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Register a new userModern Multicore CPUs are not Energy Proportional: Opportunity for Bi-objective Optimization for Performance and Energy
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Added by
Alexey Lastovetsky
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Energy proportionality is the key design goal followed by architects of modern multicore CPUs. One of its implications is that optimization of an application for performance will also optimize it for energy. In this work, we show that energy proportionality does not hold true for multicore CPUs. This finding creates the opportunity for bi-objective optimization of applications for performance and energy. We propose and study the first application-level method for bi-objective optimization of multithreaded data-parallel applications for performance and energy. The method uses two decision variables, the number of identical multithreaded kernels (threadgroups) executing the application and the number of threads in each threadgroup, with the workload always partitioned equally between the threadgroups. We experimentally demonstrate the efficiency of the method using four highly optimized multithreaded data-parallel applications, 2D fast Fourier transform based on FFTW and Intel MKL, and dense matrix-matrix multiplication using OpenBLAS and Intel MKL. Four modern multicore CPUs are used in the experiments. The experiments show that optimization for performance alone results in the increase in dynamic energy consumption by up to 89% and optimization for dynamic energy alone degrades the performance by up to 49%. By solving the bi-objective optimization problem, the method determines up to 11 globally Pareto-optimal solutions. Finally, we propose a qualitative dynamic energy model employing performance monitoring counters as parameters, which we use to explain the discovered energy nonproportionality and the Pareto-optimal solutions determined by our method. The model shows that the energy nonproportionality in our case is due to the activity of the data translation lookaside buffer (dTLB), which is disproportionately energy expensive.
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Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost generation of data underscores the need for commensurate acceleration in downstream computational analysis of the sequencing data. A fundamental step in downstream analysis is mapping of the reads to a long reference DNA sequence, such as a reference human genome. Sequence mapping is a compute-intensive step that accounts for more than 30% of the overall time of the GATK workflow. BWA-MEM is one of the most widely used tools for sequence mapping and has tens of thousands of users. In this work, we focus on accelerating BWA-MEM through an efficient architecture aware implementation, while maintaining identical output. The volume of data requires distributed computing environment, usually deploying multicore processors. Since the application can be easily parallelized for distributed memory systems, we focus on performance improvements on a single socket multicore processor. BWA-MEM run time is dominated by three kernels, collectively responsible for more than 85% of the overall compute time. We improved the performance of these kernels by 1) improving cache reuse, 2) simplifying the algorithms, 3) replacing small fragmented memory allocations with a few large contiguous ones, 4) software prefetching, and 5) SIMD utilization wherever applicable - and massive reorganization of the source code enabling these improvements. As a result, we achieved nearly 2x, 183x, and 8x speedups on the three kernels, respectively, resulting in up to 3.5x and 2.4x speedups on end-to-end compute time over the original BWA-MEM on single thread and single socket of Intel Xeon Skylake processor. To the best of our knowledge, this is the highest reported speedup over BWA-MEM.
Homomorphic encryption (HE) allows direct computations on encrypted data. Despite numerous research efforts, the practicality of HE schemes remains to be demonstrated. In this regard, the enormous size of ciphertexts involved in HE computations degrades computational efficiency. Near-memory Processing (NMP) and Computing-in-memory (CiM) - paradigms where computation is done within the memory boundaries - represent architectural solutions for reducing latency and energy associated with data transfers in data-intensive applications such as HE. This paper introduces CiM-HE, a Computing-in-memory (CiM) architecture that can support operations for the B/FV scheme, a somewhat homomorphic encryption scheme for general computation. CiM-HE hardware consists of customized peripherals such as sense amplifiers, adders, bit-shifters, and sequencing circuits. The peripherals are based on CMOS technology, and could support computations with memory cells of different technologies. Circuit-level simulations are used to evaluate our CiM-HE framework assuming a 6T-SRAM memory. We compare our CiM-HE implementation against (i) two optimized CPU HE implementations, and (ii) an FPGA-based HE accelerator implementation. When compared to a CPU solution, CiM-HE obtains speedups between 4.6x and 9.1x, and energy savings between 266.4x and 532.8x for homomorphic multiplications (the most expensive HE operation). Also, a set of four end-to-end tasks, i.e., mean, variance, linear regression, and inference are up to 1.1x, 7.7x, 7.1x, and 7.5x faster (and 301.1x, 404.6x, 532.3x, and 532.8x more energy efficient). Compared to CPU-based HE in a previous work, CiM-HE obtain 14.3x speed-up and >2600x energy savings. Finally, our design offers 2.2x speed-up with 88.1x energy savings compared to a state-of-the-art FPGA-based accelerator.
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