We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size.

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The paper presents state of the art of energy-aware high-performance computing (HPC), in particular identification and classification of approaches by system and device types, optimization metrics, and energy/power control methods. System types include single device, clusters, grids, and clouds while considered device types include CPUs, GPUs, multiprocessor, and hybrid systems. Optimization goals include various combinations of metrics such as execution time, energy consumption, and temperature with consideration of imposed power limits. Control methods include scheduling, DVFS/DFS/DCT, power capping with programmatic APIs such as Intel RAPL, NVIDIA NVML, as well as application optimizations, and hybrid methods. We discuss tools and APIs for energy/power management as well as tools and environments for prediction and/or simulation of energy/power consumption in modern HPC systems. Finally, programming examples, i.e., applications and benchmarks used in particular works are discussed. Based on our review, we identified a set of open areas and important up-to-date problems concerning methods and tools for modern HPC systems allowing energy-aware processing.

Two new algorithms for the all-reduce operation, optimized for imbalanced process arrival patterns (PAPs) are presented: (i) sorted linear tree (SLT), (ii) pre-reduced ring (PRR) as well as a new way of on-line PAP detection, including process arrival time (PAT) estimations and their distribution between cooperating processes was introduced. The idea, pseudo-code, implementation details, benchmark for performance evaluation and a real case example for machine learning are provided. The results of the experiments were described and analyzed, showing that the proposed solution has high scalability and improved performance in comparison with the usually used ring and Rabenseifner algorithms.Collective communication [2] is frequently used by the programmers and designers of parallel programs, especially in high performance computing (HPC) applications related to scientific simulations and data analysis, including machine learning calculations. Usually, collective operations, e.g. implemented in MPI [6], are based on algorithms optimized for the simultaneous entering of all participants into the operation, i.e. they do not take into consideration possible differences in process arrival times (PATs), thus, in real environment, where such imbalances are ubiquitous, they can have significant performance

The recently deployed supercomputer Tryton, located