295 research outputs found
PGPG: An Automatic Generator of Pipeline Design for Programmable GRAPE Systems
We have developed PGPG (Pipeline Generator for Programmable GRAPE), a
software which generates the low-level design of the pipeline processor and
communication software for FPGA-based computing engines (FBCEs). An FBCE
typically consists of one or multiple FPGA (Field-Programmable Gate Array)
chips and local memory. Here, the term "Field-Programmable" means that one can
rewrite the logic implemented to the chip after the hardware is completed, and
therefore a single FBCE can be used for calculation of various functions, for
example pipeline processors for gravity, SPH interaction, or image processing.
The main problem with FBCEs is that the user need to develop the detailed
hardware design for the processor to be implemented to FPGA chips. In addition,
she or he has to write the control logic for the processor, communication and
data conversion library on the host processor, and application program which
uses the developed processor. These require detailed knowledge of hardware
design, a hardware description language such as VHDL, the operating system and
the application, and amount of human work is huge. A relatively simple design
would require 1 person-year or more. The PGPG software generates all necessary
design descriptions, except for the application software itself, from a
high-level design description of the pipeline processor in the PGPG language.
The PGPG language is a simple language, specialized to the description of
pipeline processors. Thus, the design of pipeline processor in PGPG language is
much easier than the traditional design. For real applications such as the
pipeline for gravitational interaction, the pipeline processor generated by
PGPG achieved the performance similar to that of hand-written code. In this
paper we present a detailed description of PGPG version 1.0.Comment: 24 pages, 6 figures, accepted PASJ 2005 July 2
PROGRAPE-1: A Programmable, Multi-Purpose Computer for Many-Body Simulations
We have developed PROGRAPE-1 (PROgrammable GRAPE-1), a programmable
multi-purpose computer for many-body simulations. The main difference between
PROGRAPE-1 and "traditional" GRAPE systems is that the former uses FPGA (Field
Programmable Gate Array) chips as the processing elements, while the latter
rely on the hardwired pipeline processor specialized to gravitational
interactions. Since the logic implemented in FPGA chips can be reconfigured, we
can use PROGRAPE-1 to calculate not only gravitational interactions but also
other forms of interactions such as van der Waals force, hydrodynamical
interactions in SPH calculation and so on. PROGRAPE-1 comprises two Altera
EPF10K100 FPGA chips, each of which contains nominally 100,000 gates. To
evaluate the programmability and performance of PROGRAPE-1, we implemented a
pipeline for gravitational interaction similar to that of GRAPE-3. One pipeline
fitted into a single FPGA chip, which operated at 16 MHz clock. Thus, for
gravitational interaction, PROGRAPE-1 provided the speed of 0.96
Gflops-equivalent. PROGRAPE will prove to be useful for wide-range of
particle-based simulations in which the calculation cost of interactions other
than gravity is high, such as the evaluation of SPH interactions.Comment: 20 pages with 9 figures; submitted to PAS
Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis
Kawasaki disease (KD) is an acute febrile illness of early childhood. Previous reports have suggested that genetic disease susceptibility factors, together with a triggering infectious agent, could be involved in KD pathogenesis; however, the precise etiology of this disease remains unknown. Additionally, previous culture-based studies have suggested a possible role of intestinal microbiota in KD pathogenesis. In this study, we performed metagenomic analysis to comprehensively assess the longitudinal variation in the intestinal microbiota of twenty-eight KD patients. Several notable bacterial genera were commonly extracted during the acute phase, whereas a relative increase in the number of Ruminococcus bacteria was observed during the non-acute phase of KD. The metagenomic analysis results based on bacterial species classification suggested that the number of sequencing reads with similarity to five Streptococcus spp. (S. pneumonia, pseudopneumoniae, oralis, gordonii, and sanguinis), in addition to patient-derived Streptococcus isolates, markedly increased during the acute phase in most patients. Streptococci include a variety of pathogenic bacteria and probiotic bacteria that promote human health; therefore, this further species discrimination could comprehensively illuminate the KD-associated microbiota. The findings of this study suggest that KD-related Streptococci might be involved in the pathogenesis of this disease
Bag of Timestamps: A Simple and Efficient Bayesian Chronological Mining
In this paper, we propose a new probabilistic model, Bag of Timestamps (BoT), for chronological text mining. BoT is an extension of latent Dirichlet allocation (LDA), and has two remarkable features when compared with a previously proposed Topics over Time (ToT), which is also an extension of LDA. First, we can avoid overfitting to temporal data, because temporal data are modeled in a Bayesian manner similar to word frequencies. Second, BoT has a conditional probability where no functions requiring time-consuming computations appear. The experiments using newswire documents show that BoT achieves more moderate fitting to temporal data in shorter execution time than ToT.Advances in Data and Web Management. Joint International Conferences, APWeb/WAIM 2009 Suzhou, China, April 2-4, 2009 Proceeding
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