23,124 research outputs found
Highly scalable parallel sorting
Abstract — Sorting is a commonly used process with a wide breadth of applications in the high performance computing field. Early research in parallel processing has provided us with comprehensive analysis and theory for parallel sorting algorithms. However, modern super-computers have advanced rapidly in size and changed significantly in architecture, forcing new adaptations to these algorithms. To fully utilize the potential of highly parallel machines, tens of thousands of processors are used. Efficiently scaling parallel sorting on machines of this magnitude is inhibited by the communication-intensive problem of migrating large amounts of data between processors. The challenge is to design a highly scalable sorting algorithm that uses minimal communication, max-imizes overlap between computation and communication, and uses memory efficiently. This paper presents a scal-able extension of the Histogram Sorting method, making fundamental modifications to the original algorithm in order to minimize message contention and exploit overlap. We implement Histogram Sort, Sample Sort, and Radix Sort in CHARM++ and compare their performance. The choice of algorithm as well as the importance of the optimizations is validated by performance tests on two predominant modern supercomputer architectures: XT4 at ORNL (Jaguar) and Blue Gene/P at ANL (Intrepid). I
GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays
Modern day analytics deals with big datasets from diverse fields. For many application the data is in the form of an array which consists of large number of smaller arrays. Existing techniques focus on sorting a single large array and cannot be used for sorting large number of smaller arrays in an efficient manner. Currently no such algorithm is available which can sort such large number of arrays utilizing the massively parallel architecture of GPU devices. In this paper we present a highly scalable parallel algorithm, called GPU-ArraySort, for sorting large number of arrays using a GPU. Our algorithm performs in-place operations and makes minimum use of any temporary run-time memory. Our results indicate that we can sort up to 2 million arrays having 1000 elements each, within few seconds. We compare our results with the unorthodox tagged array sorting technique based on NVIDIAs Thrust library. GPU-ArraySort out-performs the tagged array sorting technique by sorting three times more data in a much smaller time. The developed tool and strategy will be made available at https://github.com/pcdslab
Rumble: Data Independence for Large Messy Data Sets
This paper introduces Rumble, an engine that executes JSONiq queries on
large, heterogeneous and nested collections of JSON objects, leveraging the
parallel capabilities of Spark so as to provide a high degree of data
independence. The design is based on two key insights: (i) how to map JSONiq
expressions to Spark transformations on RDDs and (ii) how to map JSONiq FLWOR
clauses to Spark SQL on DataFrames. We have developed a working implementation
of these mappings showing that JSONiq can efficiently run on Spark to query
billions of objects into, at least, the TB range. The JSONiq code is concise in
comparison to Spark's host languages while seamlessly supporting the nested,
heterogeneous data sets that Spark SQL does not. The ability to process this
kind of input, commonly found, is paramount for data cleaning and curation. The
experimental analysis indicates that there is no excessive performance loss,
occasionally even a gain, over Spark SQL for structured data, and a performance
gain over PySpark. This demonstrates that a language such as JSONiq is a simple
and viable approach to large-scale querying of denormalized, heterogeneous,
arborescent data sets, in the same way as SQL can be leveraged for structured
data sets. The results also illustrate that Codd's concept of data independence
makes as much sense for heterogeneous, nested data sets as it does on highly
structured tables.Comment: Preprint, 9 page
The Reverse Cuthill-McKee Algorithm in Distributed-Memory
Ordering vertices of a graph is key to minimize fill-in and data structure
size in sparse direct solvers, maximize locality in iterative solvers, and
improve performance in graph algorithms. Except for naturally parallelizable
ordering methods such as nested dissection, many important ordering methods
have not been efficiently mapped to distributed-memory architectures. In this
paper, we present the first-ever distributed-memory implementation of the
reverse Cuthill-McKee (RCM) algorithm for reducing the profile of a sparse
matrix. Our parallelization uses a two-dimensional sparse matrix decomposition.
We achieve high performance by decomposing the problem into a small number of
primitives and utilizing optimized implementations of these primitives. Our
implementation shows strong scaling up to 1024 cores for smaller matrices and
up to 4096 cores for larger matrices
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
GraphSE: An Encrypted Graph Database for Privacy-Preserving Social Search
In this paper, we propose GraphSE, an encrypted graph database for online
social network services to address massive data breaches. GraphSE preserves
the functionality of social search, a key enabler for quality social network
services, where social search queries are conducted on a large-scale social
graph and meanwhile perform set and computational operations on user-generated
contents. To enable efficient privacy-preserving social search, GraphSE
provides an encrypted structural data model to facilitate parallel and
encrypted graph data access. It is also designed to decompose complex social
search queries into atomic operations and realise them via interchangeable
protocols in a fast and scalable manner. We build GraphSE with various
queries supported in the Facebook graph search engine and implement a
full-fledged prototype. Extensive evaluations on Azure Cloud demonstrate that
GraphSE is practical for querying a social graph with a million of users.Comment: This is the full version of our AsiaCCS paper "GraphSE: An
Encrypted Graph Database for Privacy-Preserving Social Search". It includes
the security proof of the proposed scheme. If you want to cite our work,
please cite the conference version of i
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