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The week's events

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News
- Journée au vert POLARIS 2022/05/23
- DATAMOVE/POLARIS picnic 2021/06/22
- DATAMOVE/POLARIS BBQ 2019 2019/06/14
- POLARIS Bootcamp (May 2019) 2019/05/24
- slides of Andras Gyorgy 2016/01/15
Next seminars

Events in January–February 2018

M	T	W	T	F	S	S
January 1	2	3	4	5	6	7
8	9	10	11 Keynote 2:00 pm – 3:00 pm January 11, 2018 Read more	12	13	14
15	16	17	18 Predicting the Energy-Consumption of MPI Applications at Scale Using Only a Single Node, by Christian Heinrich (Polaris) 3:00 pm – 4:00 pm January 18, 2018 Monitoring and assessing the energy efficiency of supercomputers and data centers is crucial in order to limit and reduce their energy consumption. Applications from the domain of High Performance Computing (HPC), such as MPI applications, account for a significant fraction of the overall energy consumed by HPC centers. Simulation is a popular approach for studying the behavior of these applications in a variety of scenarios, and it is therefore advantageous to be able to study their energy consumption in a cost-efficient, controllable, and also reproducible simulation environment. Alas, simulators supporting HPC applications commonly lack the capability of predicting the energy consumption, particularly when target platforms consist of multi-core nodes. In this work, we aim to accurately predict the energy consumption of MPI applications via simulation. Firstly, we introduce the models required for meaningful simulations: The computation model, the communication model, and the energy model of the target platform. Secondly, we demonstrate that by carefully calibrating these models on a single node, the predicted energy consumption of HPC applications at a larger scale is very close (within a few percents) to real experiments. We further show how to integrate such models into the SimGrid simulation toolkit. In order to obtain good execution time predictions on multi-core architectures, we also establish that it is vital to correctly account for memory effects in simulation. The proposed simulator is validated through an extensive set of experiments with well-known HPC benchmarks. Lastly, we show the simulator can be used to study applications at scale, which allows researchers to save both time and resources compared to real experiments Bâtiment IMAG (442) Saint-Martin-d'Hères, 38400 France View Location Map Read more	19	20	21
22	23	24	25	26	27	28
29	30	31	February 1 Keynote 2:00 pm – 3:00 pm February 1, 2018 Read more	2	3	4
5	6	7	8 Datamove workshop N/A February 8, 2018 Read more	9	10	11
12	13	14	15 Untitled Event N/A February 15, 2018 Read more Parallel Sequence Alignment of Whole Chromosomes with Hundreds of GPUs and Pruning (by Alba Cristina Magalhaes Alves de Melo, University of Brasilia ) 2:00 pm – 3:00 pm February 15, 2018 Biological Sequence Alignment is a very basic operation in Bioinformatics used routinely worldwide. Smith-Waterman is the exact algorithm used to compare two sequences, obtaining the optimal alignment in quadratic time and space. In order to accelerate Smith-Waterman, many GPU-based strategies were proposed in the literature. However, aligning DNA sequences of millions of characters, or Base Pairs (MBP), is still a very challenging task. In this talk, we discuss related work in the area of parallel biological sequence alignment and present our multi-GPU strategy to align DNA sequences with up to 249 millions of characters in 384 GPUs. In order to achieve this, we propose an innovative speculation technique, which is able to parallelize a phase of the Smith-Waterman algorithm that is inherently sequential. We combined our speculation technique with sophisticated buffer management and fine-grain linear space matrix processing strategies to obtain our parallel algorithm. As far as we know, this is the first implementation of Smith-Waterman able to retrieve the optimal alignment between sequences with more than 50 millions of characters. We will also present a pruning technique for one GPU that is able to prune more than 50% of the Smith-Waterman matrix and still retrieve the optimal alignment. We will show the results obtained in the Keeneland cluster (USA), where we compared all the human x chimpanzee homologous chromosomes (ranging from 26 MBP to 249 MBP). The human_chimpanzee chromosome 5 comparison (180 MBP x 183 MBP) attained 10.35 TCUPS (Trillions of Cells Updated per Second) using 384 GPUs. In this case, we processed 45 petacells, being able to produce the optimal alignment in 53 minutes and 7 seconds, with a speculation hit ratio of 98.2%. Short Bio: Alba Cristina Magalhaes Alves de Melo obtained her PhD degree in Computer Science from the Institut National Polytechnique de Grenoble (INPG), France, in 1996. In 2008, she did a postdoc at the University of Ottawa, Canada; in 2011, she was invited as Guest Scientist at Université Paris-Sud, France; and in 2013 she did a sabbatical at the Universitat Polytecnica de Catalunya, Spain. Since 1997, she works at the Department of Computer Science at the University of Brasilia (UnB), Brazil, where she is now a Full Professor. She is also a CNPq Research Fellow level 1D in Brazil. She was the Coordinator of the Graduate Program in Informatics at UnB for several years (2000-2002, 2004-2006, 2008, 2010, 2014) and she coordinated international collaboration projects with the Universitat Politecnica de Catalunya, Spain (2012, 2014-2016) and with the University of Ottawa, Canada (2012-2015). In 2016, she received the Brazilian Capes Award on “Advisor of the Best PhD Thesis in Computer Science”. Her research interests are High Performance Computing, Bioinformatics and Cloud Computing. She advised 2 postdocs, 4 PhD Thesis and 22 MsC Dissertations. Currently, she advises 4 PhD students and 2 MsC students. She is Senior Member of the IEEE Society and Member of the Brazilian Computer Society. She gave invited talks at Universitat Karlshure, Germany, Université Paris-Sud, France, Universitat Polytecnica de Catalunya, Spain, University of Ottawa, Canada and at Universidad del Chile, Chile. She has currently 91 papers listed at DBLP (www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Melo:Alba_Cristina_Magalhaes_Alves_de.html). Read more	16	17	18
19	20	21	22 Seminar recess (vacation) N/A February 22, 2018 Read more	23	24	25
26	27	28	March 1 Keynote N/A March 1, 2018 Read more	2	3	4

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Calendar

The week's events

Category: Seminars Keynote

Keynote

News

Next seminars

Events

Events in January–February 2018

January

Category: Seminars Keynote

Category: Seminars Predicting the Energy-Consumption of MPI Applications at Scale Using Only a Single Node, by Christian Heinrich (Polaris)

February

Category: Seminars Keynote

Category: Seminars Datamove workshop

Category: Seminars Untitled Event

Category: Seminars Parallel Sequence Alignment of Whole Chromosomes with Hundreds of GPUs and Pruning (by Alba Cristina Magalhaes Alves de Melo, University of Brasilia )

Category: Seminars Seminar recess (vacation)

March

Category: Seminars Keynote

Meta

Keynote

Keynote

Predicting the Energy-Consumption of MPI Applications at Scale Using Only a Single Node, by Christian Heinrich (Polaris)

Keynote

Datamove workshop

Untitled Event

Parallel Sequence Alignment of Whole Chromosomes with Hundreds of GPUs and Pruning (by Alba Cristina Magalhaes Alves de Melo, University of Brasilia )

Seminar recess (vacation)

Keynote