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.

The paper presents a complete solution for modeling scientific and business workflow applications, static and just-in-time QoS selection of services and workflow execution in a real environment. The workflow application is modeled as an acyclic directed graph where nodes denote tasks and edges denote dependencies between the tasks. The BeesyCluster middleware is used to allow providers to publish services from sequential or parallel applications, from their servers or clusters. Optimization algorithms are proposed to select a capable service for each task so that a global criterion is optimized such as a product of workflow execution time and cost, a linear combination of those or minimization of the time with a cost constraint. The paper presents implementation details of the multithreaded workflow execution engine implemented in JEE. Several tests were performed for three different optimization goals for two business and scientific workflow applications. Finally, the overhead of the solution is presented.

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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.

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