| 1. |
- Andersson, Måns
(author)
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Leveraging Intermediate Representations for High-Performance Portable Discrete Fourier Transform Frameworks : with Application to Molecular Dynamics
- 2023
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Licentiate thesis (other academic/artistic)abstract
- The Discrete Fourier Transform (DFT) and its improved formulations, the Fast Fourier Transforms (FFTs), are vital for scientists and engineers in a range of domains from signal processing to the solution of partial differential equations. A growing trend in Scientific Computing is heterogeneous computing, where accelerators are used instead or together with CPUs. This has led to problems for developers in unifying portability, performance, and productivity. This thesis first motivates this work by showing the importance of having efficient DFT calculations, describes the DFT algorithm and a formulation based on matrix-factorizations which has been developed to formulate FFT algorithms and express their parallelism to exploit modern computer architectures, such as accelerators.The first paper is a motivating study of the breakdown of the performance and scalability of the high-performance Molecular Dynamics code GROMACS where DFT calculations are a main performance bottleneck. In particular, the long-range interactions are solved with the Particle-Mesh Ewald algorithm which uses a three-dimensional Fast Fourier Transform. The two following papers present two approaches to leverage factorization with the help of two different frameworks using Intermediate Representation and compiler technology, for the development of fast and portable code. The second paper presents a front-end and a pipeline for code generation in a domain-specific language based on Multi-Level Intermediate Representation (MLIR) for developing Fast Fourier Transform libraries. The last paper investigates and optimizes an implementation of an important kernel within the matrix-factorization framework: the batched DFT. It is implemented with data-centric programming and a data-centric intermediate representation called Stateful Dataflow multi-graphs (SDFG). The paper evaluates strategies for complex-valued data layout for performance and portability and we show that there is a trade-off between portability and maintainability in using the native complex data type and that an SDFG-level abstraction could be beneficial for developing higher-level applications.
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| 2. |
- Anzt, Hartwig, et al.
(author)
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An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
- 2020
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In: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Journal article (peer-reviewed)abstract
- Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
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