Alexander Schoell
Name: | Dr. rer. nat. Alexander Schoell | |
Address: | University of Stuttgart | |
Room: | ||
Phone: | (+49) (0)711 / 685-88-279 | |
Telefax: | (+49) (0)711 / 685-88-288 | |
E-mail: | ||
Projects
Contributions to ongoing and completed projects:
Simulation on Reconfigurable Heterogeneous Computer Architectures
Project page: Simulation on Reconfigurable Heterogeneous Computer Architectures
Since the beginning of the DFG Cluster of Excellence "Simulation Technology" (SimTech) at the University of Stuttgart in 2008, the Institute of Computer Architecture and Computer Engineering (ITI, RA) is an active part of the research within the Stuttgart Research Center for Simulation Technology (SRC SimTech). The institute's research includes the development of fault tolerant simulation algorithms for new, tightly-coupled many-core computer architectures like GPUs, the acceleration of existing simulations on such architectures, as well as the mapping of complex simulation applications to innovative reconfigurable heterogeneous computer architectures.
Within the research cluster, Hans-Joachim Wunderlich acts as a principal investigator (PI) and he co-coordinates the research activities of the SimTech Project Network PN2 "High-Performance Simulation across Computer Architectures". This project network is unique in terms of its interdisciplinary nature and its interfaces between the participating researchers and projects. Scientists from computer science, chemistry, physics and chemical engineering work together to develop and provide new solutions for some of the major challenges in simulation technology. The classes of computational problems treated within project network PN2 comprise quantum mechanics, molecular mechanics, electronic structure methods, molecular dynamics, Markov-chain Monte-Carlo simulations and polarizable force fields.
06.2008 - 10.2017, SimTech Cluster of Excellence 
Publications
Journals and Conference Proceedings
| 9. | Energy-efficient and Error-resilient Iterative Solvers for Approximate Computing Schöll, Alexander; Braun, Claus; Wunderlich, Hans-Joachim Proceedings of the 23rd IEEE International Symposium on On-Line Testing and Robust System Design (IOLTS'17), Thessaloniki, Greece, 3-5 July 2017, pp. 237-239 |
2017 DOI PDF |
| Keywords: Approximate Computing, Energy-efficiency, Fault Tolerance, Quality Monitoring | ||
| Abstract: Iterative solvers like the Preconditioned Conjugate Gradient (PCG) method are widely-used in compute-intensive domains including science and engineering that often impose tight accuracy demands on computational results. At the same time, the error resilience of such solvers may change in the course of the iterations, which requires careful adaption of the induced approximation errors to reduce the energy demand while avoiding unacceptable results. A novel adaptive method is presented that enables iterative Preconditioned Conjugate Gradient (PCG) solvers on Approximate Computing hardware with high energy efficiency while still providing correct results. The method controls the underlying precision at runtime using a highly efficient fault tolerance technique that monitors the induced error and the quality of intermediate computational results. | ||
BibTeX:
@inproceedings{SchoeBW2017,
author = {Schöll, Alexander and Braun, Claus and Wunderlich, Hans-Joachim},
title = {{Energy-efficient and Error-resilient Iterative Solvers for Approximate Computing}},
booktitle = {Proceedings of the 23rd IEEE International Symposium on On-Line Testing and Robust System Design (IOLTS'17)},
year = {2017},
pages = {237--239},
keywords = {Approximate Computing, Energy-efficiency, Fault Tolerance, Quality Monitoring},
abstract = {Iterative solvers like the Preconditioned Conjugate Gradient (PCG) method are widely-used in compute-intensive domains including science and engineering that often impose tight accuracy demands on computational results. At the same time, the error resilience of such solvers may change in the course of the iterations, which requires careful adaption of the induced approximation errors to reduce the energy demand while avoiding unacceptable results. A novel adaptive method is presented that enables iterative Preconditioned Conjugate Gradient (PCG) solvers on Approximate Computing hardware with high energy efficiency while still providing correct results. The method controls the underlying precision at runtime using a highly efficient fault tolerance technique that monitors the induced error and the quality of intermediate computational results.},
doi = {http://dx.doi.org/10.1109/IOLTS.2017.8046244},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2017/IOLTS_SchoeBW2017.pdf}
}
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| 8. | Applying Efficient Fault Tolerance to Enable the Preconditioned Conjugate Gradient Solver on Approximate Computing Hardware Schöll, Alexander; Braun, Claus; Wunderlich, Hans-Joachim Proceedings of the IEEE International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems (DFT'16), University of Connecticut, USA, 19-20 September 2016, pp. 21-26 DFT 2016 Best Paper Award |
2016 DOI PDF |
| Keywords: Approximate Computing, Fault Tolerance, Sparse Linear System Solving, Preconditioned Conjugate Gradient | ||
| Abstract: A new technique is presented that allows to execute the preconditioned conjugate gradient (PCG) solver on approximate hardware while ensuring correct solver results. This technique expands the scope of approximate computing to scientific and engineering applications. The changing error resilience of PCG during the solving process is exploited by different levels of approximation which trade off numerical accuracy and hardware utilization. Such approximation levels are determined at runtime by periodically estimating the error resilience. An efficient fault tolerance technique allows reductions in hardware utilization by ensuring the continued exploitation of maximum allowed energy-accuracy trade-offs. Experimental results show that the hardware utilization is reduced on average by 14.5% and by up to 41.0% compared to executing PCG on accurate hardware. | ||
BibTeX:
@inproceedings{SchoeBW2016,
author = {Schöll, Alexander and Braun, Claus and Wunderlich, Hans-Joachim},
title = {{Applying Efficient Fault Tolerance to Enable the Preconditioned Conjugate Gradient Solver on Approximate Computing Hardware}},
booktitle = {Proceedings of the IEEE International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems (DFT'16)},
year = {2016},
pages = {21-26},
keywords = {Approximate Computing, Fault Tolerance, Sparse Linear System Solving, Preconditioned Conjugate Gradient},
abstract = {A new technique is presented that allows to execute the preconditioned conjugate gradient (PCG) solver on approximate hardware while ensuring correct solver results. This technique expands the scope of approximate computing to scientific and engineering applications. The changing error resilience of PCG during the solving process is exploited by different levels of approximation which trade off numerical accuracy and hardware utilization. Such approximation levels are determined at runtime by periodically estimating the error resilience. An efficient fault tolerance technique allows reductions in hardware utilization by ensuring the continued exploitation of maximum allowed energy-accuracy trade-offs. Experimental results show that the hardware utilization is reduced on average by 14.5% and by up to 41.0% compared to executing PCG on accurate hardware.},
doi = {http://dx.doi.org/10.1109/DFT.2016.7684063},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2016/DFT_SchoeBW2016.pdf}
}
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| 7. | Pushing the Limits: How Fault Tolerance Extends the Scope of Approximate Computing Wunderlich, Hans-Joachim; Braun, Claus; Schöll, Alexander Proceedings of the 22nd IEEE International Symposium on On-Line Testing and Robust System Design (IOLTS'16), Sant Feliu de Guixols, Catalunya, Spain, 4-6 July 2016, pp. 133-136 |
2016 DOI PDF |
| Keywords: Approximate Computing, Variable Precision, Metrics, Characterization, Fault Tolerance | ||
| Abstract: Approximate computing in hardware and software promises significantly improved computational performance combined with very low power and energy consumption. This goal is achieved by both relaxing strict requirements on accuracy and precision, and by allowing a deviating behavior from exact Boolean specifications to a certain extent. Today, approximate computing is often limited to applications with a certain degree of inherent error tolerance, where perfect computational results are not always required. However, in order to fully utilize its benefits, the scope of applications has to be significantly extended to other compute-intensive domains including science and engineering. To meet the often rather strict quality and reliability requirements for computational results in these domains, the use of appropriate characterization and fault tolerance measures is highly required. In this paper, we evaluate some of the available techniques and how they may extend the scope of application for approximate computing. | ||
BibTeX:
@inproceedings{WundeBS2016,
author = {Wunderlich, Hans-Joachim and Braun, Claus and Schöll, Alexander},
title = {{Pushing the Limits: How Fault Tolerance Extends the Scope of Approximate Computing}},
booktitle = {Proceedings of the 22nd IEEE International Symposium on On-Line Testing and Robust System Design (IOLTS'16)},
year = {2016},
pages = {133--136},
keywords = {Approximate Computing, Variable Precision, Metrics, Characterization, Fault Tolerance},
abstract = {Approximate computing in hardware and software promises significantly improved computational performance combined with very low power and energy consumption. This goal is achieved by both relaxing strict requirements on accuracy and precision, and by allowing a deviating behavior from exact Boolean specifications to a certain extent. Today, approximate computing is often limited to applications with a certain degree of inherent error tolerance, where perfect computational results are not always required. However, in order to fully utilize its benefits, the scope of applications has to be significantly extended to other compute-intensive domains including science and engineering. To meet the often rather strict quality and reliability requirements for computational results in these domains, the use of appropriate characterization and fault tolerance measures is highly required. In this paper, we evaluate some of the available techniques and how they may extend the scope of application for approximate computing.},
doi = {http://dx.doi.org/10.1109/IOLTS.2016.7604686},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2016/IOLTS_WundeBS2016.pdf}
}
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| 6. | Efficient Algorithm-Based Fault Tolerance for Sparse Matrix Operations Schöll, Alexander; Braun, Claus; Kochte, Michael A.; Wunderlich, Hans-Joachim Proceedings of the 46th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN'16), Toulouse, France, 28 June-1 July 2016, pp. 251-262 |
2016 DOI PDF |
| Keywords: Fault Tolerance, Sparse Linear Algebra, ABFT, Online Error Localization | ||
| Abstract: We propose a fault tolerance approach for sparse matrix operations that detects and implicitly locates errors in the results for efficient local correction. This approach reduces the runtime overhead for fault tolerance and provides high error coverage. Existing algorithm-based fault tolerance approaches for sparse matrix operations detect and correct errors, but they often rely on expensive error localization steps. General checkpointing schemes can induce large recovery cost for high error rates. For sparse matrix-vector multiplications, experimental results show an average reduction in runtime overhead of 43.8%, while the error coverage is on average improved by 52.2% compared to related work. The practical applicability is demonstrated in a case study using the iterative Preconditioned Conjugate Gradient solver. When scaling the error rate by four orders of magnitude, the average runtime overhead increases only by 31.3% compared to low error rates. | ||
BibTeX:
@inproceedings{SchoeBKW2016,
author = {Schöll, Alexander and Braun, Claus and Kochte, Michael A. and Wunderlich, Hans-Joachim},
title = {{Efficient Algorithm-Based Fault Tolerance for Sparse Matrix Operations}},
booktitle = {Proceedings of the 46th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN'16)},
year = {2016},
pages = {251--262},
keywords = {Fault Tolerance, Sparse Linear Algebra, ABFT, Online Error Localization},
abstract = {We propose a fault tolerance approach for sparse matrix operations that detects and implicitly locates errors in the results for efficient local correction. This approach reduces the runtime overhead for fault tolerance and provides high error coverage. Existing algorithm-based fault tolerance approaches for sparse matrix operations detect and correct errors, but they often rely on expensive error localization steps. General checkpointing schemes can induce large recovery cost for high error rates. For sparse matrix-vector multiplications, experimental results show an average reduction in runtime overhead of 43.8%, while the error coverage is on average improved by 52.2% compared to related work. The practical applicability is demonstrated in a case study using the iterative Preconditioned Conjugate Gradient solver. When scaling the error rate by four orders of magnitude, the average runtime overhead increases only by 31.3% compared to low error rates.},
doi = {http://dx.doi.org/10.1109/DSN.2016.31},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2016/DSN_SchoeBKW2016.pdf}
}
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| 5. | Fault Tolerance of Approximate Compute Algorithms Wunderlich, Hans-Joachim; Braun, Claus; Schöll, Alexander Proceedings of the 34th VLSI Test Symposium (VTS'16), Caesars Palace, Las Vegas, Nevada, USA, 25-27 April 2016 |
2016 DOI PDF |
| Abstract: Approximate computing algorithms cover a wide range of different applications and the boundaries to domains like variable-precision computing, where the precision of the computations can be online adapted to the needs of the application [1, 2], as well as probabilistic and stochastic computing [3], which incorporate stochastic processes and probability distributions in the target computations, are sometimes blurred. The central idea of purely algorithm-based approximate computing is to transform algorithms, without necessarily requiring approximate hardware, to trade-off accuracy against energy. Early termination of algorithms that exhibit incremental refinement [4] reduces iterations at the cost of accuracy. Loop perforation [5] approximates iteratively-computed results by identifying and reducing loops that contribute only insignificantly to the solution. Another group of approximate algorithms is represented by neural networks, which can be trained to mimic certain algorithms and to compute approximate results [6]. Today, approximate computing is predominantly proposed for applications in multimedia and signal processing with a certain degree of inherent error tolerance. However, in order to fully utilize the benefits of these architectures, the scope of applications has to be significantly extended to other computeintensive tasks, for instance, in science and engineering. Such an extension requires that the allowed error or the required minimum precision of the application is either known beforehand or reliably determined online to deliver trustworthy and useful results. Errors outside the allowed range have to be reliably detected and tackled by appropriate fault tolerance measures. | ||
BibTeX:
@inproceedings{WundeBS2016a,
author = {Wunderlich, Hans-Joachim and Braun, Claus and Schöll, Alexander},
title = {{Fault Tolerance of Approximate Compute Algorithms}},
booktitle = {Proceedings of the 34th VLSI Test Symposium (VTS'16)},
year = {2016},
abstract = {Approximate computing algorithms cover a wide range of different applications and the boundaries to domains like variable-precision computing, where the precision of the computations can be online adapted to the needs of the application [1, 2], as well as probabilistic and stochastic computing [3], which incorporate stochastic processes and probability distributions in the target computations, are sometimes blurred. The central idea of purely algorithm-based approximate computing is to transform algorithms, without necessarily requiring approximate hardware, to trade-off accuracy against energy. Early termination of algorithms that exhibit incremental refinement [4] reduces iterations at the cost of accuracy. Loop perforation [5] approximates iteratively-computed results by identifying and reducing loops that contribute only insignificantly to the solution. Another group of approximate algorithms is represented by neural networks, which can be trained to mimic certain algorithms and to compute approximate results [6]. Today, approximate computing is predominantly proposed for applications in multimedia and signal processing with a certain degree of inherent error tolerance. However, in order to fully utilize the benefits of these architectures, the scope of applications has to be significantly extended to other computeintensive tasks, for instance, in science and engineering. Such an extension requires that the allowed error or the required minimum precision of the application is either known beforehand or reliably determined online to deliver trustworthy and useful results. Errors outside the allowed range have to be reliably detected and tackled by appropriate fault tolerance measures.},
doi = {http://dx.doi.org/10.1109/VTS.2016.7477307},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2016/VTS_WundeBS2016.pdf}
}
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| 4. | Low-Overhead Fault-Tolerance for the Preconditioned Conjugate Gradient Solver Schöll, Alexander; Braun, Claus; Kochte, Michael A.; Wunderlich, Hans-Joachim Proceedings of the International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems (DFT'15), Amherst, Massachusetts, USA, 12-14 October 2015, pp. 60-65 |
2015 DOI PDF |
| Keywords: Fault Tolerance, Sparse Linear System Solving, Preconditioned Conjugate Gradient, ABFT | ||
| Abstract: Linear system solvers are an integral part for many different compute-intensive applications and they benefit from the compute power of heterogeneous computer architectures. However, the growing spectrum of reliability threats for such nano-scaled CMOS devices makes the integration of fault tolerance mandatory. The preconditioned conjugate gradient (PCG) method is one widely used solver as it finds solutions typically faster compared to direct methods. Although this iterative approach is able to tolerate certain errors, latest research shows that the PCG solver is still vulnerable to transient effects. Even single errors, for instance, caused by marginal hardware, harsh environments, or particle radiation, can considerably affect execution times, or lead to silent data corruption. In this work, a novel fault-tolerant PCG solver with extremely low runtime overhead is proposed. Since the error detection method does not involve expensive operations, it scales very well with increasing problem sizes. In case of errors, the method selects between three different correction methods according to the identified error. Experimental results show a runtime overhead for error detection ranging only from 0.04% to 1.70%. | ||
BibTeX:
@inproceedings{SchoeBKW2015a,
author = {Schöll, Alexander and Braun, Claus and Kochte, Michael A. and Wunderlich, Hans-Joachim},
title = {{Low-Overhead Fault-Tolerance for the Preconditioned Conjugate Gradient Solver}},
booktitle = {Proceedings of the International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems (DFT'15)},
year = {2015},
pages = {60-65},
keywords = { Fault Tolerance, Sparse Linear System Solving, Preconditioned Conjugate Gradient, ABFT },
abstract = {Linear system solvers are an integral part for many different compute-intensive applications and they benefit from the compute power of heterogeneous computer architectures. However, the growing spectrum of reliability threats for such nano-scaled CMOS devices makes the integration of fault tolerance mandatory. The preconditioned conjugate gradient (PCG) method is one widely used solver as it finds solutions typically faster compared to direct methods. Although this iterative approach is able to tolerate certain errors, latest research shows that the PCG solver is still vulnerable to transient effects. Even single errors, for instance, caused by marginal hardware, harsh environments, or particle radiation, can considerably affect execution times, or lead to silent data corruption. In this work, a novel fault-tolerant PCG solver with extremely low runtime overhead is proposed. Since the error detection method does not involve expensive operations, it scales very well with increasing problem sizes. In case of errors, the method selects between three different correction methods according to the identified error. Experimental results show a runtime overhead for error detection ranging only from 0.04% to 1.70%. },
doi = {http://dx.doi.org/10.1109/DFT.2015.7315136},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2015/DFTS_SchoeBKW2015.pdf}
}
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| 3. | Efficient On-Line Fault-Tolerance for the Preconditioned Conjugate Gradient Method Schöll, Alexander; Braun, Claus; Kochte, Michael A.; Wunderlich, Hans-Joachim Proceedings of the 21st IEEE International On-Line Testing Symposium (IOLTS'15), Elia, Halkidiki, Greece, 6-8 July 2015, pp. 95-100 |
2015 DOI PDF |
| Keywords: Sparse Linear System Solving, Fault Tolerance, Preconditioned Conjugate Gradient, ABFT | ||
| Abstract: Linear system solvers are key components of many scientific applications and they can benefit significantly from modern heterogeneous computer architectures. However, such nano-scaled CMOS devices face an increasing number of reliability threats, which make the integration of fault tolerance mandatory. The preconditioned conjugate gradient method (PCG) is a very popular solver since it typically finds solutions faster than direct methods, and it is less vulnerable to transient effects. However, as latest research shows, the vulnerability is still considerable. Even single errors caused, for instance, by marginal hardware, harsh operating conditions or particle radiation can increase execution times considerably or corrupt solutions without indication. In this work, a novel and highly efficient fault-tolerant PCG method is presented. The method applies only two inner products to reliably detect errors. In case of errors, the method automatically selects between roll-back and efficient on-line correction. This significantly reduces the error detection overhead and expensive re-computations. | ||
BibTeX:
@inproceedings{SchoeBKW2015,
author = {Schöll, Alexander and Braun, Claus and Kochte, Michael A. and Wunderlich, Hans-Joachim},
title = {{Efficient On-Line Fault-Tolerance for the Preconditioned Conjugate Gradient Method}},
booktitle = {Proceedings of the 21st IEEE International On-Line Testing Symposium (IOLTS'15)},
year = {2015},
pages = {95--100},
keywords = {Sparse Linear System Solving, Fault Tolerance, Preconditioned Conjugate Gradient, ABFT},
abstract = {Linear system solvers are key components of many scientific applications and they can benefit significantly from modern heterogeneous computer architectures. However, such nano-scaled CMOS devices face an increasing number of reliability threats, which make the integration of fault tolerance mandatory. The preconditioned conjugate gradient method (PCG) is a very popular solver since it typically finds solutions faster than direct methods, and it is less vulnerable to transient effects. However, as latest research shows, the vulnerability is still considerable. Even single errors caused, for instance, by marginal hardware, harsh operating conditions or particle radiation can increase execution times considerably or corrupt solutions without indication. In this work, a novel and highly efficient fault-tolerant PCG method is presented. The method applies only two inner products to reliably detect errors. In case of errors, the method automatically selects between roll-back and efficient on-line correction. This significantly reduces the error detection overhead and expensive re-computations.},
doi = {http://dx.doi.org/10.1109/IOLTS.2015.7229839},
file = {http://www.iti.uni-stuttgart.de/fileadmin/rami/files/publications/2015/IOLTS_SchoeBKW2015.pdf}
}
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| 2. | Adaptive Parallel Simulation of a Two-Timescale-Model for Apoptotic Receptor-Clustering on GPUs Schöll, Alexander; Braun, Claus; Daub, Markus; Schneider, Guido; Wunderlich, Hans-Joachim Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'14), Belfast, United Kingdom, 2-5 November 2014, pp. 424-431 SimTech Best Paper Award |
2014 DOI PDF |
| Keywords: Heterogeneous computing, GPU computing, parallel particle simulation, multi-timescale model, adaptive Euler-Maruyama approximation, ligand-receptor aggregation | ||
| Abstract: Computational biology contributes important solutions for major biological challenges. Unfortunately, most applications in computational biology are highly computeintensive and associated with extensive computing times. Biological problems of interest are often not treatable with traditional simulation models on conventional multi-core CPU systems. This interdisciplinary work introduces a new multi-timescale simulation model for apoptotic receptor-clustering and a new parallel evaluation algorithm that exploits the computational performance of heterogeneous CPU-GPU computing systems. For this purpose, the different dynamics involved in receptor-clustering are separated and simulated on two timescales. Additionally, the time step sizes are adaptively refined on each timescale independently. This new approach improves the simulation performance significantly and reduces computing times from months to hours for observation times of several seconds. |
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BibTeX:
@inproceedings{SchoeBDSW2014,
author = {Schöll, Alexander and Braun, Claus and Daub, Markus and Schneider, Guido and Wunderlich, Hans-Joachim},
title = {{Adaptive Parallel Simulation of a Two-Timescale-Model for Apoptotic Receptor-Clustering on GPUs}},
booktitle = {Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'14)},
year = {2014},
pages = {424--431},
keywords = {Heterogeneous computing, GPU computing, parallel particle simulation, multi-timescale model, adaptive Euler-Maruyama approximation, ligand-receptor aggregation},
abstract = {Computational biology contributes important solutions for major biological challenges. Unfortunately, most applications in computational biology are highly computeintensive and associated with extensive computing times. Biological problems of interest are often not treatable with traditional simulation models on conventional multi-core CPU systems. This interdisciplinary work introduces a new multi-timescale simulation model for apoptotic receptor-clustering and a new parallel evaluation algorithm that exploits the computational performance of heterogeneous CPU-GPU computing systems. For this purpose, the different dynamics involved in receptor-clustering are separated and simulated on two timescales. Additionally, the time step sizes are adaptively refined on each timescale independently. |
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| 1. | Parallel Simulation of Apoptotic Receptor-Clustering on GPGPU Many-Core Architectures Braun, Claus; Daub, Markus; Schöll, Alexander; Schneider, Guido; Wunderlich, Hans-Joachim Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'12), Philadelphia, Pennsylvania, USA, 4-7 October 2012, pp. 1-6 |
2012 DOI PDF |
| Keywords: GPGPU; parallel particle simulation; numerical modeling; apoptosis; receptor-clustering | ||
| Abstract: Apoptosis, the programmed cell death, is a physiological process that handles the removal of unwanted or damaged cells in living organisms. The process itself is initiated by signaling through tumor necrosis factor (TNF) receptors and ligands, which form clusters on the cell membrane. The exact function of this process is not yet fully understood and currently subject of basic research. Different mathematical models have been developed to describe and simulate the apoptotic receptor-clustering. In this interdisciplinary work, a previously introduced model of the apoptotic receptor-clustering has been extended by a new receptor type to allow a more precise description and simulation of the signaling process. Due to the high computational requirements of the model, an ef?cient algorithmic mapping to a modern many-core GPGPU architecture has been developed. Such architectures enable high-performance computing (HPC) simulation tasks on the desktop at low costs. The developed mapping reduces average simulation times from months to days (peak speedup of 256x), allowing the productive use of the model in research. |
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BibTeX:
@inproceedings{BraunDSSW2012,
author = {Braun, Claus and Daub, Markus and Schöll, Alexander and Schneider, Guido and Wunderlich, Hans-Joachim},
title = {{Parallel Simulation of Apoptotic Receptor-Clustering on GPGPU Many-Core Architectures}},
booktitle = {Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'12)},
year = {2012},
pages = {1--6},
keywords = {GPGPU; parallel particle simulation; numerical modeling; apoptosis; receptor-clustering},
abstract = {Apoptosis, the programmed cell death, is a physiological process that handles the removal of unwanted or damaged cells in living organisms. The process itself is initiated by signaling through tumor necrosis factor (TNF) receptors and ligands, which form clusters on the cell membrane. The exact function of this process is not yet fully understood and currently subject of basic research. Different mathematical models have been developed to describe and simulate the apoptotic receptor-clustering. |
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Teaching
Lectures, Exercises and Seminars
Master/Diploma Theses and Student Research Projects
2016 | Evaluation of the Fault Tolerance of Artificial Neuronal Networks and Investigation of their Precision Requirement Development of a Model-based Characterization Software Framework for Approximate Computing Applications Adaptive Approximate Computing for Image Filtering using Dynamic Partial Reconfiguration | |
2014 | Tailoring and Optimization of a GPU Simulation Environment on Apoptotic Receptor-Clustering to OpenCL | |
2013 | Integration von algorithmenbasierter Fehlertoleranz in grundlegende Operationen der linearen Algebra auf GPGPUs |
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