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Florian Büren

dblp:243/3645 · DBLP profile ↗
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1ranked-venue papers
1as first author
0since 2021 · last 2019
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Systems, architecture and hardware · 1 · 1 first-author

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Computer architecture, parallel and distributed computing, and storage systems
1 paper
GPUs and heterogeneous computing · 77% High-performance computing · 23%
Theoretical computer science
1 paper
Algorithms and data structures · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
GPUs and heterogeneous computing
multi-GPU computing
0.412019
Suffix Array Construction on Multi-GPU Systems · HPDC 2019
Algorithms and data structures › sequence algorithms › string algorithms › string indexing
suffix array
0.412019
Suffix Array Construction on Multi-GPU Systems · HPDC 2019
High-performance computing › scientific data analysis
genome sequence analysis
0.112019
Suffix Array Construction on Multi-GPU Systems · HPDC 2019

Methods — techniques the papers use, named apart from their topics

partitioning search · 0.8inter-GPU merging · 0.8NVLink · 0.8
YearPublicationVenuePosition
2019 Suffix Array Construction on Multi-GPU Systems
abstract
Suffix arrays are prevalent data structures being fundamental to a wide range of applications including bioinformatics, data compression, and information retrieval. Therefore, various algorithms for (parallel) suffix array construction both on CPUs and GPUs have been proposed over the years. Although providing significant speedup over their CPU-based counterparts, existing GPU implementations share a common disadvantage: input text sizes are limited by the scarce memory of a single GPU. In this paper, we overcome aforementioned memory limitations by exploiting multi-GPU nodes featuring fast NVLink interconnects. In order to achieve high performance for this communication-intensive task, we design a parallel inter-GPU (re-)merging scheme. To handle segments spanning multiple GPUs, we propose an efficient strategy for the merging phase facilitated by a fast partitioning search. On 8 GPUs our implementation achieves speedups between 133 and 354 over sequential CPU-based libdivsufsort, between 30 and 68 over its multi-threaded shared memory version using 80 threads on 40 CPU cores for large datasets ranging from 697M to 3159M characters in size. For medium-sized datasets ranging between 104M and 236M, our approach yields maximum (minimum) speedups of 11.7 (4.5) and 6.45 (4.5) over existing single-GPU implementations (CUDPP, NVBIO). We are able to construct the suffix array of a full human genome on a single DGX-1 server within a runtime of 3.44~seconds which is faster than the 4.8 seconds that were previously reported employing 1600 cores on 100 nodes on a CPU-based HPC cluster. Our implementation is publicly available at https://gitlab.rlp.net/pararch/multi-gpu-suffix-array/.
Florian Büren, Daniel Jünger, Robin Kobus, Christian Hundt 0002, Bertil Schmidt
HPDC1