CD
C. I. De Zeeuw
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The cloud has become a powerful and useful environment for the deployment of High-Performance Computing (HPC) applications, but the large number of available instance types poses a challenge in selecting the optimal platform. Users often do not have the time or knowledge necessary to make an optimal choice. Recommender systems have been developed for this purpose but current state-of-the-art systems either require large amounts of training data, or require running the application multiple times; this is costly. In this work, we propose Oikonomos-II, a resource-recommendation system based on reinforcement learning for HPC applications in the cloud. Oikonomos-II models the relationship between different input parameters, instance types, and execution times. The system does not require any preexisting training data or repeated job executions, as it gathers its own training data opportunistically using user-submitted jobs, employing a variant of the Neural-LinUCB algorithm. When deployed on a mix of HPC applications, Oikonomos-II quickly converged towards an optimal policy. The system eliminates the need for preexisting training data or auxiliary runs, providing an economical, general-purpose, resource-recommendation system for cloud HPC.
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The cloud has become a powerful and useful environment for the deployment of High-Performance Computing (HPC) applications, but the large number of available instance types poses a challenge in selecting the optimal platform. Users often do not have the time or knowledge necessary to make an optimal choice. Recommender systems have been developed for this purpose but current state-of-the-art systems either require large amounts of training data, or require running the application multiple times; this is costly. In this work, we propose Oikonomos-II, a resource-recommendation system based on reinforcement learning for HPC applications in the cloud. Oikonomos-II models the relationship between different input parameters, instance types, and execution times. The system does not require any preexisting training data or repeated job executions, as it gathers its own training data opportunistically using user-submitted jobs, employing a variant of the Neural-LinUCB algorithm. When deployed on a mix of HPC applications, Oikonomos-II quickly converged towards an optimal policy. The system eliminates the need for preexisting training data or auxiliary runs, providing an economical, general-purpose, resource-recommendation system for cloud HPC.
Journal article
(2019)
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G. Chatzikonstantis, H. Sidiropoulos, C. Strydis, M. Negrello, G. Smaragdos, C. I. De Zeeuw, D. J. Soudris
Mathematical models with varying degrees of complexity have been proposed and simulated in an attempt to represent the intricate mechanisms of the human neuron. One of the most biochemically realistic and analytical models, based on the Hodgkin–Huxley (HH) model, has been selected for study in this paper. In order to satisfy the model's computational demands, we present a simulator implemented on Intel Xeon Phi Knights Landing manycore processors. This high-performance platform features an x86-based architecture, allowing our implementation to be portable to other common manycore processing machines. This is reinforced by the fact that Phi adopts the popular OpenMP and MPI programming models. The simulator performance is evaluated when calculating neuronal networks of varying sizes, density and network connectivity maps. The evaluation leads to an analysis of the neuronal synaptic patterns and their impact on performance when tackling this type of workload on a multinode system. It will be shown that the simulator can calculate 100 ms of simulated brain activity for up to 2 millions of biophysically-accurate neurons and 2 billion neuronal synapses within one minute of execution time. This level of performance renders the application an efficient solution for large-scale detailed model simulation.
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Mathematical models with varying degrees of complexity have been proposed and simulated in an attempt to represent the intricate mechanisms of the human neuron. One of the most biochemically realistic and analytical models, based on the Hodgkin–Huxley (HH) model, has been selected for study in this paper. In order to satisfy the model's computational demands, we present a simulator implemented on Intel Xeon Phi Knights Landing manycore processors. This high-performance platform features an x86-based architecture, allowing our implementation to be portable to other common manycore processing machines. This is reinforced by the fact that Phi adopts the popular OpenMP and MPI programming models. The simulator performance is evaluated when calculating neuronal networks of varying sizes, density and network connectivity maps. The evaluation leads to an analysis of the neuronal synaptic patterns and their impact on performance when tackling this type of workload on a multinode system. It will be shown that the simulator can calculate 100 ms of simulated brain activity for up to 2 millions of biophysically-accurate neurons and 2 billion neuronal synapses within one minute of execution time. This level of performance renders the application an efficient solution for large-scale detailed model simulation.
Conference paper
(2018)
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S. K.E. Koekkoek, S. Soloukeytbalvandany, B. S. Generowicz, W. S. Vanhoogstraten, N. L. Deoude, H. J. Boele, C. Strydis, G. Leus, C. I. De Zeeuw, More Authors...
Functional ultrasound (fUS) is a relatively new imaging modality to study the brain with a high spatiotemporal resolution and a wide field-of-view. In fUS detailed images of cerebral blood flow and volume are used to derive functional information, as changes in local flow and/or volume may reflect neuronal activation through neurovascular coupling. Most fUS studies so far have been performed in rats. Translating fUS to mice, which is a favorable animal model for neuroscience, pleads for a higher spatial resolution than what has been reported so far. As a consequence the temporal sampling of the blood flow should also be increased in order to adequately capture the wide range in blood velocities, as the Doppler shifts are inversely proportional to the spatial resolution. Here we present our first detailed images of the mouse brain vasculature at high spatiotemporal resolution. In addition we show some early experimental work on tracking brain activity upon local electrical stimulation.
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Functional ultrasound (fUS) is a relatively new imaging modality to study the brain with a high spatiotemporal resolution and a wide field-of-view. In fUS detailed images of cerebral blood flow and volume are used to derive functional information, as changes in local flow and/or volume may reflect neuronal activation through neurovascular coupling. Most fUS studies so far have been performed in rats. Translating fUS to mice, which is a favorable animal model for neuroscience, pleads for a higher spatial resolution than what has been reported so far. As a consequence the temporal sampling of the blood flow should also be increased in order to adequately capture the wide range in blood velocities, as the Doppler shifts are inversely proportional to the spatial resolution. Here we present our first detailed images of the mouse brain vasculature at high spatiotemporal resolution. In addition we show some early experimental work on tracking brain activity upon local electrical stimulation.