| 1. |
- Aguilar, Xavier, et al.
(författare)
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Scalability analysis of Dalton, a molecular structure program
- 2013
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Ingår i: Future generations computer systems. - : Elsevier BV. - 0167-739X .- 1872-7115. ; 29:8, s. 2197-2204
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.
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| 2. |
- Aguilar, Xavier, et al.
(författare)
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Scaling Dalton, a molecular electronic structure program
- 2011
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Ingår i: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden. - : IEEE conference proceedings. - 9781457721632 ; , s. 256-262
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Konferensbidrag (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.
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| 3. |
- Donos, Nikos, et al.
(författare)
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Impact of timing of dental implant placement and loading : Summary and consensus statements of group 1—The 6th EAO Consensus Conference 2021
- 2021
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Ingår i: Clinical Oral Implants Research. - : John Wiley & Sons. - 0905-7161 .- 1600-0501. ; 32:S21, s. 85-92
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: This publication reports on the EAO workshop group 1 summaries, discussions and consensus statements based on four systematic reviews evaluating the impact of timing of dental implant placement and loading.Materials and methods: The first of the systematic reviews was on the influence of the timing of implant placement and loading in the biological outcomes of implant-supported fixed partial dentures. The second systematic review evaluated the influence of the timing of implant placement and loading on the aesthetic outcomes in single-tooth implants. The third systematic review was on the long-term outcomes of maxillary single-tooth implants in relation to timing protocols of implant placement and loading and the fourth on patient's perception of timing concepts in implant dentistry. The group evaluated these systematic reviews, provided comments and additions as required and agreed on the relevant consensus statements as well as on clinical and research recommendations.Results: Different timings of implant placement/loading presented with high implant survival rates. The systematic reviews evaluated from this working group provided a number of conclusions based on the available/current literature. However, the specific topic of timing is an area that further research is required in order to provide detailed guidelines for the different protocols to be employed.
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| 4. |
- Gong, Jing, et al.
(författare)
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Nek5000 with OpenACC
- 2015
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Ingår i: Solving software challenges for exascale. - Cham : Springer International Publishing. - 9783319159751 - 9783319159768 ; , s. 57-68
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Konferensbidrag (refereegranskat)abstract
- Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flows. We follow up on an earlier study which ported the simplified version of Nek5000 to a GPU-accelerated system by presenting the hybrid CPU/GPU implementation of the full Nek5000 code using OpenACC. The matrix-matrix multiplication, the Nek5000 gather-scatter operator and a preconditioned Conjugate Gradient solver have implemented using OpenACC for multi-GPU systems. We report an speed-up of 1.3 on single node of a Cray XK6 when using OpenACC directives in Nek5000. On 512 nodes of the Titan supercomputer, the speed-up can be approached to 1.4. A performance analysis of the Nek5000 code using Score-P and Vampir performance monitoring tools shows that overlapping of GPU kernels with host-accelerator memory transfers would considerably increase the performance of the OpenACC version of Nek5000 code.
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| 5. |
- Gong, Jing, et al.
(författare)
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NekBone with Optimizaed OpenACC directives
- 2015
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Konferensbidrag (refereegranskat)abstract
- Accelerators and, in particular, Graphics Processing Units (GPUs) have emerged as promising computing technologies which may be suitable for the future Exascale systems. Here, we present performance results of NekBone, a benchmark of the Nek5000 code, implemented with optimized OpenACC directives and GPUDirect communications. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. Results of an optimized NekBone version lead to 78 Gflops performance on a single node. In addition, a performance result of 609 Tflops has been reached on 16, 384 GPUs of the Titan supercomputer at Oak Ridge National Laboratory.
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| 6. |
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| 7. |
- Hilbel, T., et al.
(författare)
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Performance and productivity benefits using multi-core processors for the analysis of digital long-term ECG recordings
- 2008
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Ingår i: Computers in Cardiology, 2008. ; , s. 1069-1072
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Konferensbidrag (refereegranskat)abstract
- Modern Holter recorders allow the acquisition of 12 lead ECGs with a sampling rate of IKHz or higher and a resolution of 16 bits over more than 24h. While large volumes of data can be easily stored on flash memory cards the analysis of these biosignals requires considerable calculation power and network bandwidth. In general, processing time is important when hundreds of digital recordings from large study groups need to be analyzed The objective of the following investigation is to address the question: Can performance and productivity benefits in ECG analysis be achieved using multi-core processor technology? Because these processors have two or more processing cores they can perform parallel processing. The results show that segmentation of Holter data and running the same program multiple times simultaneously can dramatically speedup the computing performance.
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| 8. |
- Markidis, Stefano, et al.
(författare)
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OpenACC acceleration of the Nek5000 spectral element code
- 2015
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Ingår i: The international journal of high performance computing applications. - : Sage Publications. - 1094-3420 .- 1741-2846. ; 29:3, s. 311-319
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Tidskriftsartikel (refereegranskat)abstract
- We present a case study of porting NekBone, a skeleton version of the Nek5000 code, to a parallel GPU-accelerated system. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. The original NekBone Fortran source code has been used as the base and enhanced by OpenACC directives. The profiling of NekBone provided an assessment of the suitability of the code for GPU systems, and indicated possible kernel optimizations. To port NekBone to GPU systems required little effort and a small number of additional lines of code (approximately one OpenACC directive per 1000 lines of code). The naïve implementation using OpenACC leads to little performance improvement: on a single node, from 16 Gflops obtained with the version without OpenACC, we reached 20 Gflops with the naïve OpenACC implementation. An optimized NekBone version leads to a 43 Gflop performance on a single node. In addition, we ported and optimized NekBone to parallel GPU systems, reaching a parallel efficiency of 79.9% on 1024 GPUs of the Titan XK7 supercomputer at the Oak Ridge National Laboratory.
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| 9. |
- Markidis, Stefano, et al.
(författare)
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Paving the path to exascale computing with CRESTA development environment
- 2013
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The development and implementation of efficient computer codes for exascale supercomputers will require combined advancement of all development environment components: compilers, automatic tuning frameworks, run-time systems, debuggers and performance monitoring and analysis tools. The exascale era poses unprecedented challenges. Because the presence of accelerators is more and more common among the fastest supercomputer and will play a role in exascale computing, compilers will need to support hybrid computer architectures and generate efficient code hiding the complexity of programming accelerators. Hand optimization of the code will be very difficult on exascale machine and will be increasingly assisted by automatic tuners. Application tuning will be more focus on parallel aspects of the computation because of large amount of available parallelism. The application workload will be distributed over million of processes, and to implement ad-hoc strategies directly in the application will be probably unfeasible while an adaptive run-time system will provide automatic load balancing. Debuggers and performance monitoring tools will deal with million processes and with huge amount of data from application and hardware counters, but they will still be required to minimize the overhead and retain scalability. In this talk, we present how the development environment of the CRESTA exascale EC project meets all these challenges by advancing the state of the art in the field.An investigation of compiler support for hybrid GPU programming, the design concepts, and the main characteristics of the alpha prototype implementation of the CRESTA development environment components for exascale computing are presented. A performance study of OpenACC compiler directives has been carried out, showing very promising results and indicating OpenACC as viable approach for programming hybrid exascale supercomputer. A new Domain-Specific Language (DSL) has been defined for the expression of parallel auto-tuning at very large scale. The focus of on the extension of the auto-tuning approach into the parallel domain to enable tuning of communication-related aspects of application. A new adaptive run-time system has been designed to schedule processes depending on the resource availability, on the workload, and on the run-time analysis of the application performance. The Allinea DDT debugger and the Dresden University of Technology MUST MPI correctness checker are being extended to provide a unified interface, to improve scalability, and to include new disruptive technology based on statistical analysis of run-time behavior of the application for anomalies detection. The new exascale prototypes of the Dresden University of Technology Vampir, VampirTrace and Score-P performance monitoring and analysis tools have been released. The new features include the possibility of applying filtering technique before loading performance data to drastically reduce memory needs during the performance analysis. The initial evaluation study of the development environment is targeted on the CRESTA project applications to determine how the development environment could be coupled into a production suite for exascale computing.
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