11,083 research outputs found
Cache-Oblivious Peeling of Random Hypergraphs
The computation of a peeling order in a randomly generated hypergraph is the
most time-consuming step in a number of constructions, such as perfect hashing
schemes, random -SAT solvers, error-correcting codes, and approximate set
encodings. While there exists a straightforward linear time algorithm, its poor
I/O performance makes it impractical for hypergraphs whose size exceeds the
available internal memory.
We show how to reduce the computation of a peeling order to a small number of
sequential scans and sorts, and analyze its I/O complexity in the
cache-oblivious model. The resulting algorithm requires
I/Os and time to peel a random hypergraph with edges.
We experimentally evaluate the performance of our implementation of this
algorithm in a real-world scenario by using the construction of minimal perfect
hash functions (MPHF) as our test case: our algorithm builds a MPHF of
billion keys in less than hours on a single machine. The resulting data
structure is both more space-efficient and faster than that obtained with the
current state-of-the-art MPHF construction for large-scale key sets
khmer: Working with Big Data in Bioinformatics
We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source
Application
Using Hashing to Solve the Dictionary Problem (In External Memory)
We consider the dictionary problem in external memory and improve the update
time of the well-known buffer tree by roughly a logarithmic factor. For any
\lambda >= max {lg lg n, log_{M/B} (n/B)}, we can support updates in time
O(\lambda / B) and queries in sublogarithmic time, O(log_\lambda n). We also
present a lower bound in the cell-probe model showing that our data structure
is optimal.
In the RAM, hash tables have been used to solve the dictionary problem faster
than binary search for more than half a century. By contrast, our data
structure is the first to beat the comparison barrier in external memory. Ours
is also the first data structure to depart convincingly from the indivisibility
paradigm
GPU LSM: A Dynamic Dictionary Data Structure for the GPU
We develop a dynamic dictionary data structure for the GPU, supporting fast
insertions and deletions, based on the Log Structured Merge tree (LSM). Our
implementation on an NVIDIA K40c GPU has an average update (insertion or
deletion) rate of 225 M elements/s, 13.5x faster than merging items into a
sorted array. The GPU LSM supports the retrieval operations of lookup, count,
and range query operations with an average rate of 75 M, 32 M and 23 M
queries/s respectively. The trade-off for the dynamic updates is that the
sorted array is almost twice as fast on retrievals. We believe that our GPU LSM
is the first dynamic general-purpose dictionary data structure for the GPU.Comment: 11 pages, accepted to appear on the Proceedings of IEEE International
Parallel and Distributed Processing Symposium (IPDPS'18
Fast Scalable Construction of (Minimal Perfect Hash) Functions
Recent advances in random linear systems on finite fields have paved the way
for the construction of constant-time data structures representing static
functions and minimal perfect hash functions using less space with respect to
existing techniques. The main obstruction for any practical application of
these results is the cubic-time Gaussian elimination required to solve these
linear systems: despite they can be made very small, the computation is still
too slow to be feasible.
In this paper we describe in detail a number of heuristics and programming
techniques to speed up the resolution of these systems by several orders of
magnitude, making the overall construction competitive with the standard and
widely used MWHC technique, which is based on hypergraph peeling. In
particular, we introduce broadword programming techniques for fast equation
manipulation and a lazy Gaussian elimination algorithm. We also describe a
number of technical improvements to the data structure which further reduce
space usage and improve lookup speed.
Our implementation of these techniques yields a minimal perfect hash function
data structure occupying 2.24 bits per element, compared to 2.68 for MWHC-based
ones, and a static function data structure which reduces the multiplicative
overhead from 1.23 to 1.03
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