Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations
In this paper, we describe the Desmos supercomputer that consists of 32 hybrid nodes connected by a low-latency highbandwidth Angara interconnect with torus topology. This supercomputer is aimed at cost-effective classical molecular dynamics calculations. Desmos serves as a test bed for the Angara interconnect that supports 3D and 4D torus network topologies, and verifies its ability to unite massively-parallel programming systems speeding-up effectively MPI-based applications. We describe the Angara interconnect presenting typical MPI benchmarks. Desmos benchmarks results for GROMACS, LAMMPS, VASP and CP2K are compared with the data for other HPC systems. Also, we consider the job scheduling statistics for several months of Desmos deployment.
In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energy when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.
In this paper, we present an approach to scalable co-scheduling in distributed computing for complex sets of interrelated tasks(jobs). The scalability means that schedules are formed for job models with various levels of task granularity, data replication policies, and processor resource and memory can be upgraded. The necessary of guaranteed job execution at the required quality of service causes taking into account the distributed environment dynamics, namely, changes in the number of jobs for servicing, volumes of computations, possible failures of processor nodes, etc. At a consequence, in the general case, a set of versions of scheduling, or a strategy, is required instead of a single version. We propose a callable model of scheduling based on multicriteria strategies. The choice of the specific schedule depends on the load level of the resource dynamics and is formed as a resource query which is sent to a local batch-job management system.
We simulate model for evolution of local virtual time profile in conservative parallel discrete event the simulation (PDES) algorithm with long-range communication links. The main findings of simulation are that i) growth exponent depends logarithmically on the concentration p of long-range links; ii) utilisation of processing elements time decreases slowly with p. Thismeans that the conservative PDES with long-range communication links is fully scalable.
Population annealing is a novel Monte Carlo algorithm designed for simulations of systems of statistical mechanics with rugged free-energy landscapes. We discuss a realization of the algorithm for the use on a hybrid computing architecture combining CPUs and GPGPUs. The particular advantage of this approach is that it is fully scalable up to many thousands of threads. We report on applications of the developed realization to several interesting problems, in particular the Ising and Potts models, and review applications of population annealing to further systems.
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.
Generalized error-locating codes are discussed. An algorithm for calculation of the upper bound of the probability of erroneous decoding for known code parameters and the input error probability is given. Based on this algorithm, an algorithm for selection of the code parameters for a specified design and input and output error probabilities is constructed. The lower bound of the probability of erroneous decoding is given. Examples of the dependence of the probability of erroneous decoding on the input error probability are given and the behavior of the obtained curves is explained.
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
Let G be a semisimple algebraic group whose decomposition into the product of simple components does not contain simple groups of type A, and P⊆G be a parabolic subgroup. Extending the results of Popov , we enumerate all triples (G, P, n) such that (a) there exists an open G-orbit on the multiple flag variety G/P × G/P × . . . × G/P (n factors), (b) the number of G-orbits on the multiple flag variety is finite.
I give the explicit formula for the (set-theoretical) system of Resultants of m+1 homogeneous polynomials in n+1 variables