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My thoughts of Dec 2 readings -- Gordon Bell Prizes

The Anton paper deals with a specific application molecular dynamics. The amazing part to me is that they do both software and hardware design to run MD applications on HPC computers. Before that, I have a naive thought that HPC is mainly the algorithms research on similar HPC clusters or computers. Kind of combining MPI and OpenMP code together, transforming serial algorithms into parallel algorithms, CUDA programming in GPUs, etc. It seems that there is not a general platform where people in…See More
Blog post by Fei Ye Dec 2, 2010
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Maybe we should start a hedge fund so we can fund our own work...

Millisedon-Scale Molecular Dynamics Simulation on Anton: The work presented in this paper was sheer awesomeness! They built their own system, and not just any system, but the most kick-ass system they could design to compute exactly what they wanted... How cool is that? Special-purpose platforms for in-demand areas obviously has value, proven by this paper. The progress made by this specialized system could potentially lead to advancements in medical research that would have been out of reach…See More
Blog post by David Noble Dec 2, 2010
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Gordon Bell Prizes

A first thought I had about the MD simulation on Anton was: "Do I have the patience to get excited about femtosecond time step simulations where it takes an entire DAY to simulate on the order of 10 microseconds?" They did not discuss this, but I'm assuming that a femtosecond time step is necessary in order to accurately capture the molecular dynamics, therefore getting to a microsecond requires 1 billion steps. Being deep into orbital simulation where time steps are usually more than 1 second…See More
Blog post by Danny Browne Dec 2, 2010
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12/02 ANTON

The Anton paper describes the special purpose Anton supercomputer designed for only one thing: Molecular Dynamics simulations of biomolecular systems. It is stated that the architecture and the algorithm were developed together to have highly optimized system. The results obtained are very impressive with Anton outperforming x86 by about two orders. If i have understood the Gordon Bell Prize correctly, it is for systems that demonstrate performance in terms of highest FLOPS of useful work.…See More
Blog post by Srinivasa Manohar Karlapalem Dec 2, 2010
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Millisecond-scale molecular dynamics simulations on Anton

The Anton paper mainly talks about designs for molecular dynamic (MD) simulations of bio-molecular systems. Detailed report on Anton’s performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations. The paper also shows how different algorithms have been coordinated with Anton to achieve these results.I personally found this paper very interesting considering the picture of classical molecular dynamics…See More
Blog post by Abhinesh Krishnaraj Rao Dec 2, 2010
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Blood Flow

...........I read both Molecular Dynamics papers. They were incredible.I'm not good enough at math or science to do them justice in this blog post.So I won't.Simply amazing work though.I imagine the blood flow simulation will be huge for helping medical researchers.See More
Blog post by Puyan Lotfi Dec 2, 2010
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Anton: A True General Purpose Processor

This paper describes a specialized parallel hardware named Anton, that is designed to accelerate MD simulations by two orders of magnitude, down to millisecond-scale level for molecular systems involving tens of thousands of atoms. The machine consists of 512 parallel processing nodes, each containing a specialized single ASIC for the MD computation engine. A natural first question is whether building a specialized machine for molecular simulation can gain a significant performance advantage…See More
Blog post by Chris McClanahan Dec 2, 2010
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Gordon Bell

This paper on molecular dynamics is interesting but I think the notion of designing a computer to solve particular problems is the more relevant topic. Anton is designedfor the specific purpose of solving the MD on the millisecond scale. My thought that Anton’s architecturecould be extended to solve any fluid dynamics type problem on a large scalemore efficiently than commodity-style super computers. What I found also unique is that theydesigned the algorithm specific to the architecture, which…See More
Blog post by Adam Springer Dec 2, 2010
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Gordon Bell Prizes

“Millisecond-Scale Molecular Dynamics Simulations on Anton” by Shaw et al, presents a special-purpose hardware architecture for molecular dynamics. It poses an interesting question: given a computation task, how much could you improve performance if you had complete freedom to redesign the hardware and algorithms? The authors found that they were able to improve the performance of MD simulations by two orders of magnitude by developing a new architecture that does not resemble the x86 design at…See More
Blog post by Kent Czechowski Dec 2, 2010
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Richard (Rich) Vuduc commented on Kent Czechowski's blog post 'Autotuning: Compilers for general programs'
Some of my notes from today's discussion. - Programming model vs. compilers * Limited expressivity? - Parallelizing compilers - Blame the hardware guys - Lack of security is not a hardware thing - Assumptions/fundamental limits about…
Nov 30, 2010
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Blog posts by Abtin Nov 30, 2010
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Compilers... Ehh...

Compiler research: The next 50 years. They clearly identify the problem in the first page of the paper, in that the direction computing is going in is parallelism, but there is a lack of language and compiler support for ease of development for parallel programs. They mention the changes that will have to be made within the community in order to contiinue contributing in the same fashion that they have over the history of computing. The paper was pretty straight forward, but nothing really…See More
Blog post by David Noble Nov 30, 2010
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Autotuning: Compilers for general programs

'Compiler Research: The Next 50 Years', by Hall et al, is a manifesto on the future of compiler innovation. The paper starts out as a wishlist of future accomplishments (all of which are too general to ever to be reached) but ends with a reasonable set of recommendations. The main point being that compiler technology is still an integral part of computer science, but unlike the rest of the field, the scope and complicity of compiler technology significantly limits the contribution that an…See More
A blog post by Kent Czechowski was featured Nov 30, 2010
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Autotuning: Compilers for general programs

[UPDATED 11/30/2010 @ 7:35a]The Hall paper was published shortly after the 50th anniversary of IBM's release of the first optimizing compiler and gave insight into the needs and trends of the next 50 years. I liked the statistic given early on which indicated the ~$60B or 0.6% of the U.S. GDP is spent on correcting software defects; that is a good indication of the need for better tools to identify program bugs. One of the main points addressed both early and late in the article was the need to…See More
A blog post by Danny Browne was featured Nov 30, 2010
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My thoughts of Nov 30 readings -- Autotuning -- Compilers for general programs

The next 50 years describes a beautiful picture compilers and HPC research would become central to the future computer science and information technology. It talks about a wide range of topics including cost of programming, system security and reliability, accomplishments and future challenges. It then recommends more investment of money on compiler research and more attention of researchers and students. I have to say that this paper is like an advertisement of encouraging students to…See More
Blog post by Fei Ye Nov 30, 2010
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Compiler Optimizations and Auto-tuning

Compiler Research: The next 50 yearsThis article was a good read because it started by telling of all the achievements that compiler optimizations and compilers in general have done thus far and it discussed the need for compilers in optimizing for modern multi and many core architectures for the next 10 years. The article then moved into discussion of auto-tuning in optimizing compilers. There was a lot of discussion on the need to create compiler infrastructures that are open and easy to read…See More
Blog post by Puyan Lotfi Nov 30, 2010
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11/30 Autotuning

The 'Next 50 Years' paper tries to predict the research of Compiler technology in the next 50 years. The paper starts off with some figures on the bad state of existing software and it's impact on the economy as one of the driving causes to change the existing designs. The authors speak about the emerging mulitcore architectures and emphasize on solving the problem of choosing the right optimization strategy for the architecture at hand. Importance of compilers for parallel platforms is also…See More
Blog post by Srinivasa Manohar Karlapalem Nov 30, 2010
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Autotuning: Compilers for general programs

The first paper Compiler research: The Next 50 years, provides a general perspective on the past contributions, current status, and future directions of compiler technology and makes four main recommendations in support of a vibrant compiler field in the years to come. The paper is more of a general overview of the state of the compiler research in the modern day world. It mentions that still there are plenty of challenges, problems, etc in the field of compilers, for example: in multi-core…See More
Blog post by Abhinesh Krishnaraj Rao Nov 30, 2010
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Autotuning: Compilers for general programs

'Compiler Research: The Next 50 Years', by Hall et al, is a manifesto on the future of compiler innovation. The paper starts out as a wishlist of future accomplishments (all of which are too general to ever to be reached) but ends with a reasonable set of recommendations. The main point being that compiler technology is still an integral part of computer science, but unlike the rest of the field, the scope and complicity of compiler technology significantly limits the contribution that an…See More
Blog post by Kent Czechowski Nov 30, 2010
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Compiler Stuff

The first paper discusses the trends compilers will take in the next 50 years. It’s a bold assumption in computing to state the trend of anything for 2 years, let alone50 years but getting passed that…the authors bring out some importantquestions. One point is thediscussion of security of programs and how much time/money is spent on justthat issue. Now, I have noidea if improving compilers will fix the security issues but it will be moneywell spent if they do. I am alsocurious if parallel…See More
Blog post by Adam Springer Nov 30, 2010

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Srinivasa Manohar Karlapalem

reading submission for tomorrow? 3 Replies

hi, i know that it is a bit too late for me to be posting this, but could anybody please let me know which of the 4 papers are we supposed to critique? i have been actually waiting for sometime to…Continue

Started by Srinivasa Manohar Karlapalem. Last reply by Srinivasa Manohar Karlapalem Sep 14, 2010.

 

Blog Posts

Kent Czechowski

Autotuning: Compilers for general programs

'Compiler Research: The Next 50 Years', by Hall et al, is a manifesto on the future of compiler innovation. The paper starts out as a wishlist of future accomplishments (all of which are too general to ever to be reached) but ends with a reasonable set of recommendations. The main point being that compiler technology is still an integral part of computer science, but unlike the rest of the field, the scope and complicity of compiler technology significantly limits the contribution that an… Continue

Posted by Kent Czechowski on November 30, 2010 at 12:00am — 1 Comment

Danny Browne

Autotuning: Compilers for general programs

[UPDATED 11/30/2010 @ 7:35a]


The Hall paper was published shortly after the 50th anniversary of IBM's release of the first optimizing compiler and gave insight into the needs and trends of the next 50 years. I liked the statistic given early on which indicated the ~$60B or 0.6% of the U.S. GDP is spent on correcting software defects; that is a good indication of the need for better tools to identify program bugs. One of the main points addressed both early and late… Continue

Posted by Danny Browne on November 29, 2010 at 5:30pm

Danny Browne

Complexity Models for Energy and Power

First looking at the Agha paper, this is the one I read last fall and am now revisiting. I recall that a take-away last year was that I wish they had spent more time on iso-energy or iso-power applications rather than iso-performance. Thinking through it more I can come up with more iso-performance applications than last year (basically anything real-time), but in general it seems that iso-energy and iso-power are more common in today's problems. If there is a mobile device with a battery,…
Continue

Posted by Danny Browne on November 10, 2010 at 9:40pm

Kent Czechowski

Data centers: Architectural issues

Internet-scale applications cannot sustain current trends in growth without significants power efficiency improvements. The power efficient Atom processors offer an alternative to the high-end Xeon processors, but with a significant cost to performance. This leads to an interesting question: to appease the data center customers, should Intel focus on making its Xeon processor more power efficient or improving the performance of the Atom processor? Unfortunately, the paper does not provide a… Continue

Posted by Kent Czechowski on November 9, 2010 at 1:27am

Scott McManus

Going even further with non-ACID, non-SQL databases

I want to point out that being non-SQL does not mean that a database is non-ACID. Note that BigTable uses Chubby as its locking manager, which should ensure consistency. BigTable relies on the Google File System, which stores at least three copies of the data, so data is certainly durable. Atomicity and isolation do not appear to be guaranteed, but so what? If you have 1,000 disks, then atomicity is no longer as big an issue, and isolation seems to fall by the wayside as well. With BigTable, we… Continue

Posted by Scott McManus on November 1, 2010 at 9:55pm

Abhinesh Krishnaraj Rao

Apps, Big and Small

The first paper namely "Parallelizing the Web browser" is mainly motivated by the need for browser improvements especially on hand-held devices and mainly discusses how parallelism may help to achieve the goals of generating Responsive and energy efficient browsers. I personally feel this a very informative paper in the modern day context as many of us are looking for substitutes for laptops and hand-held devices could be the same if we overcome the problem of parallelizing browser access on… Continue

Posted by Abhinesh Krishnaraj Rao on October 28, 2010 at 8:45am — 1 Comment

Puyan Lotfi

Has the web browser as a platform just gone too far?

I worked on a BI related application in my last job, and I hate the whole field and don't like to read papers on it.


But I also hate on web browsers and I actually enjoy hating on them:


So having JIT compilation in web browsers wasn't enough, and apparently no one decided it would be too hectic to add more features given that Javascript lacks of strong types and rigid structures. Let's back up a bit: anyone reading this paper should also read…
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Posted by Puyan Lotfi on October 28, 2010 at 8:59am

Chris McClanahan

BIG A, little a, what begins with 'A'?

Application - ASCII - ARPANET ... A - a - A… Continue

Posted by Chris McClanahan on October 27, 2010 at 11:00pm

Abtin

MAD

Am I going MAD?

Posted by Abtin on October 28, 2010 at 7:30am

Kent Czechowski

MPI





“MPI on a Million Processors” by Balaji et al asks an important question: how scalable is MPI? As HPC clusters continue to grow in size to truly colossal shared-memory machines, it is important to consider how the size of the cluster impacts MPI. In the end, the study finds that MPI implementations must continue to pay close attention to the memory requirements, but is ready to scale to a million processor machine . Although, I do not find the experiments to be particularly rigorous… Continue

Posted by Kent Czechowski on October 25, 2010 at 8:48pm — 1 Comment

 
 
 

This graduate-level seminar surveys current topics in parallel computing, through research paper discussions and a major term project.

Members

  • Richard (Rich) Vuduc
  • Puyan Lotfi
  • Fei Ye
  • David Noble
  • Danny Browne
  • Srinivasa Manohar Karlapalem
  • Abhinesh Krishnaraj Rao
  • Chris McClanahan
  • Adam Springer
  • Kent Czechowski
  • Abtin
  • Scott McManus

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