Analysis of hybrid parallelization strategies: simulation of Anderson localization and Kalman Filter for LHCb triggers

This thesis presents two experiences of hybrid programming applied to condensed matter and high energy physics. The two projects differ in various aspects, but both of them aim to analyse the benefits of using accelerated hardware to speedup the calculations in current science-research scenarios. The first project enables massively parallelism in a simulation of the Anderson localisation phenomenon in a disordered quantum system. The code represents a Hamiltonian in momentum space, then it executes a diagonalization of the corresponding matrix using linear algebra libraries, and finally it analyses the energy-levels spacing statistics averaged over several realisations of the disorder. The implementation combines different parallelization approaches in an hybrid scheme. The averaging over the ensemble of disorder realisations exploits massively parallelism with a master-slave configuration based on both multi-threading and message passing interface (MPI). This framework is designed and implemented to easily interface similar application commonly adopted in scientific research, for example in Monte Carlo simulations. The diagonalization uses multi-core and GPU hardware interfacing with MAGMA, PLASMA or MKL libraries. The access to the libraries is modular to guarantee portability, maintainability and the extension in a near future. The second project is the development of a Kalman Filter, including the porting on GPU architectures and autovectorization for online LHCb triggers. The developed codes provide information about the viability and advantages for the application of GPU technologies in the first triggering step for Large Hadron Collider beauty experiment (LHCb). The optimisation introduced on both codes for CPU and GPU delivered a relevant speedup on the Kalman Filter. The two GPU versions in CUDA R and OpenCLTM have similar performances and are adequate to be considered in the upgrade and in the corresponding implementations of the Gaudi framework. In both projects we implement optimisation techniques in the CPU code. This report presents extensive benchmark analyses of the correctness and of the performances for both projects

Near Deterministic Signal Processing Using GPU, DPDK, and MKL

RÉSUMÉ En radio défnie par logiciel, le traitement numcrique du signal impose le traitement en temps réel des donnés et des signaux. En outre, dans le développement de systèmes de communication sans fil basées sur la norme dite Long Term Evolution (LTE), le temps réel et une faible latence des processus de calcul sont essentiels pour obtenir une bonne experience utilisateur. De plus, la latence des calculs est une clé essentielle dans le traitement LTE, nous voulons explorer si des unités de traitement graphique (GPU) peuvent être utilisées pour accélérer le traitement LTE. Dans ce but, nous explorons la technologie GPU de NVIDIA en utilisant le modéle de programmation Compute Unified Device Architecture (CUDA) pour réduire le temps de calcul associé au traitement LTE. Nous présentons briévement l'architecture CUDA et le traitement paralléle avec GPU sous Matlab, puis nous comparons les temps de calculs avec Matlab et CUDA. Nous concluons que CUDA et Matlab accélérent le temps de calcul des fonctions qui sont basées sur des algorithmes de traitement en paralléle et qui ont le même type de données, mais que cette accélération est fortement variable en fonction de l'algorithme implanté. Intel a proposé une boite à outil pour le développement de plan de données (DPDK) pour faciliter le développement des logiciels de haute performance pour le traitement des fonctionnalités de télécommunication. Dans ce projet, nous explorons son utilisation ainsi que celle de l'isolation du système d'exploitation pour réduire la variabilité des temps de calcul des processus de LTE. Plus précisément, nous utilisons DPDK avec la Math Kernel Library (MKL) pour calculer la transformée de Fourier rapide (FFT) associée avec le processus LTE et nous mesurons leur temps de calcul. Nous évaluons quatre cas: 1) code FFT dans le cœur esclave sans isolation du CPU, 2) code FFT dans le cœur esclave avec l'isolation du CPU, 3) code FFT utilisant MKL sans DPDK et 4) code FFT de base. Nous combinons DPDK et MKL pour les cas 1 et 2 et évaluons quel cas est plus déterministe et réduit le plus la latence des processus LTE. Nous montrons que le temps de calcul moyen pour la FFT de base est environ 100 fois plus grand alors que l'écart-type est environ 20 fois plus élevé. On constate que MKL offre d'excellentes performances, mais comme il n'est pas extensible par lui-même dans le domaine infonuagique, le combiner avec DPDK est une alternative très prometteuse. DPDK permet d'améliorer la performance, la gestion de la mémoire et rend MKL évolutif.----------ABSTRACT In software defined radio, digital signal processing requires strict real time processing of data and signals. Specifically, in the development of the Long Term Evolution (LTE) standard, real time and low latency of computation processes are essential to obtain good user experience. As low latency computation is critical in real time processing of LTE, we explore the possibility of using Graphics Processing Units (GPUs) to accelerate its functions. As the first contribution of this thesis, we adopt NVIDIA GPU technology using the Compute Unified Device Architecture (CUDA) programming model in order to reduce the computation times of LTE. Furthermore, we investigate the efficiency of using MATLAB for parallel computing on GPUs. This allows us to evaluate MATLAB and CUDA programming paradigms and provide a comprehensive comparison between them for parallel computing of LTE processes on GPUs. We conclude that CUDA and Matlab accelerate processing of structured basic algorithms but that acceleration is variable and depends which algorithm is involved. Intel has proposed its Data Plane Development Kit (DPDK) as a tool to develop high performance software for processing of telecommunication data. As the second contribution of this thesis, we explore the possibility of using DPDK and isolation of operating system to reduce the variability of the computation times of LTE processes. Specifically, we use DPDK along with the Math Kernel Library (MKL) provided by Intel to calculate Fast Fourier Transforms (FFT) associated with LTE processes and measure their computation times. We study the computation times in different scenarios where FFT calculation is done with and without the isolation of processing units along the use of DPDK. Our experimental analysis shows that when DPDK and MKL are simultaneously used and the processing units are isolated, the resulting processing times of FFT calculation are reduced and have a near-deterministic characteristic. Explicitly, using DPDK and MKL along with the isolation of processing units reduces the mean and standard deviation of processing times for FFT calculation by 100 times and 20 times, respectively. Moreover, we conclude that although MKL reduces the computation time of FFTs, it does not offer a scalable solution but combining it with DPDK is a promising avenue

Image Data Processing System (IDAPS) software documentation, S-056 experiment. Volume 1: System software description

Information for personnel with programming backgrounds to understand and follow the logic of the software which supports the IDAPS system hardware configuration is presented

Leveraging elasticity theory to calculate cell forces: From analytical insights to machine learning

Living cells possess capabilities to detect and respond to mechanical features of their surroundings. In traction force microscopy, the traction of cells on an elastic substrate is made visible by observing substrate deformation as measured by the movement of embedded marker beads. Describing the substrates by means of elasticity theory, we can calculate the adhesive forces, improving our understanding of cellular function and behavior. In this dissertation, I combine analytical solutions with numerical methods and machine learning techniques to improve traction prediction in a range of experimental applications. I describe how to include the normal traction component in regularization-based Fourier approaches, which I apply to experimental data. I compare the dominant strategies for traction reconstruction, the direct method and inverse, regularization-based approaches and find, that the latter are more precise while the former is more stress resilient to noise. I find that a point-force based reconstruction can be used to study the force balance evolution in response to microneedle pulling showing a transition from a dipolar into a monopolar force arrangement. Finally, I show how a conditional invertible neural network not only reconstructs adhesive areas more localized, but also reveals spatial correlations and variations in reliability of traction reconstructions