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An adaptive packed-memory array

Michael A. Bender, Haodong Hu
2006 Proceedings of the twenty-fifth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems - PODS '06  
Specifically, the cost to scan L consecutive elements is O(1 + L/B) memory transfers. This paper gives the first adaptive packed-memory array (APMA), which automatically adjusts to the input pattern.  ...  The packed-memory array (PMA) is a data structure that maintains a dynamic set of N elements in sorted order in a Θ(N)-sized array.  ...  ACKNOWLEDGMENTS We are grateful to Ziyang Duan for proposing an early uneven-rebalance strategy. We are grateful to Bradley Kuszmaul for suggesting that we focus on sequential inserts.  ... 
doi:10.1145/1142351.1142355 dblp:conf/pods/BenderH06 fatcat:o3vi5njpzjgklnackhwywby3gi

An adaptive packed-memory array

Michael A. Bender, Haodong Hu
2007 ACM Transactions on Database Systems  
Specifically, the cost to scan L consecutive elements is O(1 + L/B) memory transfers. This paper gives the first adaptive packed-memory array (APMA), which automatically adjusts to the input pattern.  ...  The packed-memory array (PMA) is a data structure that maintains a dynamic set of N elements in sorted order in a Θ(N)-sized array.  ...  ACKNOWLEDGMENTS We are grateful to Ziyang Duan for proposing an early uneven-rebalance strategy. We are grateful to Bradley Kuszmaul for suggesting that we focus on sequential inserts.  ... 
doi:10.1145/1292609.1292616 fatcat:jtzzfsfbwfbifhsbfngoudthsy

GPU memory model overview

Aaron Lefohn
2005 ACM SIGGRAPH 2005 Courses on - SIGGRAPH '05  
-Save up to 16, 32-bit floating values per pixel • Multiple Render Targets (MRTs) on ATI and NVIDIASparse/Adaptive Data Structures Sparse/Adaptive Data StructuresTexture access is like an array lookup.The  ...  GPU Arrays • Higher Dimensional Arrays -Pack into 2D buffers -N-D to 2D address translation -Same problems as 3D arrays if data does not fit in a single 2D texture 33 Sparse/Adaptive Data  ... 
doi:10.1145/1198555.1198775 dblp:conf/siggraph/Lefohn05 fatcat:ftovz5bsxfe2hng5rtfne7y6ya

DaStGen—A Data Structure Generator for Parallel C++ HPC Software [chapter]

Hans–Joachim Bungartz, Wolfgang Eckhardt, Miriam Mehl, Tobias Weinzierl
2008 Lecture Notes in Computer Science  
Simulation codes often suffer from high memory requirements.  ...  This holds in particular if they are memory-bounded, and, with multicore systems coming up, the problem will become even worse as more and more cores have to share the memory connections.  ...  An Adaptive Grid Management Besides the solver, we implemented a grid management for adaptive Cartesian grids [8] .  ... 
doi:10.1007/978-3-540-69389-5_25 fatcat:4cvsxg3a5zadxbxichtsd6yu3u

Signal Integration by Bacterial Chemosensory Complexes

Victor Sourjik
2015 Biophysical Journal  
The resulting core complexes display native receptor-stimulated kinase activities that are fully regulated by attractant binding to the receptor, or covalent modification of the receptor adaptation sites  ...  We are reconstituting core units on isolated bacterial membranes, yielding individual core units and oligomers of core units ranging in size up to small hexagonal arrays.  ...  Loosely packed methylation helices produce kinase-off output and serve as substrates for subsequent receptor modifications that enhance MH packing during the sensory adaptation phase of an attractant response  ... 
doi:10.1016/j.bpj.2014.11.260 fatcat:62djvnijgveyrpexu7n4dsnkfq

Improving Locality for Adaptive Irregular Scientific Codes [chapter]

Hwansoo Han, Chau-Wen Tseng
2001 Lecture Notes in Computer Science  
An important class of scientific codes access memory in an irregular manner.  ...  Researchers have shown that consecutively packing data relative to traversal order can significantly reduce cache miss rates by increasing spatial locality.  ...  to create an adaptive code.  ... 
doi:10.1007/3-540-45574-4_12 fatcat:arh6n3y75netpai2q2bxmxqx4i

H.264/AVC In-Loop De-Blocking Filter Targeting a Dynamically Reconfigurable Instruction Cell Based Architecture

A. Major, I. Nousias, S. Khawam, M. Milward, Ying Yi, T. Arslan
2007 Second NASA/ESA Conference on Adaptive Hardware and Systems (AHS 2007)  
Second NASA/ESA Conference on Adaptive Hardware and Systems(AHS 2007) 0-7695-2866-X/07 $25.00  ...  Packed Pixel-Memory Access Image data in the h.264 decoder is stored in arrays of 8bit chars and therefore all pixel reads operate on 8-bits at a time.  ...  This enables the proposed filter module to access four packed pixels in a single 32-bit read operation and hence reduces memory access by a factor of four.  ... 
doi:10.1109/ahs.2007.58 dblp:conf/ahs/MajorNKMYA07 fatcat:mmqmqb6xrfdsfiyph3mdwxxeje

Improving cache performance in dynamic applications through data and computation reorganization at run time

Chen Ding, Ken Kennedy
1999 SIGPLAN notices  
With the rapid improvement of processor speed, performance of the memory hierarchy has become the principal bottleneck for most applications.  ...  A number of compiler transformations have been developed to improve data reuse in cache and registers, thus reducing the total number of direct memory accesses in a program.  ...  However, in an irregular or adaptive computation, the order of data access is not known until run time and that order may change dynamically.  ... 
doi:10.1145/301631.301670 fatcat:g74dpsrsevfnnloo54g3pqaklq

Improving cache performance in dynamic applications through data and computation reorganization at run time

Chen Ding, Ken Kennedy
1999 Proceedings of the ACM SIGPLAN 1999 conference on Programming language design and implementation - PLDI '99  
With the rapid improvement of processor speed, performance of the memory hierarchy has become the principal bottleneck for most applications.  ...  A number of compiler transformations have been developed to improve data reuse in cache and registers, thus reducing the total number of direct memory accesses in a program.  ...  However, in an irregular or adaptive computation, the order of data access is not known until run time and that order may change dynamically.  ... 
doi:10.1145/301618.301670 dblp:conf/pldi/DingK99 fatcat:2d6ey3fe2nbjditdkb7ajuca6u

Optimizing irregular shared-memory applications for clusters

Seung-Jai Min, Rudolf Eigenmann
2008 Proceedings of the 22nd annual international conference on Supercomputing - ICS '08  
A parallel array reduction transformation reduces overheads in the analysis.  ...  A packed communication optimization and a differential communication optimization effectively eliminate unnecessary and redundant messages.  ...  Since the input integer list, key_array, is used as an indirection array and updated on every iteration, IS is an adaptive irregular benchmark.  ... 
doi:10.1145/1375527.1375566 dblp:conf/ics/MinE08 fatcat:4gozlvtnojfovf52tq2darod4y

H.264/AVC In-Loop De-Blocking Filter Targeting a Dynamically Reconfigurable Instruction Cell Based Architecture

Adam Major, Ioannis Nousias, Sami Khawam, Mark Milward, Ying Yi, Mark Muir, Tughrul Arslan
2007 2007 International Conference on Field Programmable Logic and Applications  
Second NASA/ESA Conference on Adaptive Hardware and Systems(AHS 2007) 0-7695-2866-X/07 $25.00  ...  Packed Pixel-Memory Access Image data in the h.264 decoder is stored in arrays of 8bit chars and therefore all pixel reads operate on 8-bits at a time.  ...  This enables the proposed filter module to access four packed pixels in a single 32-bit read operation and hence reduces memory access by a factor of four.  ... 
doi:10.1109/fpl.2007.4380652 dblp:conf/fpl/MajorNKMYMA07 fatcat:efeyar3275dqxlnyayakcal57m

Flagellar Motor Architecture

Frederick W. Dahlquist
2015 Biophysical Journal  
Thus HDX-MS provides an important tool in a hybrid approach for understanding structure and mechanism in membrane-bound, multi-protein complexes.  ...  The resulting core complexes display native receptor-stimulated kinase activities that are fully regulated by attractant binding to the receptor, or covalent modification of the receptor adaptation sites  ...  Loosely packed methylation helices produce kinase-off output and serve as substrates for subsequent receptor modifications that enhance MH packing during the sensory adaptation phase of an attractant response  ... 
doi:10.1016/j.bpj.2014.11.257 fatcat:d33behwmarcfljha6oiscpvm5a

Structure and Dynamics of the Receptor:Kinase Complex that Mediates Bacterial Chemotaxis

Brian R. Crane
2015 Biophysical Journal  
Thus HDX-MS provides an important tool in a hybrid approach for understanding structure and mechanism in membrane-bound, multi-protein complexes.  ...  The resulting core complexes display native receptor-stimulated kinase activities that are fully regulated by attractant binding to the receptor, or covalent modification of the receptor adaptation sites  ...  Loosely packed methylation helices produce kinase-off output and serve as substrates for subsequent receptor modifications that enhance MH packing during the sensory adaptation phase of an attractant response  ... 
doi:10.1016/j.bpj.2014.11.258 fatcat:qwvq2q6zvbh4xmpwc2xre72o44

HAMP: The CPU Domain of Bacterial Chemoreceptors

John Parkinson
2015 Biophysical Journal  
Thus HDX-MS provides an important tool in a hybrid approach for understanding structure and mechanism in membrane-bound, multi-protein complexes.  ...  The resulting core complexes display native receptor-stimulated kinase activities that are fully regulated by attractant binding to the receptor, or covalent modification of the receptor adaptation sites  ...  Loosely packed methylation helices produce kinase-off output and serve as substrates for subsequent receptor modifications that enhance MH packing during the sensory adaptation phase of an attractant response  ... 
doi:10.1016/j.bpj.2014.11.259 fatcat:2yrh7tbrbrbvvoyjklcaoiqxwe

Bacterial chemoreceptors: providing enhanced features to two-component signaling

Gerald L Hazelbauer, Wing-Cheung Lai
2010 Current Opinion in Microbiology  
Homodimer signaling initiates with helical piston sliding that is converted to modulation of competing packing modes of adjacent segments of an extended helical coiled coil.  ...  Bacteria perform chemotaxis utilizing core two-component signaling systems to which have been added enhanced features of signal amplification, sensory adaptation, molecular memory and high sensitivity  ...  They carry sites of covalent modification that enable molecular memory, sensory adaptation and wide dynamic range.  ... 
doi:10.1016/j.mib.2009.12.014 pmid:20122866 pmcid:PMC2863001 fatcat:f7iiqmdlprhp5pvxxyfqwd7wdq
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