we have that understands this problem incredibly well because we’ve been dealing with it for so long.

TER: To what extent do you think this can be automated with the use of compilers and tools?

WILLIAMS: So I actually think we’re going to see more of this–and we’re building a programming environment that does this.

You’re going to have to have a more integrated look between the application developer and the tool set going back and forth.

First of all, you have whatever language you ended up with or whatever way you use for the application to express its parallelism.  Right now we are working with the model of extensions to Open MP directives and MPI.  But there has to be a loop between the application guy and the tool set that says, well, he’s put in his directives into Open MP, and the compiler runs it and the compiler looks at it and there’s  a set of  decisions it can make and a set of decisions it can’t make because it doesn’t have enough information.   There has to be the feedback loop back to the code developer that says if you could tell me these three things I could do a better job.  And then let the application developer look at that and see if he can provide more hints and tips into the compiler to do some of that. Then you go through the performance analysis loop, you grab performance data and then there’s another set of things that the compilers and the tools can tell you about your execution and feed you back data.  And at that point you can come back in and optimize.  So I actually think that there has got to be a tight relationship – there’s got to be a way to do a tight marriage between the application developer and the toolset that you build so there’s a communication that can go on.  I do think a lot of that can be automated but there has to be a lot of interaction initially to do that.  I do think you could take the burden down.  A guideline I’ve been giving my programming environment team is this:  If through the automated systems they can build, if they could get 80% of the performance on 20% of the effort on the application developer side, we’re good.  That’s the 80/20 I want to look at.  And we think we can get there.  But indeed there is a learning curve for all of us to go through as we start to work with these accelerators.

TER:  So what words of advice do you have for the new guys coming in to HPC?

WILLIAMS: You know, I like to think of it more in line with what advice do they have for me?   The folks coming out of school today are quite different than the traditional users of supercomputers.  I’ll give you a side story here.  We had some folks come in this summer to help us do an evaluation of the productivity of some of our tools.  We wanted to do some experiments and we were describing the environment that we wanted them to run in, and when we suggested they run Fortran codes, they looked at us with total and complete blank stares. So, we changed it and let them work in C++ and they were fine.  The times are certainly changing.

So what advice do I have for them?  I think they have to come in with complete openness and flexibility and not get locked into the models that we’ve had in the past. I’m a realist in the sense that a lot of the codes we have today have been running for years and people tweak them and they change them and they adapt them for the current architecture, but for those who are developing applications from scratch, my advice is be flexible, be open, and be creative, because with the kinds of architectures we have today, creativity can be rewarded. Think outside the box.

Related posts:

• Interview with Peter Ungaro, President & CEO of Cray Inc.
• Senior executive departure leaves us wondering about Cray’s market direction
• An Interview with The Portland Group’s Doug Miles

The post EXECUTIVE INTERVIEW – Peg Williams, Senior Vice President HPC Systems, Cray Inc. appeared first on insideHPC.

Contents

• Welcome Letter – Peter Ungaro, President and CEO, Cray Inc.
• Interview – Peg Williams, Senior Vice President HPC Systems, Cray Inc.
• Interview – Doug Miles, Director, The Portland Group
• Interview – Steve Scott, CTO, Tesla Business Unit, NVIDIA
• Interview – Jack Wells, Director of Science, NCCS at ORNL
• Interview – Peter Ungaro, President and CEO, Cray Inc., on TITAN
• Restaurant Reviews – Trey’s Corner: local foodie reviews the best Seattle has to offer
• SCI-FI Original – The Three Gifts of the Magi by Rich Brueckner

http://www.youtube.com/watch?v=8x_Vi-Z6Tvk

You can still download the Print ‘n Fly PDF (15 Mbytes). If your IT crowd blocks Dropbox, please Download here.

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The award of Titan to Cray is a milestone event for the HPC community.  But for many of the hardware and software engineers at Cray, it’s just another day in the office.

This is what Cray does.  They build very large systems and they push the envelope.

But when the team at Cray talks about Jaguar and the other milestone systems they have delivered to their customers, they don’t brag about their engineering prowess.  They beam with pride talking about the science and discovery their systems are making possible.

The Exascale Report is pleased to bring you this feature interview with Pete Ungaro, CEO of Cray, Inc.

The Exascale Report: So Pete, congratulations on behalf of an entire community on what you’ve been able to accomplish here – I know it’s been a very long time, and a lot of work put into this, and now we’re finally able to talk about Titan and all the great things this system will be able to do.

UNGARO: I just want to say thanks.  It’s been a long road but it’s been a great one.

TER: So I’d like to start off by asking you what Cray has learned over the past year that you believe will enable Titan to hit its goals.

UNGARO: Well we know now that we can build systems at this scale.  Jaguar was roughly the same size machine – 200 cabinets, so we know that we can build systems at that size and scale them up and hand them over to the researchers who can get some incredible science out of them.  We feel like this is a pretty straightforward process for us.  We’ve been able to get our architecture, our interconnect, our software all up to this scale and we think Titan just represents one more turn of the crank for us along that line.

TER: But this is obviously beyond anything that’s taken place up to this point, and knowing how volatile we are when we start to push the envelope, why do you have such confidence that Cray can deliver on such an ambitious project especially after what we saw with IBM / NCSA / Blue Waters this year?

UNGARO: I really think that the key for us is that we’ve really built our company to be focused on delivering these kinds of systems to the market. We’ve delivered the most high-end supercomputers in the world.  We’ve been able to deliver systems like this over and over again. And while you are absolutely correct that Titan is going to a huge step beyond where we’ve been in the past, from a systems architecture and from a delivering the systems standpoint, we believe that it’s a pretty straightforward path for us.  I think our sole focus on supercomputing, is really the biggest area that differentiates us from our competition today.  Not just about our technology which is also pretty strong, but I think it’s building a company like we’ve done that focuses on one part of the market and doing things like this, along with some great partnerships with our customers like Oak Ridge, we’re able to do this pretty successfully and we’re able to repeat it over and over again.

TER: How about for the users? They are going to be exposed to an application development environment that in some ways may be unlike anything they have had to deal with in the past – the programming environment for sure – so what will you be able to do to help transition the users from Jaguar to Titan?

UNGARO: That’s a great question Mike.  And maybe even the most important part of our story and one that we spend a lot of time with Oak Ridge talking about.  All the applications that today run on Jaguar will be able to be run on Titan, so there is a similar AMD Opteron computing environment, a similar program model and such.  Where the difference comes in is all the GPUs that we’re adding.  And so we’ve developed a programming model that allows users to much more easily take advantage of GPUs.  So in addition to just using CUDA programming which most people use today, we can take advantage of a more directives-based approach using our complier or Portland Group’s.  I think one big advantage to our roadmap right now, with our overall vision of adaptive supercomputing, it really says that within a programming environment, or programming model, we can take advantage of these different kinds of processing capabilities.  In fact, we have a lot of experience that says when we start to use our programming model to code for a GPU it actually improves its performance on a CPU.  That’s been a big leverage point for a lot of users to go through the effort of programming for GPUs because they know that their codes will not just run faster consistent with GPUs but also on systems with CPUs and today, being able to be portable among many different machines  is very important for the user community.  So I think you have to have a programming environment that allows for that smooth and easy transition but also compels the programmers or scientists to want to do the extra work to take advantage of the underlying hardware.

TER: So, as you are figuring out what the production environments will look like for a system like Titan, will the compilers and debuggers, you mentioned Cray’s and the Portland Group’s, will they have to be modified to a significant level in order to work for that environment?

UNGARO: Yeah, there is definitely work that needs to be done in companies like us and The Portland Group, and Pathscale, you know a number of companies that we’ve worked with have been starting that work for over a year or two now, so there’s been a lot of progress in the marketplace to enable for these new kinds of hybrid architectures, especially where you have a CPU and a GPU which is a quite different architecture than the more traditional one where you have a couple of CPUs on a single node.  So it’s been something that we’ve worked with our partners quite a bit with over time and we also of course have a lot of our own tools from compilers to debuggers to performance toolkits to different monitoring applications that we’ve had to enable for this type of environment.  So it is a lot of work, but the key has been to try to do that work without forcing the user to completely rewrite their entire application.  So, how can we do that in such a way that allows the user to bridge from one environment to the other – and back and forth.

TER: So Pete what is really different about building a system the size of Titan as compared to some of the commodity clusters with GPUs?

UNGARO: Part of what goes on today is that we get so focused on talking about the peak performance of the machine or the Linpack performance of the machine, that we forget that there are different types of machines, and that real sustained performance is really key.  I think that what makes a Cray system different from building a ten petaflops GPU system out of commodity components is our whole system environment.  We very tightly integrate the hardware with our software with our interconnect, and we build that all together from a single system view, not just aggregating a lot of components from a lot of different places and trying to tie it together and integrate them, but building the system from the ground up.  I think that’s what has really been, quite honestly, the success of systems like Jaguar, and what I think is going to be the difference for systems like Titan in the market, from people that just go out and get a bunch of fast processors or GPUs and put them together with Infiniband.

TER: What impact do you see Titan having on science and industry and let’s try to put this in a timeframe.  Will the system be up and running with users by the time we roll into supercomputing 2012?

UNGARO: Oak Ridge has laid out a timeframe for the system and actually the first phase of the system is upgrading all of the system to the latest AMD Interlagos processors and our brand new Gemini interconnect and that should be available for users in early 2012.  And then we’ll start to bring on the GPUs later in 2012 and it should be up for users kind of late 2012 or early 2013 as that gets integrated and through its acceptance process and into the Department of Energy allocation process that they use at Oak Ridge. So that’s the current timeline that we have Mike.

TER: So, we’re probably looking at somewhere in the 2013, 2014, 2015 timeframe to seeing some pretty significant developments based on applications finally figuring their way around the system, and by that time, you guys will probably be ready for another phase – or Titan Plus – won’t you?

UNGARO: LOL.  You know one of the interesting things that happened with Jaguar was – within the first couple weeks of Jaguar being up, even before it got through its acceptance process, we already had world record science being done on the machine. So I think that one of the big differences that Oak Ridge has done with their user community is – they have a great team there that works very closely with our team at Cray that help enable their scientists to really take advantage of the machine right when it comes up.  So I will be really disappointed if we don’t have some breakthrough science even next year before the machine is fully in production.  I know that they are working very hard with their science teams around that and I expect that we’ll have a lot of success there.  So hopefully we won’t have to wait until 2013, 2014, or 2015, but we do already have some ideas on what Titan Plus might look like.

TER: So I spoke with Jack Wells at Oak Ridge, and Steve Scott at NVIDIA, and I get the sense that – and I know there are other players involved and I don’t mean to exclude other companies, but from the three of you as the hub of what’s going on here, I sense higher levels of enthusiasm and energy and excitement than I’ve seen with many projects over the past years.  It just seems to me, as someone looking at this from the outside, that you guys do have an unusually good synergy established between Oak Ridge, NVIDIA, and Cray.  Thoughts?

UNGARO: I would agree and I’d actually include AMD and a couple of other companies into that mix, but I definitely agree with that.  We have a long term partnership that we’ve established with Oak Ridge as we went from kind of one machine generation to the next.  I think that’s really started to build a cohesiveness, and not just between the vendor community companies like Cray and AMD and NVIDIA, with an organization like Oak Ridge, but also extending out into the user community.  We’ve had so many opportunities to spend direct time with the people using these machines and understanding what their needs are so when we bring the next machine out it’s even more ready for what the user community needs.  I believe Titan is going to be a big step forward, not just in performance but also in functionality that the user community needs to be very successful within the Office of Science.  I’m pretty excited about it and I can’t wait. You know, building machines like this is something that makes me get up in the morning so I’m pretty excited and I know our partners are to.

TER: So Pete, some people in the press are already making a big deal out of Titan being able to challenge Japan for the title of the world’s fastest supercomputer, so I have to ask you, is this really even important?

UNGARO: If you mention the world’s fastest supercomputer as what is number one on the Top 500 list, I actually don’t believe that’s very important.  I would tell you clearly that’s not a goal of ours at Cray and I can tell you that’s not the goal of Oak Ridge or the Department of Energy.  I think what’s really important is being the system that delivers world class science off the machine.  So how can we find alternative energy sources and what simulations can we do and how realistic can we make those simulations to convince us about developing alternative energy sources, or about understanding climate change and the impact of energy policy on climate change.  Those are things that are going to really be a difference maker for us.  Curing cancer on a supercomputer would be something that I think is way more important than being number one on the Top 500 list.  Not to say that that isn’t a great thing too. One of the things that Jaguar has done, is the first system in the world to sustain petaFLOPS performance across a set of applications. There are five applications right now that are running at over a petFLOPS of performance on Jaguar which is pretty amazing.  I think that number is going to grow quite immensely when we get to Titan.

TER: Fantastic.  Very well said.  I’ve been saying for some time that if we really are serious in this country about ending the nation’s dependence on oil, we should be putting more money into exascale research and not into offshore drilling –but I don’t want to make a political statement of course!

But I’m also very excited about the potential.  I wish you all the luck in the world and we’ll check back in with you on a regular basis to report on Titan’s progress.  So any closing comments for the user community?

UNGARO: Mike I just want to thank you for the interview.  Obviously this is a huge milestone for Cray. It has a big impact on our company overall and we couldn’t be happier for what this machine is going to do, and even more so, we’re super excited to be able to deliver it to Oak Ridge and the Office of Science.

This article reprinted with permission of The Exascale Report™.

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Less than a month ago, ORNL was finally able to announce a significant award to Cray for the next stage of Jaguar, growing the system into the ten to twenty petaFLOPS range with the addition of GPU accelerators from NVIDIA.

The new system will be called Titan.

We caught up with Jack Wells, Director of Science for the National Center for Computational Sciences, a U.S. Department of Energy (DOE) Office of Science user facility at ORNL, to talk about Titan.

The Exascale Report: How many individual users or organizations do you see accessing Titan in 2012 – 2013?

WELLS: I think that we would be able to maintain a population of projects similar to what we have now. Through the INCITE [Innovative and Novel Computational Impact on Theory and Experiment] program at our leadership computing facility at Oak Ridge, we support and collaborate with 32 projects in 2011, and the available resources are oversubscribed. We also support nine projects through the ASCR Leadership Computing Challenge (ALCC) program and a larger number of smaller projects through our Director’s Discretionary Access Program. I expect the demand and our ability to support that number of projects will be sustained.

TER: Do you have any sense of the number of individual users?

WELLS: We do track the number of individual users. Our current number on the Jaguar supercomputer is approximately 800, and we expect this to remain fairly constant. Our users work on grand challenges in science and engineering. They engage in simulations to understand the molecular basis of disease, the intricacies of climate change, and the chemistry of a car battery that can last for 500 miles. They may be working on a biofuel that is economically viable or a fusion reactor that may someday provide clean, abundant energy. They have one thing in common—they use computing to solve some of the planet’s biggest problems. These individual users are participants in projects that can have, say, a dozen users, so the number of awards through INCITE, ALCC, and Director’s Discretion is small enough to keep the time allocations large. In the 2011 calendar year, for example, the average INCITE allocation was 27 million processor hours. One project received 110 million hours.

TER: How will the user access to the systems and their ability to develop and test applications change from Jaguar to Titan?

WELLS: We are working with Cray, PGI, CAPS, Allinea, Vampir, and the scientific library teams to have optimized tools for the users. We are also working now to get a core set of projects ready for Titan. One of the main questions that arose two years ago when we proposed the hybrid architecture focused on the usability of the future computer: Would researchers be able to squeeze results out of a GPU-accelerated machine without too much programming pain? So we have focused on a set of six applications that are representative of our workload, and are working with the architects of the codes and some of the main users to get these codes ready—and it’s actually become part of the project. We have also developed a training curriculum, consisting of conferences, workshops, tutorials, case studies, and lessons learned, that covers tools and techniques for realizing the benefits of hybrid architecture.

TER: And could you clarify for us what those six applications are?

WELLS: One is S3D (Direct Numerical Simulation of Turbulent Combustion), a chemical combustion code out of Sandia used by Principal Investigator Jackie Chen to simulate burning fuels. Another is the Wang-Landau LSMS code (Wang-Landau Linear Scaling Multiple Scattering), a materials first-principles code that’s been developed here at Oak Ridge National Laboratory. Another code is LAAMPS (Los Alamos Molecular Dynamics code) authored by colleagues at Los Alamos and used here to simulate lignocellulose. Another is PFLOTRAN (Modeling Multiscale-Multiphase-Multicomponent Subsurface flows), a subsurface transport code that Peter Lichtner from Los Alamos uses to study carbon sequestration and underground transport of contaminants. Another is CAM-SE (a scalable, spectral element dynamical core for the Community Atmosphere Model), a community atmospheric code from the climate community. And the sixth is DENOVO, a neutron transport code. That’s a part of the workload within the Consortium for the Advanced Simulation of Light-Water Reactors—the DOE [Department of Energy] nuclear energy modeling and simulation hub led here at Oak Ridge.

TER: So Jack, when you say there is work being done now, what do the users – the application developers –the programmers – the scientists – what do they actually do now in order to get ready for Titan?

WELLS: When we started the work on these codes, there were few tools to help with the work. The teams have spent most of the time restructuring codes to expose more levels of parallelism and promote data locality. These are exactly the type of transformations that make codes run better on both accelerators and multicore CPUs. Some of the codes have kernels in CUDA, others are using directives with the compilers. Still others are using optimized libraries.

TER: Would you say there is a lot of manual work at this point?

WELLS: Things are improving in that regard as compiler directives are advanced. So many of the compiler companies are coming out with common compiler directives that help a great deal.

TER: So you have a very unique perspective on this – you have the experience on the user side and you have the experience on the leadership side – would you say that from the early days of being a user on very large, advanced computing systems – to today, are things easier for the user or are they more difficult

WELLS: If you take the 15- or 20-year view, I’m not sure. There are many new challenges, for example, the increasingly massive parallelism. But, I think the challenge of utilizing parallel computing in the early days was similar in character. If you think about message passing hardware before MPI, there was a lot of diversity. But then standards developed and our investments in software had a longer life. I think that’s what we’ll see here. Some people may tell you it’s a really big change—and it certainly is—but from my point of view, the fundamental issue of revealing new levels of parallelism reminds me of attempts to use the hierarchical memory and processor structure within the Intel Paragon supercomputers that we used in our laboratory during the 1990s.

Now the dramatic difference is the number of processing threads, and this has increased rather steadily. There was a time when 100-way parallelism was a big deal, and then 1,000 and 10,000, and now we have on the order of 100,000 processing cores, and they keep increasing. So, this is a big challenge, and what we see is that many of the applications that are doing well dealing with very large core counts—making progress using a large fraction of the full capability—many of them have taken on bigger, more realistic problems—problems that implement high degrees of fidelity and embrace more physical phenomena, stochastic behavior, ensemble behavior. These kinds of applications are the ones that are advancing science and engineering using the full capability of the machine.

TER: A number of people still question why we need to continue to push the technology envelope. They don’t get it – in terms of the importance. So Jack, what gets you the most excited when you think about how this processing capability may impact science and discovery? How do you see life changing when 20 petaFLOPS becomes the bottom of the production and performance scale.

WELLS: This is a very exciting question. Having such broad access to predictive simulation capability would dramatically advance many areas of science and engineering. I believe that we would dramatically accelerate the invention of new energy technologies, such as a 500-mile battery for transportation or very efficient solar cells, or the safe life extension of nuclear reactors. For scientists and engineers, this would revolutionize the practice of research. Simulation would not replace experiment’s role in the scientific method or in engineering design principles. But it would allow us to be very focused and efficient with the most interesting and important experiments to perform conceptual designs to construct prototypes.

TER: And in terms of an access convention, do you see cloud playing a role at all?

WELLS: Oh yes, I do. I think that is part of the story of computational science and engineering. There’s no doubt that this will be a cost-effective solution for some, maybe many, users. Scientists will take advantage of these resources—where it makes sense for them—and that is the way it should be.

TER: And on an international scale, do you see the U.S., because of efforts like Titan and what will be coming after that, maintaining some level of technology leadership?

WELLS: My understanding of U.S. science and engineering policy is that there’s a broad consensus around the role of the federal government in advancing supercomputing and then using supercomputing as a tool for advancing science, technology, U.S. competitiveness in general. I think there’s a strong bipartisan consensus there.

Of course, other countries also perceive the value of supercomputing, and they are investing as well. I think leadership should be defined in terms of impact—and that’s measured over an extended period of time. We’re committed to leadership in impact. Now certainly Europe and Asia are making significant investments in supercomputing. Some of the investments in Europe that stand out to me are their investments in application software. There are strong European research teams and computational science programs in Europe that are funding these integrated code teams to advance particular areas of engineering and science in which they feel they have leadership. And I think that’s significant.

TER: What steps are you taking at ORNL and the Leadership Computing Facility to ensure long term program success and to keep Oak Ridge and all your suppliers and partners working in harmony moving forward?

WELLS: We’ve touched on several points that are relevant to this question, but for long-term program success I’d emphasize the importance of a sustained policy on the role of supercomputing in science and engineering. And I think we have that. If that continues, it’s a strong foundation on which to build the future.

Relative to the current inflection point we have in technology, the energy consumption of these large machines necessitates energy-aware computing as we move forward. The broader industry is already doing this with investments in mobile computing and game hardware. The broader IT industry is making significant investments in these accelerator processors. So the technology risks of our platforms, going forward, are really quite modest. There’s always a risk of putting these machines together at scale, but that’s something we have a track record of managing through years of deploying leadership-class computing systems. And we have tremendous confidence in our vendor. Certainly the biggest perceived risk over the last two and one-half years as we’ve planned for Titan has been its usability by science and engineering teams. As I tried to emphasize previously, we are playing a role, in concert with our vendor partners, in making sure the machine is demonstrably useable. Computer science researchers will also have a role in generalizing or extracting the lessons that are learned throughout the Titan project and making them more readily available to a broader community.

This interview appears here courtesy of The Exascale Report.

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Dahlia Lounge—Cuisine:Asian Influenced North- west: 2001 Fourth Ave. (Virginia St.) Seattle, WA 98121 206-682-4142

This 20+year veteran of the Seattle scene is still going strong with a super-loyal local following that mixes with out-of-town foodies looking for a unique Seattle experience. Chef Tom Douglas will take you on a culinary journey using Asian ingredients and tech- niques along with the freshest Northwest offerings. All of this in a sophisticated, yet comfort- able urban-chic dining room with professional, informed and unstuffy service. Don’t miss the raw bar, the crab cakes and a chance to see why salmon is king in the world of Cascadia cuisine. Certainly do not leave without having something sweet from one of the most expertly de- signed dessert menus in town.

Le Pichet—French Cuisine 1933 First Ave. (Virginia St.) Seattle, WA 98101 206-256-1499

Take a trip to Paris without leaving this fair city by stop- ping by the gorgeous, yet simply designed bistro. Named after the vesicles by which you can (and should) order expertly chosen wine from a value-based list, this long time Belltown favorite is for the Francophile in all of us. Choose from a number of crisp, properly dressed, seasonal salads and a charcuterie plate, then move on to perhaps the best chicken dish in Seattle—a whole bird perfectly roasted to order for two. Of course, the French love their desserts and Le Pichet delivers not only the classics like chocolate mousse and crème brulee but other nicely done modern takes as well.

Matt’s in the Market—Local, Seasonal NW Cuisine 94 Pike St # 32 Seattle, WA 98101-2066 (206) 467-7909

Located on the 3rd floor of the Corner Market Building in the world famous Pike Place Market, this simply, yet tastefully de- signed restaurant offers spectac- ular views of the Puget Sound. With the market directly

across the street the chef and his staff have access to an amaz- ing bounty of the freshest local ingredients. Try the absurdly flavorful pork belly or grilled octopus then have anything involving the always fresh fish or a locally sourced lamb dish. It is every chef’s dream to not have to get in a truck to find the fresh- est, most local of ingredients and even more of a dream to have an endless supply right at your doorstep—Matt’s makes this a dream come true.

“Start with the wicked shrimp, have the tuxedoed waiters make you a before-your-eyes caeser, then experience a table-side carved Chateubriand…”

El Gaucho—Steakhouse 2505 First Ave. (Wall St.)Seattle, WA 98121 206-728-1337

The restaurant to see local sports celebrities, broker a multi-million dollar deal or plain just be seen, El Gaucho is a Seattle institution for movers and shakers. Step back in time in this ultra swank, darkly lit supper club style restaurant and re-live the glory days. Steak, of course, is star of the show here and the 28 day dry-aged, hand picked, Mid-West prime beef does not disappoint. Start with the wicked shrimp, have the tux- edoed waiters make you a before- your-eyes caeser then experience a table-side carved Chateubriand and finish with Bananas Foster. With live Latin music nightly, a happening bar scene and a well- dressed crowd, you’ll feel like Frank and Dean could walk in at any moment.

Wild Ginger—Modern Pan-Asian 1401 3rd Ave Seattle, WA 98101 206-623-450

Wild Ginger has been around since 1989—an eon in restaurant years—and in it’s current stunningly beautiful digs for the past 11 years. A certain testament to the fantastic job the kitchen has been doing over this span in serving up perfectly executed Pan- Asian cuisine that takes advantage of the local access to Asian ingredients and the freshness that the local water and land provide. Try the satay bar where you can savor a lovely skewered prawn

or Vietnamese Hawker Beef that comes with various dipping sauces that are superbly paired. Duck, a staple course in Asian cuisine, is rendered grandly here with crispy skin enveloping the smoky, gamy meat inside. Dungeness crab, a Northwest staple, is also prepared magnificently and served with

a black bean sauce, ginger and chiles that will take you on a tour of Southeast Asia in one dish. 22 years in the business and Wild Ginger’s atmosphere, food and service have only seemed to got- ten better over time—a remark- able feat.

Salumi—Artisan Cured Meats 309 Third Ave South Seattle, WA 98104 206-621-8772

This cured meats (salumi) shop run by Armandino Batali—yes, father of star Chef Mario—in Pioneer Square is a closet of a restaurant/deli that has a very NYish feel.

Mr. Batali cures all meats in- house and serves other more entrée like items including a to-die-for porchetta lasagna or an excellent wild mushroom gnocchi. Sit down at the long communal table and rub el- bows with local business people, tourists and hipsters and have a glass of excellent, inexpensive wine poured in a juice glass. If that is too cozy, the line for to go sandwiches–while often long– moves rather quickly and is more than worth the wait to have some of this wildly popular establishments homey, yet fantastic fare.

Reprinted from the Print’nFly Guide to SC11 Seattle, an in-flight magazine custom-tailored for your trip to the biggest Supercomputing conference ever. Download the PDF (15 Mbytes). If your IT crowd blocks Dropbox, please Download here.

Related posts:

• Smartphone Version – Guide to SC11 Seattle
• Print ‘n Fly Guide to SC11 Seattle
• SC11 to Return to Seattle

The post Get Hungry – Seattle Recommendations from a Local Foodie appeared first on insideHPC.

By Peter Ungaro, President and CEO, Cray, Inc.

On behalf of everyone at Cray, let me be the first to say, welcome to Seattle!

People often think of Cray as a Midwest-based company, and while we still maintain a large presence in St. Paul, Minnesota and Chippewa Falls, Wisconsin, Seattle has been home to our company’s corporate head- quarters for more than 10 years now. Actually, we like to think that Cray has three hometowns! As the HPC industry descends upon Seattle for the 2011 Supercomputing Conference, our Seattle-based “Crayons” are very excited to be the unofficial hosts this year.

If the 23 previous conferences are any indication, this 24th annual gathering will successfully continue the great tradition of showcasing the best our industry has to offer. Each year brings another opportunity to col- lectively discuss, explore and experience the latest trends in HPC. This year is no exception as we analyze the merging of scientific simulation and big data – an exciting topic that will no doubt be talked about this week and for years to come.

SC is also a great time to have fun and celebrate our industry. Last year, we did this with gumbo, po’ boys and hurricanes. This year, we get to enjoy salmon, crab, microbrews, Washington wines and, of course, great coffee!

Seattle is a beautiful city, even in November, so enjoy your time here and be sure to visit some of the many sights, restaurants and entertainment options Seattle has to offer. A few of our Seattle Crayons have even shared some of their favorites to help guide you to some of the can’t-miss spots.

Enjoy Seattle and welcome to SC11!

Reprinted from the Print’nFly Guide to SC11 Seattle, an in-flight magazine custom-tailored for your trip to the biggest Supercomputing conference ever. Download the PDF (15 Mbytes). If your IT crowd blocks Dropbox, please Download here.

Related posts:

• Print ‘n Fly Guide to SC11 Seattle
• Interview with Peter Ungaro, President & CEO of Cray Inc.
• Video: Cray’s Peter Ungaro on the Challenges of Exascale

The post Sponsored Post: Welcome to Seattle – Peter Ungaro, CEO, Cray Inc. appeared first on insideHPC.

As a destination city, Seattle has much to offer in the way of sights, food, and entertainment. But when we asked a Cray employees for their recommendations, they really stepped up with lots of great tips for a fabulous week.

We hope that you find this Print ‘n Fly magazine useful. Besides entertainment guides, we’ve included feature interviews as well as a science fiction original story I wrote that takes place at an SC conference 20 years in the future.

Contents

• Welcome Letter – Peter Ungaro, President and CEO, Cray Inc.
• Executive Interview – Peg Williams, Senior Vice President HPC Systems, Cray Inc.
• Interview – Doug Miles, Director, The Portland Group
• Interview – Steve Scott, CTO, Tesla Business Unit, NVIDIA
• Interview – Jack Wells, Director of Science, NCCS at ORNL
• Interview – Peter Ungaro, President and CEO, Cray Inc., on TITAN
• Restaurant Reviews – Trey’s Corner: local foodie reviews the best Seattle has to offer
• Best of Seattle – Cray employees share their favorite spots for food, coffee, and more
• SCI-FI Original – The Three Gifts of the Magi by Rich Brueckner

Download the PDF (15 Mbytes).

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• Sponsored Post: Welcome to Seattle – Peter Ungaro, CEO, Cray Inc.

The post Print ‘n Fly Guide to SC11 Seattle appeared first on insideHPC.

This “story trailer” video previews The Three Gifts of the Magi, a new SCI-FI original by Rich Brueckner that will appear in the Print ‘n Fly Guide to SC11 Seattle.

This is the continuing story of The Three Magi of Katrina, a science fiction story set in New Orleans at SC30.

Tagline: Released from prison, a convicted assassin races to SC31 in Seattle to find the Artificial Intelligence known as Adom.

Update: You can now read the story online.

The Print ‘n Fly Guide to SC11 Seattle is now available. Download the PDF (15 Mbytes). If your IT crowd blocks Dropbox, please Download here.

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• Fiction: The Three Magi of Katrina — SCI-FY Set at SC30 in New Orleans
• SCI-FI Original: The Three Gifts of the Magi
• Video: SC30 – The Movie Trailer Number 3

The post Video Trailer: The Three Gifts of the Magi – SCI-FI for SC11 appeared first on insideHPC.

According to Steve Scott, recently appointed CTO of the Tesla Business Unit at NVIDIA, “Oak Ridge’s decision to base Titan on Tesla GPUs underscores the growing belief that GPU-based heterogeneous computing is the best approach to reach exascale computing levels within the next decade.”

In the first phase of the Titan deployment, which is currently underway, Oak Ridge will upgrade its existing Jaguar supercomputer with 960 Tesla M2090 GPUs, based on the NVIDIA® “Fermi” architecture. These GPUs will serve as companion processors to the AMD multi-core CPUs. In the second phase, expected to begin in 2012, Oak Ridge plans to deploy up to 18,000 Tesla GPUs based on the next-generation architecture code-named “Kepler.”

We spoke with Steve Scott to discuss the role of the GPU in this important milestone system and what Titan will mean to the HPC user community. Here is that interview.

The Exascale Report: NVIDIA is a leader in the mobile and desktop chip market, and now you are solidifying a position as a leader in the supercomputing market and have both ends of the market covered quite nicely. I also see that NVIDIA’s stock was up 4.4% as of yesterday, and that’s a 44% increase above the 52-week low. The company is in a very strong position right now of exuding confidence. It seems to me that NVIDIA is doing a tremendous job of figuring out a business model that can survive, or maybe we should say surpass, the volatile nature of the HPC market segment. Would you care to comment on this?

SCOTT: Well, the business model is key. One of the things that attracted me to NVIDIA is that I believe NVIDIA has the right technology to get to exaFLOPS computing, and drive High Performance Computing in general, because of its unique approach to heterogeneous computing that results in greater energy efficiency. But also because of NVIDIA’s business model that allows us to support that development. It costs on the order of a billion dollars to create each new generation of high-performance processor, and the HPC market simply isn’t big enough to support that level of development. The fact that we have a very high volume market for our graphics processors, and that we can use the same chips for high-end graphics workloads as we can for HPC, allows us to get the best of each new generation. We simply couldn’t do what we are doing if we weren’t leveraging that large consumer-driven market.

TER: So it’s a matter of striking a pretty good balance in terms of your future R&D investment as well – and maintaining both sides of the equation?

SCOTT: Exactly.

TER: So Steve, you’ve seen a tremendous amount of new technology during your career, and I imagine it’s difficult for you to get really excited about new developments when they come along – but you do seem to be very enthusiastic about what’s going on here with Titan. What do you find most exciting – or most interesting, about this important milestone on the journey to exascale?

SCOTT: Well, Oak Ridge National Labs is really the world’s premier open computing facility. They have a tremendous track record of delivering large-scale systems with their partnership with Cray – and delivering science out of those systems, so I’m particularly excited to have this caliber of organization look to the future and make an ‘all in’ bet on GPU computing. I think they’ll do tremendous things with this system, and I’m looking forward to the many teams of scientists they will have generating results and moving their codes forward to what I think will prove to be a hybrid multicore future.

TER: And you’ve been involved with Titan for what…maybe 3-4 years now?

SCOTT: I’ve been involved with Oak Ridge through my position at Cray for, well, it must be 8 or 9 years now.

TER: So specific to this new system, what are some of the tradeoffs that had to be considered – or perhaps still need to be considered when it comes to building such a complicated hardware system, yet still creating a workable user environment?

SCOTT: Cray is really expert at building large, useable systems from their custom interconnect to their software stack, but the NVIDIA component is really about how we’re going to move the compute nodes forward. And, we’re in a new era now where we are completely constrained by power. So, power efficiency equals performance. NVIDIA’s architecture is explicitly heterogeneous with the GPUs being designed from the ground up to be energy efficient when running parallel workloads. So we can really concentrate on the compute node itself, the memory system, and the functional units and memory hierarchy that will allow us to deliver more performance at much lower power consumption than a traditional CPU architecture. And, the scalable aspects of the system are being addressed by the Cray interconnect and software stack.

TER: So Steve, give us a picture of what you see for next year – as we are getting ready for Supercomputing 2012 – and what will NVIDIA’s role be in the global HPC market at that point?

SCOTT: Well I can’t comment specifically on the schedule for upgrading the Titan system with next generation Tesla GPUs – they will be doing that during the second half of next year and I imagine there will be a lot of excitement and activity around the Titan system as we prepare for Supercomputing 2012. I expect that this system is a signpost of where we will see momentum shifting in the high-end HPC market, and actually in the broader HPC market.

If you would have looked at the Top 500 list three years ago – the June of 2008 list – you would have seen no GPU-based supercomputers on that list. Now we’re in a situation where 3 out of the top 5 systems are powered by NVIDIA Tesla GPUs, and the number 3 system, Jaguar, is about to be upgraded to use NVIDIA GPUs. We’ve seen a tremendous amount of uptake in just a very short period of time. And because this fundamental shift that has taken place in terms of power, I think we’re going to see continued uptake over the next several years.

We’re just excited to see Oak Ridge embracing this technology – and we’re excited to see what the world is going to do with this technology. It’s very gratifying to have customers that are doing the kinds of work that Oak Ridge and others are doing with high performance computing.

Read the full piece at The Exascale Report.

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The post An Interview With Steve Scott, CTO Tesla Business Unit, NVIDIA appeared first on insideHPC.

Discussions around Titan always circle back around to the tools and the programming environment. As the systems get more complex, we all agree there will be an increasing need for enhanced compilers and development tools.  At the core of this discussion, we always hear reference to the same company – The Portland Group.

It’s no surprise to many that PGI compilers will be an integral component of the user application development environment, not just for Titan, but for many generations of systems to come.

To talk about the compiler heartbeat of this new system and the changing user environments of larger petascale deployments, The Exascale Report talked with the Director of The Portland Group, Doug Miles,

The Exascale Report: Most Cray systems include PGI compilers. Will PGI compilers be available on Titan?

MILES: Yes, in fact Oak Ridge upgraded some time ago to our GPU-enabled PGI Accelerator compiler suite to enable early software work and preparation for Titan. By the time Titan is installed, the latest versions of the PGI compilers, including support for AVX and the new AMD Interlagos CPUs and the latest NVIDIA GPUs will already be in place.

TER: Titan will represent an entirely new level of complexity in terms of the programming and application development environment. What is being done today to ensure the most efficient development environments possible, with Titan and other platforms, as we start to deploy these massive and complex systems?

MILES: You are right that this is a new level of complexity. In addition to the distributed-memory dimension and the SMP dimension, developers now need to consider the accelerator dimension when porting and optimizing applications. Fortunately, with the right compiler and tools support, it is all very tractable. PGI’s approach is based on 3 elements: aggressive x86 optimization and OpenMP directives for efficient use of CPU resources, GPU directives to make it easy to get started accelerating applications with GPUs, and native CUDA Fortran/C/C++ language support for full control over GPU porting and optimization. Obviously debugging will also be a key factor, and companies like Allinea and Totalview are doing great work in that area and we’ll be working with them to ensure our tools are interoperable.

TER: What are the biggest considerations / challenges users will face in moving from Jaguar to Titan?

MILES: In moving from Jaguar to Titan, one factor that stands out is the sheer number of cores that will be available in the full-up Titan system – into the millions if you count each CUDA core individually. Developers and users will need to either run much larger problems or expose orders of magnitude more parallelism in their algorithms in order to use the system efficiently.

Another challenge will be to minimize the cost of data movement between CPU memory and GPU memory. We’ve added features to the PGI Accelerator compilers in the past year that enable developers to allocate data in GPU memory and re-use it across kernel invocations and even up and down procedure call chains. That is a big step forward in enabling whole program data management between CPU memory and device memory, which doesn’t eliminate all data movement but ensures it can be minimized.

Another issue in the move from Jaguar to Titan will be effectively using CPU and GPU resources *together*. You don’t want to write code in a way that leaves 16 very powerful CPU cores idle while the GPUs are in use. Users will need to determine which parts of their applications are most suitable for GPU acceleration, which parts are most suitable for execution on the CPU cores, and structure their codes to maximize use of all the available computing resources. Programming in CUDA (C/C++ or Fortran), this is supported by default in the programming model.
The PGI Accelerator compilers will support asynchronous execution of GPU regions and CPU regions by early next year.

TER: Has the criticism regarding the difficulty in programming the GPU been fair and accurate – and what is PGI’s perspective on this?

MILES: Look, NVIDIA did a beautiful job of opening up GPUs for general-purpose parallel computation using CUDA. It was just about the right mix of API and language extensions to allow skilled programmers to extract the performance of GPUs on a wide variety of algorithms. If they had gone completely with an API approach, a la OpenCL, it would have been so low-level as to be almost unusable by scientists and engineers. If they had taken a purely high-level language-based approach out of the gate, they would have been betting the success or failure of GPGPU on some extremely complex and advanced compiler technology. I think we’ve all seen cases before where that has not panned out so well.

All that said, the barriers to getting started with GPUs can and are being lowered rapidly. We’re at the point in the adoption curve where higher-level programming models for GPUs are appearing from all sides – PGI with OpenMP- like directives, Microsoft with AMP, the OpenCL committee with their HLM initiatives, and even Google’s Renderscript for Android is touted as a way to write portable GPGPU code for mobile devices. All of these are recognition of the fundamental value of GPGPU, and all will likely make contributions in certain disciplines to ensure that GPGPU programming becomes progressively easier and more mainstream for all types of developers.

TER: What role will PGI compilers play in creating useable, productive environments as we move into 20 Petaflops and larger systems?

MILES: Back when we started working on the PGI Accelerator directive-based GPU compilers in early 2008, we made a bet that accelerators would become a mainstream technology in technical computing. Our goal in the race to 20 PFLOPs and beyond is to deliver compilers and tools that allow PGI users to extract the full performance potential of many-core and accelerator-based systems without getting locked in to any specific architecture or platform. We do of course aggressively react to demand, and in that sense we do put more emphasis on some platforms than others, but fundamentally PGI is agnostic regarding processors and operating systems. That objectivity is what gives PGI its unique position in the HPC market, and why we have historically been a bellweather on HPC market directions – from microprocessor-based scalable systems, to Linux/x86 clusters, to the rise of x86-64, and now toward GPGPU and beyond. I think you’ll continue to see us play that role on the inexorable march toward Exascale systems.

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The post An Interview with The Portland Group’s Doug Miles appeared first on insideHPC.