Many-Core CPUs Can Deliver Scalable Performance to Stochastic Simulations of Large-Scale Biochemical Reaction Networks

Stochastic simulation of large-scale biochemical reaction networks is becoming essential for Systems Biology. It enables the in-silico investigation of complex biological system dynamics under different conditions and intervention strategies, while also taking into account the inherent "biological noise" especially present in the low species count regime. It is however a great computational challenge since in practice we need to execute many repetitions of a complex simulation model to assess the average and extreme cases behavior of the dynamical system it represents. The problem's work scales quickly, with the number of repetitions required and the number of reactions in the bio-model. The worst case scenario s when there is a need to run thousands of repetitions of a complex model with thousands of reactions. We have developed a stochastic simulation software framework for many- and multi-core CPUs. It is evaluated using Intel's experimental many-cores Single-chip Cloud Computer (SCC) CPU and the latest generation consumer grade Core i7 multi-core Intel CPU, when running Gillespie's First Reaction Method exact stochastic simulation algorithm. It is shown that emerging many-core NoC processors can provide scalable performance achieving linear speedup as simulation work scales in both dimensions

Harnessing Performance Variability in Embedded and High-performance Many/Multi-core Platforms

This book describes the state-of-the art of industrial and academic research in the architectural design of heterogeneous, multi/many-core processors. The authors describe methods and tools to enable next-generation embedded and high-performance heterogeneous processors to confront cost-effectively the inevitable variations by providing Dependable-Performance: correct functionality and timing guarantees throughout the expected lifetime of a platform under thermal, power, and energy constraints. Various aspects of the reliability problem are discussed, at both the circuit and architecture level, the intelligent selection of knobs and monitors in multicore platforms, and systematic design methodologies. The authors demonstrate how new techniques have been applied in real case studies from different applications domain and report on results and conclusions of those experiments. Enables readers to develop performance-dependable heterogeneous multi/many-core architectures Describes system software designs that support high performance dependability requirements Discusses and analyzes low level methodologies to tradeoff conflicting metrics, i.e. power, performance, reliability and thermal management Includes new application design guidelines to improve performance dependabilit

The Unexpected Efficiency of Bin Packing Algorithms for Dynamic Storage Allocation in the Wild: An Intellectual Abstract

Recent work has shown that viewing allocators as black-box 2DBP solvers bears meaning. For instance, there exists a 2DBP-based fragmentation metric which often correlates monotonically with maximum resident set size (RSS). Given the field's indeterminacy with respect to fragmentation definitions, as well as the immense value of physical memory savings, we are motivated to set allocator-generated placements against their 2DBP-devised, makespan-optimizing counterparts. Of course, allocators must operate online while 2DBP algorithms work on complete request traces; but since both sides optimize criteria related to minimizing memory wastage, the idea of studying their relationship preserves its intellectual--and practical--interest. Unfortunately no implementations of 2DBP algorithms for DSA are available. This paper presents a first, though partial, implementation of the state-of-the-art. We validate its functionality by comparing its outputs' makespan to the theoretical upper bound provided by the original authors. Along the way, we identify and document key details to assist analogous future efforts. Our experiments comprise 4 modern allocators and 8 real application workloads. We make several notable observations on our empirical evidence: in terms of makespan, allocators outperform Robson's worst-case lower bound $93.75\%$ of the time. In $87.5\%$ of cases, GNU's \texttt{malloc} implementation demonstrates equivalent or superior performance to the 2DBP state-of-the-art, despite the second operating offline. Most surprisingly, the 2DBP algorithm proves competent in terms of fragmentation, producing up to $2.46$x better solutions. Future research can leverage such insights towards memory-targeting optimizations.Comment: 13 pages, 10 figures, 3 tables. To appear in ISMM '2

Adjacent LSTM-Based Page Scheduling for Hybrid DRAM/NVM Memory Systems

Recent advances in memory technologies have led to the rapid growth of hybrid systems that combine traditional DRAM and Non Volatile Memory (NVM) technologies, as the latter provide lower cost per byte, low leakage power and larger capacities than DRAM, while they can guarantee comparable access latency. Such kind of heterogeneous memory systems impose new challenges in terms of page placement and migration among the alternative technologies of the heterogeneous memory system. In this paper, we present a novel approach for efficient page placement on heterogeneous DRAM/NVM systems. We design an adjacent LSTM-based approach for page placement, which strongly relies on page accesses prediction, while sharing knowledge among pages with behavioral similarity. The proposed approach leads up to 65.5% optimized performance compared to existing approaches, while achieving near-optimal results and saving 20.2% energy consumption on average. Moreover, we propose a new page replacement policy, namely clustered-LRU, achieving up to 8.1% optimized performance, compared to the default Least Recently Used (LRU) policy

Resource Aware GPU Scheduling in Kubernetes Infrastructure

Nowadays, there is an ever-increasing number of artificial intelligence inference workloads pushed and executed on the cloud. To effectively serve and manage the computational demands, data center operators have provisioned their infrastructures with accelerators. Specifically for GPUs, support for efficient management lacks, as state-of-the-art schedulers and orchestrators, threat GPUs only as typical compute resources ignoring their unique characteristics and application properties. This phenomenon combined with the GPU over-provisioning problem leads to severe resource under-utilization. Even though prior work has addressed this problem by colocating applications into a single accelerator device, its resource agnostic nature does not manage to face the resource under-utilization and quality of service violations especially for latency critical applications. In this paper, we design a resource aware GPU scheduling framework, able to efficiently colocate applications on the same GPU accelerator card. We integrate our solution with Kubernetes, one of the most widely used cloud orchestration frameworks. We show that our scheduler can achieve 58.8% lower end-to-end job execution time 99%-ile, while delivering 52.5% higher GPU memory usage, 105.9% higher GPU utilization percentage on average and 44.4% lower energy consumption on average, compared to the state-of-the-art schedulers, for a variety of ML representative workloads

EDEN: A high-performance, general-purpose, NeuroML-based neural simulator

Modern neuroscience employs in silico experimentation on ever-increasing and more detailed neural networks. The high modelling detail goes hand in hand with the need for high model reproducibility, reusability and transparency. Besides, the size of the models and the long timescales under study mandate the use of a simulation system with high computational performance, so as to provide an acceptable time to result. In this work, we present EDEN (Extensible Dynamics Engine for Networks), a new general-purpose, NeuroML-based neural simulator that achieves both high model flexibility and high computational performance, through an innovative model-analysis and code-generation technique. The simulator runs NeuroML v2 models directly, eliminating the need for users to learn yet another simulator-specific, model-specification language. EDEN's functional correctness and computational performance were assessed through NeuroML models available on the NeuroML-DB and Open Source Brain model repositories. In qualitative experiments, the results produced by EDEN were verified against the established NEURON simulator, for a wide range of models. At the same time, computational-performance benchmarks reveal that EDEN runs up to 2 orders-of-magnitude faster than NEURON on a typical desktop computer, and does so without additional effort from the user. Finally, and without added user effort, EDEN has been built from scratch to scale seamlessly over multiple CPUs and across computer clusters, when available.Comment: 29 pages, 9 figure

BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling the Inferior- Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal- network dimensions but also different network-connectivity circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table

Co-Design of Approximate Multilayer Perceptron for Ultra-Resource Constrained Printed Circuits

Printed Electronics (PE) exhibits on-demand, extremely low-cost hardware due to its additive manufacturing process, enabling machine learning (ML) applications for domains that feature ultra-low cost, conformity, and non-toxicity requirements that silicon-based systems cannot deliver. Nevertheless, large feature sizes in PE prohibit the realization of complex printed ML circuits. In this work, we present, for the first time, an automated printed-aware software/hardware co-design framework that exploits approximate computing principles to enable ultra-resource constrained printed multilayer perceptrons (MLPs). Our evaluation demonstrates that, compared to the state-of-the-art baseline, our circuits feature on average 6x (5.7x) lower area (power) and less than 1% accuracy loss