GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP
Classical molecular dynamics (MD) calculations represent a significant part of the utilization time of high-performance computing systems. As usual, the efficiency of such calculations is based on an interplay of software and hardware that are nowadays moving to hybrid GPU-based technologies. Several well-developed open-source MD codes focused on GPUs differ both in their data management capabilities and in performance. In this work, we analyze the performance of LAMMPS, GROMACS and OpenMM MD packages with different GPU backends on Nvidia Volta and AMD Vega20 GPUs. We consider the efficiency of solving two identical MD models (generic for material science and biomolecular studies) using different software and hardware combinations. We describe our experience in porting the CUDA backend of LAMMPS to ROCm HIP that shows considerable benefits for AMD GPUs comparatively to the OpenCL backend.
We present optimization guidelines and implementations of cryptographic hash functions GOST R 34.11-94 and GOST R 34.11-2012. Results for x86_64 CPUs and NVIDIA CUDA-capable GPUs are provided for our and several other well-known implementations. It is shown that the new standard may be twice as fast as the old one on modern CPUs, but it may be slower on embedded devices and GPUs. The results given for our implementation are the fastest among all the tested implementations on both platforms.
An approach is described to implementation of the Method of Four Russians for reducing the dense matrices over GF(2) to row echelon form using the NVIDIA CUDA platform. Estimates of the algorithm running time and recommendations on choosing the algorithm parameters are given. It is shown that the developed implementation is most effective in comparison with the existing solutions for matrices of a size 2^17 x 2^17.
Energy consumption of hybrid systems is an actual problem of modern high-performance computing. The trade-off between power consumption and performance becomes more and more prominent. In this paper, we discuss the energy and power efficiency of two modern hybrid minicomputers Jetson TK1 and TX1. We use the Empirical Roofline Tool to obtain peak performance data and the molecular dynamics package LAMMPS as an example of a real-world benchmark. Using the precise wattmeter, we measure Jetsons power consumption profiles. The effectiveness of DVFS is examined as well. We determine the optimal GPU and DRAM frequencies that give the minimum energy-to-solution value.
ASYS, the AIPEA School for Young Scientists. ASYS was successfully convened at the Andalusian Institute of Earth Sciences (CSIC-UGR, Granada, Spain) on July 15 and 16, 2017, under the supervision of Dr. Claro Ignacio Sainz Díaz, researcher of this centre, and in close connection to the 16th International Clay Conference in Granada (ICC 2017). Young and not so-young clay scientists actively participated in the ASYS providing a fertile cultural substratum for discussing a third volume, Computational Mineralogy in Clays.
The organization of the chapters in this book follows the didactic approach of the 3rd ASYS. The didactic material, accompanied by an extensive literature, has been collected to form 8 chapters authored by Ignacio Sainz-Díaz (Spain), Andrey Kalinichev (USA), Triq Jamil (Pakistan) and Hendrik Heinz (USA), Alfonso Hernández-Laguna (Spain), Pauline Simonnin, Duo Song, Vitali Alexandrov, Eric J. Bylaska and Kevin Rosso (USA), Sergey V. Churakov and René Schliemann (Switzerland), Edgar Galicia-Andrés, Peter Grančič, Martin. H. Gerzabek, Chris Oostenbrink and Daniel Tunega (Austria), and Ana Borrego-Sánchez and C. Ignacio Sainz-Díaz (both Spain).
Volume 3 covers aspects dealing with Introduction into Computational Mineralogy in Clays (Chapter 1) and Atomistic Modeling of Clays and Related Nanoporous Materials with ClayFF force field (Chapter 2). Chapter 3 introduces Simulations of Clay Minerals with IFF All Atom Models: Advantages, Validation, and Applications and Chapter 4 Fundamentals of Ab Initio calculations. Chapter 5 details Modeling Electron Transfer in Iron-Bearing Phyllosilicate Minerals and Chapter 6 discusses on Ab initio simulations of clay minerals reactivity and thermodynamics. And finally, Chapters 7 and 8 focus on Modeling of interactions in natural and synthetic organoclays as well as on Absorption of Pharmaceutical drugs onto clay minerals surfaces. These book chapters are milestones in a tradition of presenting status reports about Computational Mineralogy in Clays, the first one I remember was given by Kubicki and Bleam as Editors of a CMS workshop about Molecular Modeling of Clays (CMS 1998, Cleveland, Ohio). These chapters should be considered as an opportunity for continuing studies in clay science. Editorial responsibility for this volume was taken by C.Ignacio Sainz-Díaz, Saverio Fiore (Italy) took care as AES Series Editor.
Reiner Dohrmann AIPEA President
Modern Elbrus-4S and Elbrus-8S processors show floating point performance comparable to the popular Intel processors in the field of high-performance computing. Tasks oriented to take advantage of the VLIW architecture show even greater efficiency on Elbrus processors. In this paper the efficiency of the most popular materials science codes in the field of classical molecular dynamics and quantum-mechanical calculations is considered. A comparative analysis of the performance of these codes on Elbrus processor and other modern processors is carried out.
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.
Event logs collected by modern information and technical systems usually contain enough data for automated process models discovery. A variety of algorithms was developed for process models discovery, conformance checking, log to model alignment, comparison of process models, etc., nevertheless a quick analysis of ad-hoc selected parts of a journal still have not get a full-fledged implementation. This paper describes an ROLAP-based method of multidimensional event logs storage for process mining. The result of the analysis of the journal is visualized as directed graph representing the union of all possible event sequences, ranked by their occurrence probability. Our implementation allows the analyst to discover process models for sublogs defined by ad-hoc selection of criteria and value of occurrence probability
Existing approaches suggest that IT strategy should be a reflection of business strategy. However, actually organisations do not often follow business strategy even if it is formally declared. In these conditions, IT strategy can be viewed not as a plan, but as an organisational shared view on the role of information systems. This approach generally reflects only a top-down perspective of IT strategy. So, it can be supplemented by a strategic behaviour pattern (i.e., more or less standard response to a changes that is formed as result of previous experience) to implement bottom-up approach. Two components that can help to establish effective reaction regarding new initiatives in IT are proposed here: model of IT-related decision making, and efficiency measurement metric to estimate maturity of business processes and appropriate IT. Usage of proposed tools is demonstrated in practical cases.