2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines 2006
DOI: 10.1109/fccm.2006.5
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A case study in porting a production scientific supercomputing application to a reconfigurable computer

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Cited by 58 publications
(45 citation statements)
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“…An example of an MD system, NAMD was also successfully accelerated with FPGAs. 8 Another example is the ProtoMol framework, which was designed especially for computational experimentation and so has well-defined partitions among computations. 9 We have found that the acceleratable kernel not only comprises more than 90 percent of execution time with ProtoMol, but the modularity enables straightforward integration of an FPGA accelerator.…”
Section: Methods 4: Living With Amdahl's Lawmentioning
confidence: 99%
“…An example of an MD system, NAMD was also successfully accelerated with FPGAs. 8 Another example is the ProtoMol framework, which was designed especially for computational experimentation and so has well-defined partitions among computations. 9 We have found that the acceleratable kernel not only comprises more than 90 percent of execution time with ProtoMol, but the modularity enables straightforward integration of an FPGA accelerator.…”
Section: Methods 4: Living With Amdahl's Lawmentioning
confidence: 99%
“…The GRAPE PGR system [28] is one of the recent efforts in developing a design framework, but currently it does not support optimizations in the algorithmarchitecture design space. Also, some early efforts made towards modeling molecular dynamics using SRC Computers in [29], [30], involve specialized language and manual intervention in many key steps such as extracting data dependency information (used in timing analysis). In contrast, TANOR provides a fully automated framework for different N-body interaction problems.…”
Section: Scientific Application: N-body Problemsmentioning
confidence: 99%
“…The three most notable examples are a molecular dynamics application [Kindratenko and Pointer 2006;Scrofano et al 2006], a full CG solver [Morris et al 2006], and a traffic simulation engine [Tripp et al 2005]. None of these efforts have considered requirements for future systems attempting to leverage FPGAs.…”
Section: Related Workmentioning
confidence: 99%
“…While there are exceptions (notably molecular dynamics (MD) [Kindratenko and Pointer 2006;Scrofano et al 2006]), these applications tend to be hundreds of thousands of lines of code without a small section that dominates execution time. This led researchers to begin by focusing on kernel operations that are used in HPC and can be provided through a standard library interface.…”
Section: Introductionmentioning
confidence: 99%