SC16 student cluster competition challenge: Investigating the reproducibility of results for the ParConnect application
| Autor: | Mary Thomas, G. R. Williams, G. P. Behm, A. Ramos, Christopher Paolini, B. Wright, T. Nguyen, A. Esparza, V. G. Haka, James C. Otto |
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| Rok vydání: | 2017 |
| Předmět: |
De Bruijn sequence
020203 distributed computing Theoretical computer science Computer Networks and Communications Computer science Computation Message passing Breadth-first search 02 engineering and technology Parallel computing Computer Graphics and Computer-Aided Design Graph Theoretical Computer Science Data set Artificial Intelligence Hardware and Architecture Core (graph theory) 0202 electrical engineering electronic engineering information engineering Cluster (physics) Software Test data |
| Zdroj: | Parallel Computing. 70:27-34 |
| ISSN: | 0167-8191 |
| DOI: | 10.1016/j.parco.2017.07.010 |
| Popis: | At SC16, the SCC teams participated in a new application area: the Reproducibility Challenge. In this paper we report on our efforts to reproduce results presented in a paper titled “ A Parallel Connectivity Algorithm for de Bruijn Graphs in Metagenomic Applications ,” which shows that the parallel graph-based algorithm developed scales to over a thousand cores, and runs faster than traditional Breadth First Search algorithms. In general, using the smaller competition test data sets on over 128 processors, we were able to reproduce some, but not all, of the reported results: we were unable to run the D1 data set on 128 cores and 2GB/core memory; our results did show similar timing trends for the different algorithm variations; we were able to observe the trend of communication dominating the computation time; and the AP and AP_LB versions of our runs on smaller datasets only show a small time improvement in our graphs, which is similar but not exactly what was described within the paper. We believe that cluster architecture, required memory, network tuning, and number of processors available impacted our ability to exactly reproduce the results of the paper. |
| Databáze: | OpenAIRE |
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