Energy Consumption Analysis of the Nussinov RNA Folding Implementations

An energy consumption analysis of the Nussinov RNA folding algorithm implementations is discussed in this paper. We consider parallel and cache-efficient Nussinov codes generated automatically by the Traco and PluTo optimizing compilers and the manual implementation known as Transpose (Li et al.). The experimental study presents the times and power consumption of optimized code using the modern Intel i7 processor with 12 threads. We apply the Intel RAPL technique to measure energy on the processor socket, cores, and RAM. The access to the Linux kernel energy events is provided by the perf tool. We analyze the power consumption in terms of the execution times of the Nussinov codes for various RNA sequences lengths and number of threads.

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