| 1. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(författare)
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A High Performance Computing Framework for Finite Element Simulation of Blood Flow in the Left Ventricle of the Human Heart
- 2020
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Ingår i: Lecture Notes in Computational Science and Engineering. - Cham : Springer. ; , s. 155-164
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Konferensbidrag (refereegranskat)abstract
- We present a high performance computing framework for finite element simulation of blood flow in the left ventricle of the human heart. The mathematical model is described together with the discretization method and the parallel implementation in Unicorn which is part of the open source software framework FEniCS-HPC. We show results based on patient-specific data that capture essential features observed with other computational models and imaging techniques, and thus indicate that our framework possesses the potential to provide relevant clinical information for diagnosis and medical treatment. Several other studies have been conducted to simulate the three dimensional blood flow in the left ventricle of the human heart with prescribed wall movement. Our contribution to the field of cardiac research lies in establishing an open source framework modular both in modelling and numerical algorithms.
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| 2. |
- Almén, Niclas, 1971-, et al.
(författare)
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The reliability and factorial validity of different versions of the Shirom-Melamed Burnout Measure/Questionnaire and normative data for a general Swedish sample
- 2021
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Ingår i: International Journal of Stress Management. - : American Psychological Association (APA). - 1072-5245 .- 1573-3424. ; 28:4, s. 314-325
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Tidskriftsartikel (refereegranskat)abstract
- Burnout is a common problem in many countries and is associated with psychological ill health, somatic diseases, mortality and long-term sick leave. Different versions of the Shirom-Melamed Burnout Questionnaire/Measure (SMBQ/SMBM) are widely used to measure burnout. Using confirmatory factor analysis, the main purpose of the present study was to empirically evaluate different Swedish versions of the SMBQ/SMBM. A questionnaire containing 23 SMBQ/SMBM-items was sent to 4,000 randomly selected individuals of which 765 with no missing data were included in the analyses. The well-used 4-factor SMBQ/SMBM-22 including the factors emotional and physiological exhaustion (EPE), cognitive weariness (CWE), listlessness (LIS), and tension (TES) and the 3-factor SMBQ/SMBM-18 (including the EPE, the CWE, and the LIS) reached good model fit after minor modifications. Two 2-factor models (based on 12 and 11 items, respectively), including the EPE and the CWE reached good model fit without any modifications. Even though there were some concerns regarding all models with respect to discriminant validity, the factors in all models showed evidence of good composite reliability (CR) and convergent validity. Lastly, a brief six-item version of the scale based on the 12-item version of the scale indicated an excellent model fit, and the composite score of the six-item scale correlated strongly with the composite scores from the others models, suggesting that the brief version could be used with advantage. In addition, based on the LIS, a new three-item scale that measures vitality is proposed. For all measures, normative data are reported.
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| 3. |
- Almén, Niclas, et al.
(författare)
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Validation of the new brief 6-item version of the Shirom-Melamed Burnout Measure
- 2023
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Ingår i: Cogent Psychology. - : Taylor & Francis. - 2331-1908. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The Shirom-Melamed Burnout Questionnaire/Measure (SMBQ/M) is one of the most commonly used measures of burnout. Using confirmatory factor analyses, the present study aimed to evaluate the model fit, composite reliability, and factorial (i.e. convergent and discriminant) validity of the new brief Swedish version of the scale-labeled SMBM-6. In addition, we used Cronbach’s α as an indicator of the internal consistency of the total scale. The SMBM-6 consists of two subscales: the emotional and physiological exhaustion subscale (three items) and the cognitive weariness subscale (three items). A total of 1251 teachers in Sweden were included in the study. The analyses showed that the Swedish version of the SMBM-6 has an excellent model fit and good convergent validity. The discriminant validity for the cognitive weariness subscale was good, but slightly inadequate for the physiological exhaustion subscale. Composite reliability and Cronbach’s α indicated high internal consistency for the subscales and the total scale, respectively. Multi-group invariance tests for age indicated no violation of invariance. These results are consistent with those of the study by Almén and Jansson (2021), in which the SMBM-6 was developed, and a subsequent psychometric study by Sundström et al. (2022). In conclusion, there is strong support for the Swedish version of the SMBM-6 as a reliable and valid scale for measuring burnout. Testing the scale in languages other than Swedish is warranted.
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| 4. |
- Andersson, Måns
(författare)
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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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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)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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| 5. |
- Atzori, Marco, et al.
(författare)
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In-situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In-situ visualization on HPC systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We design and develop in-situ visualization with Paraview Catalyst in Nek5000, a massively parallel Fortran and C code for computational fluid dynamics applications. We perform strong scalability tests up to 2,048 cores on KTH's Beskow Cray XC40 supercomputer and assess in-situ visualization's impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in-situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ~21\% on 2,048 cores (the relative efficiency of Nek5000 without in-situ operations is ~99\%). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in-situ processing time between rank 0 and all other ranks. Better scaling and load-balancing in the parallel image composition would considerably improve the performance and scalability of Nek5000 with in-situ capabilities in large-scale simulation.
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| 6. |
- Atzori, Marco, 1992-, et al.
(författare)
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In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst
- 2022
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Ingår i: Journal of Supercomputing. - : Springer. - 0920-8542 .- 1573-0484. ; 78:3, s. 3605-3620
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Tidskriftsartikel (refereegranskat)abstract
- In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario.
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| 7. |
- Bale, Rahul, et al.
(författare)
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Stencil Penalty approach based constraint immersed boundary method
- 2020
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Ingår i: Computers & Fluids. - : Elsevier BV. - 0045-7930 .- 1879-0747. ; 2000, s. 104457-
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Tidskriftsartikel (refereegranskat)abstract
- The constraint-based immersed boundary (cIB) method has been shown to be accurate between low and moderate Reynolds number (Re) flows when the immersed body constraint is imposed as a volumetric constraint force. When the IB is modelled as a zero-thickness interface, where it is no longer possible to model a volumetric constraint force, we found that cIB is not able to produce accurate results. The main source of inaccuracies in the cIB method is the distribution of the pressure field around the IB surface. An IB surface results in a jump in the pressure field across the IB. Evaluation of the discrete gradient of pressure close to the IB leads to a pressure gradient that does not satisfy the Neumann boundary condition for pressure at the IB. Furthermore, a non-zero discrete pressure gradient on the IB results in spurious flow at grid points close to the IB. We present a novel numerical formulation which adapts the cIB formulation for ‘zero-thickness’ immersed bodies. In order to impose the Neumann boundary condition on pressure on the IB more accurately, we introduce an additional body force to the momentum equation. A WENO based stencil penalization technique is used to define the new force term. Due to the more accurate imposition on the Neumann pressure boundary condition on the IB, spurious flow is reduced and the accuracy of no penetration velocity boundary condition on the IB is improved.
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| 8. |
- Chien, Steven W.D., et al.
(författare)
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Improving Cloud Storage Network Bandwidth Utilization of Scientific Applications
- 2023
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Ingår i: Proceedings of the 7th Asia-Pacific Workshop on Networking, APNET 2023. - : Association for Computing Machinery (ACM). ; , s. 172-173
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Konferensbidrag (refereegranskat)abstract
- Cloud providers began to provide managed services to attract scientific applications, which have been traditionally executed on supercomputers. One example is AWS FSx for Lustre, a fully managed parallel file system (PFS) released in 2018. However, due to the nature of scientific applications, the frontend storage network bandwidth is left completely idle for the majority of its lifetime. Furthermore, the pricing model does not match the scalability requirement. We propose iFast, a novel host-side caching mechanism for scientific applications that improves storage bandwidth utilization and end-to-end application performance: by overlapping compute and data writeback through inexpensive local storage. iFast supports the Massage Passing Interface (MPI) library that is widely used by scientific applications and is implemented as a preloaded library. It requires no change to applications, the MPI library, or support from cloud operators. We demonstrate how iFast can accelerate the end-to-end time of a representative scientific application Neko, by 13-40%.
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| 9. |
- Choudhary, Vipin
(författare)
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Nondestructive testing and antenna measurements using UWB radar in industrial applications
- 2021
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many industries are rapidly substituting the manual test operations and move towards automated operations using modern technologies.Modern technologies such as digital cameras, sonic sensors, infrared sensors, and radar and lidar systems are used for non-destructive testingoperations. Among all the different sensors, radar systems have theability to penetrate built structures (dielectric materials), which makes them flexible and suitable for a wide range of industrial and military applications in non-destructive sensing. Such examples are the detection of damages in goods manufacturing, monitoring the health of manystructures, object detection through the wall for security purposes, etc.In particular, ultra-wide-band (UWB) radar systems are beneficial inproviding high measurement accuracy and simultaneously reduced sensitivityto passive interference (such as rain, smoke, mist etc.), immunity to external radiation and noise.The objectives of this thesis are: I) to investigate electrically small concealed structures using synthetic aperture radar (SAR), II) to determinethe complex refractive index of objects using an UWB radar system,and III) to answer to the question how we can reduce the mutual coupling (cross talk) in an UWB radar system with collocated transmitand receive antennae. In objective I, the aim is non-destructive testing of built structures, such as in concrete slab manufacturing or for use in the renovation process. In addition electrically small periodic meshes,and their orientation, could not be distinguished in conventional SAR images. The proposed polarimetric analysis method demonstrates the usefulness of the singular value decomposition (SVD) using back projection algorithm (BPA) in extracting information about shape and for classifying an electrically small object. Further in this thesis for objective II, a new method for determining the complex refractive index (or equivalently the complex relative permittivity) of objects with planar interfaces is presented. The proposed method is relatively insensitive to hardware-impairments such as frequency-dependence of antennas and analog front end. The objects can be finite in size and at a finite distance. The limits in size and distance for the method to be valid are experimentally investigated. Hence, the method is designed for industrial in-line measurements onobjects on conveyor belts. Furthermore, in the following parts of this thesis −objective III− we investigate and show how a microwave metamaterial based absorber can be used to improve the performance of aradar system for short range applications, when positioned between the transmit and receive antennas. As results, the error in estimated target distance is reduced and clutter reduction is improved.
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| 10. |
- Dykes, Tim, et al.
(författare)
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Mamba: Portable Array-based Abstractions for Heterogeneous High-Performance Systems
- 2021
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Ingår i: 2021 International Workshop on Performance, Portability and Productivity in HPC (P3HPC). - : Institute of Electrical and Electronics Engineers (IEEE).
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Konferensbidrag (refereegranskat)abstract
- High performance computing architectures have become increasingly heterogeneous in recent times. This growing architectural variety presents a multi-faceted portability problem affecting applications, libraries, programming models, languages, compilers, run-times, and system software. Approaches for performance portability typically focus heavily on efficient usage of parallel compute architectures and less on data locality abstractions and complex memory systems, with minimal support afforded to effective memory management in traditional HPC languages such as C and Fortran. We present Mamba, a library to facilitate usage of heterogeneous memory systems by high performance application/library developers through high level array-based abstractions for memory management supported by a low-level generic memory API. We detail the library design and implementation, demonstrating generic memory allocation, data layout specification, array tiling and heterogeneous transport. We evaluate performance in the context of a typical matrix transposition, DNA sequencing benchmark, and an application use case for high-order spectral element based incompressible flow.
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