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The Second Russian Supercomputing Days Conference (RuSCDays 2016) was held during September 26–27, 2016, in Moscow, Russia. It was organized by the Supercomputing Consortium of Russian Universities and the Federal Agency for Scientific Organizations. The conference was supported by the Russian Foundation for Basic Research and our respected platinum sponsors (T-Platforms, RSC, Intel, NVIDIA), gold sponsors (IBM, Mellanox, Dell EMC, Hewlett Packard Enterprise), and silver sponsor (NICEVT). The conference was organized in a partnership with the ISC High-Performance conference series and NESUS project. The conference was born in 2015 as a union of several supercomputing events in Russia and quickly became one of the most notable Russian supercomputing meetings. The conference caters to the interests of a wide range of representatives from science, industry, business, education, government, and students – anyone connected to the development or the use of supercomputing technologies. The conference topics cover all aspects of supercomputing technologies: software and hardware design, solving large tasks, application of supercomputing technologies in industry, exaflops computing issues, supercomputing co-design technologies, supercomputing education, and others. All papers submitted to the conference were reviewed by three referees and evaluated for the relevance to the conference topics, scientific contribution, presentation, approbation and related works description. For this proceedings volume, a second review round was performed. The 28 best works were carefully selected to be included in this volume.