13 research outputs found
ReCoil - an algorithm for compression of extremely large datasets of dna data
The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In this work we present ReCoil - an I/O efficient external memory algorithm designed for compression of very large collections of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate
Engineering an External Memory Minimum Spanning Tree Algorithm
We develop an external memory algorithm for computing minimum spanning trees. The algorithm is considerably simpler than previously known external memory algorithms for this problem and needs a factor of at least four less I/Os for realistic inputs. Our implementation indicates that this algorithm processes graphs only limited by the disk capacity of most current machines in time no more than a factor 2–5 of a good internal algorithm with sufficient memory space
Computational Methods in Science and Engineering : Proceedings of the Workshop SimLabs@KIT, November 29 - 30, 2010, Karlsruhe, Germany
In this proceedings volume we provide a compilation of article contributions equally covering applications from different research fields and ranging from capacity up to capability computing. Besides classical computing aspects such as parallelization, the focus of these proceedings is on multi-scale approaches and methods for tackling algorithm and data complexity. Also practical aspects regarding the usage of the HPC infrastructure and available tools and software at the SCC are presented
Engineering an External Memory Minimum Spanning Tree Algorithm
We develop an external memory algorithm for computing minimum spanning
trees. The algorithm is considerably simpler than previously known
external memory algorithms for this problem and needs a factor of at
least four less I/Os for realistic inputs.
Our implementation indicates that this algorithm processes graphs only
limited by the disk capacity of most current machines in time no more
than a factor 2--5 of a good internal algorithm with sufficient memory
space
Engineering an External Memory Minimum Spanning Tree Algorithm
We develop an external memory algorithm for computing minimum spanning
trees. The algorithm is considerably simpler than previously known
external memory algorithms for this problem and needs a factor of at
least four less I/Os for realistic inputs.
Our implementation indicates that this algorithm processes graphs only
limited by the disk capacity of most current machines in time no more
than a factor 2--5 of a good internal algorithm with sufficient memory
space
Algorithm Engineering for fundamental Sorting and Graph Problems
Fundamental Algorithms build a basis knowledge for every computer science undergraduate or a professional programmer. It is a set of basic techniques one can find in any (good) coursebook on algorithms and data structures. In this thesis we try to close the gap between theoretically worst-case optimal classical algorithms and the real-world circumstances one face under the assumptions imposed by the data size, limited main memory or available parallelism