All issues

We consider an application of the Message Passing Interface (MPI) technology for parallelization of the program code which solves equation of the linear elasticity theory. The solution of this equation describes the propagation of elastic waves in demormable rigid bodies. The solution of such direct problem of seismic wave propagation is of interest in seismics and geophysics. Our implementation of solver uses grid-characteristic method to make simulations. We consider technique to reduce time of communication between MPI processes during the simulation. This is important when it is necessary to conduct modeling in complex problem formulations, and still maintain the high level of parallelism effectiveness, even when thousands of processes are used. A solution of the problem of effective communication is extremely important when several computational grids with arbirtrary geometry of contacts between them are used in the calculation. The complexity of this task increases if an independent distribution of the grid nodes between processes is allowed. In this paper, a generalized approach is developed for processing contact conditions in terms of nodes reinterpolation from a given section of one grid to a certain area of the second grid. An efficient way of parallelization and establishing effective interprocess communications is proposed. For provided example problems we provide wave fileds and seismograms for both 2D and 3D formulations. It is shown that the algorithm can be realized both on Cartesian and on structured (curvilinear) computational grids. The considered statements demonstrate the possibility of carrying out calculations taking into account the surface topographies and curvilinear geometry of curvilinear contacts between the geological layers. Application of curvilinear grids allows to obtain more accurate results than when calculating only using Cartesian grids. The resulting parallelization efficiency is almost 100% up to 4096 processes (we used 128 processes as a basis to find efficiency). With number of processes larger than 4096, an expected gradual decrease in efficiency is observed. The rate of decline is not great, so at 16384 processes the parallelization efficiency remains at 80%.

The mathematical model, finite-difference schemes and algorithms for computation of transient thermoand hydrodynamic processes involved in commissioning the unified system including the oil producing well, electrical submersible pump and fractured-porous reservoir with bottom water are developed. These models are implemented in the computer package to simulate transient processes with simultaneous visualization of their results along with computations. An important feature of the package Oil-RWP is its interaction with the special external program GCS which simulates the work of the surface electric control station and data exchange between these two programs. The package Oil-RWP sends telemetry data and current parameters of the operating submersible unit to the program module GCS (direct coupling). The station controller analyzes incoming data and generates the required control parameters for the submersible pump. These parameters are sent to Oil-RWP (feedback). Such an approach allows us to consider the developed software as the “Intellectual Well System”.

Some principal results of the simulations can be briefly presented as follows. The transient time between inaction and quasi-steady operation of the producing well depends on the well stream watering, filtration and capacitive parameters of oil reservoir, physical-chemical properties of phases and technical characteristics of the submersible unit. For the large time solution of the nonstationary equations governing the nonsteady processes is practically identical to the inverse quasi-stationary problem solution with the same initial data. The developed software package is an effective tool for analysis, forecast and optimization of the exploiting parameters of the unified oil-producing complex during its commissioning into the operating regime.

А new cloud center of parallel computing is to be created in the Laboratory of Information Technologies (LIT) of the Joint Institute for Nuclear Research JINR) what is expected to improve significantly the efficiency of numerical calculations and expedite the receipt of new physically meaningful results due to the more rational use of computing resources. To optimize a scheme of parallel computations at a cloud environment it is necessary to test this scheme for various combinations of equipment parameters (processor speed and numbers, throughput оf а communication network etc). As a test problem, the parallel MPI algorithm for calculations of the long Josephson junctions (LDJ) is chosen. Problems of evaluating the impact of abovementioned factors of computing mean on the computing speed of the test problem are solved by simulation with the simulation program SyMSim developed in LIT.

The simulation of the LDJ calculations in the cloud environment enable users without a series of test to find the optimal number of CPUs with a certain type of network run the calculations in a real computer environment. This can save significant computational time in countable resources. The main parameters of the model were obtained from the results of the computational experiment conducted on a special cloud-based testbed. Computational experiments showed that the pure computation time decreases in inverse proportion to the number of processors, but depends significantly on network bandwidth. Comparison of results obtained empirically with the results of simulation showed that the simulation model correctly simulates the parallel calculations performed using the MPI-technology. Besides it confirms our recommendation: for fast calculations of this type it is needed to increase both, — the number of CPUs and the network throughput at the same time. The simulation results allow also to invent an empirical analytical formula expressing the dependence of calculation time by the number of processors for a fixed system configuration. The obtained formula can be applied to other similar studies, but requires additional tests to determine the values of variables.

This article reviews both historical achievements and modern results in the field of Markov Decision Process (MDP) and convex optimization. This review is the first attempt to cover the field of reinforcement learning in Russian in the context of convex optimization. The fundamental Bellman equation and the criteria of optimality of policy — strategies based on it, which make decisions based on the known state of the environment at the moment, are considered. The main iterative algorithms of policy optimization based on the solution of the Bellman equations are also considered. An important section of this article was the consideration of an alternative to the $Q$-learning approach — the method of direct maximization of the agent’s average reward for the chosen strategy from interaction with the environment. Thus, the solution of this convex optimization problem can be represented as a linear programming problem. The paper demonstrates how the convex optimization apparatus is used to solve the problem of Reinforcement Learning (RL). In particular, it is shown how the concept of strong duality allows us to naturally modify the formulation of the RL problem, showing the equivalence between maximizing the agent’s reward and finding his optimal strategy. The paper also discusses the complexity of MDP optimization with respect to the number of state–action–reward triples obtained as a result of interaction with the environment. The optimal limits of the MDP solution complexity are presented in the case of an ergodic process with an infinite horizon, as well as in the case of a non-stationary process with a finite horizon, which can be restarted several times in a row or immediately run in parallel in several threads. The review also reviews the latest results on reducing the gap between the lower and upper estimates of the complexity of MDP optimization with average remuneration (Averaged MDP, AMDP). In conclusion, the real-valued parametrization of agent policy and a class of gradient optimization methods through maximizing the $Q$-function of value are considered. In particular, a special class of MDPs with restrictions on the value of policy (Constrained Markov Decision Process, CMDP) is presented, for which a general direct-dual approach to optimization with strong duality is proposed.

One of problems in developing the gas condensate fields lies on the fact that the condensed hydrocarbons in the gas-bearing layer can get stuck in the pores of the formation and hence cannot be extracted. In this regard, research is underway to increase the recoverability of hydrocarbons in such fields. This research includes a wide range of studies on mathematical simulations of the passage of gas condensate mixtures through a porous medium under various conditions.

In the present work, within the classical approach based on the Darcy law and the law of continuity of flows, we formulate an initial-boundary value problem for a system of nonlinear differential equations that describes a depletion of a multicomponent gas-condensate mixture in porous reservoir. A computational scheme is developed on the basis of the finite-difference approximation and the fourth order Runge .Kutta method. The scheme can be used for simulations both in the spatially one-dimensional case, corresponding to the conditions of the laboratory experiment, and in the two-dimensional case, when it comes to modeling a flat gas-bearing formation with circular symmetry.

The computer implementation is based on the combination of C++ and Maple tools, using the MPI parallel programming technique to speed up the calculations. The calculations were performed on the HybriLIT cluster of the Multifunctional Information and Computing Complex of the Laboratory of Information Technologies of the Joint Institute for Nuclear Research.

Numerical results are compared with the experimental data on the pressure dependence of output of a ninecomponent hydrocarbon mixture obtained at a laboratory facility (VNIIGAZ, Ukhta). The calculations were performed for two types of porous filler in the laboratory model of the formation: terrigenous filler at 25 .„R and carbonate one at 60 .„R. It is shown that the approach developed ensures an agreement of the numerical results with experimental data. By fitting of numerical results to experimental data on the depletion of the laboratory reservoir, we obtained the values of the parameters that determine the inter-phase transition coefficient for the simulated system. Using the same parameters, a computer simulation of the depletion of a thin gas-bearing layer in the circular symmetry approximation was carried out.

This paper targets programmers and developers interested in utilizing parallel programming techniques to enhance application performance. The Oracle Solaris Studio software provides state-of-the-art optimizing and parallelizing compilers for C, C++ and Fortran, an advanced debugger, and optimized mathematical and performance libraries. Also included are an extremely powerful performance analysis tool for profiling serial and parallel applications, a thread analysis tool to detect data races and deadlock in memory parallel programs, and an Integrated Development Environment (IDE). The Oracle Message Passing Toolkit software provides the high-performance MPI libraries and associated run-time environment needed for message passing applications that can run on a single system or across multiple compute systems connected with high performance networking, including Gigabit Ethernet, 10 Gigabit Ethernet, InfiniBand and Myrinet. Examples of OpenMP and MPI are provided throughout the paper, including their usage via the Oracle Solaris Studio and Oracle Message Passing Toolkit products for development and deployment of both serial and parallel applications on SPARC and x86/x64 based systems. Throughout this paper it is demonstrated how to develop and deploy an application parallelized with OpenMP and/or MPI.

Radiopharmaceuticals with iodine radioisotopes are now widely used in imaging and non-imaging methods of nuclear medicine. When evaluating the results of radionuclide studies of the structural and functional state of organs and tissues, parallel modeling of the kinetics of radiopharmaceuticals in the body plays an important role. The complexity of such modeling lies in two opposite aspects. On the one hand, excessive simplification of the anatomical and physiological characteristics of the organism when splitting it to the compartments that may result in the loss or distortion of important clinical diagnosis information, on the other – excessive, taking into account all possible interdependencies of the functioning of the organs and systems that, on the contrary, will lead to excess amount of absolutely useless for clinical interpretation of the data or the mathematical model becomes even more intractable. Our work develops a unified approach to the construction of mathematical models of the kinetics of radiopharmaceuticals with iodine isotopes in the human body during diagnostic and therapeutic procedures of nuclear medicine. Based on this approach, three- and four-compartment pharmacokinetic models were developed and corresponding calculation programs were created in the C⁺⁺ programming language for processing and evaluating the results of radionuclide diagnostics and therapy. Various methods for identifying model parameters based on quantitative data from radionuclide studies of the functional state of vital organs are proposed. The results of pharmacokinetic modeling for radionuclide diagnostics of the liver, kidney, and thyroid using iodine-containing radiopharmaceuticals are presented and analyzed. Using clinical and diagnostic data, individual pharmacokinetic parameters of transport of different radiopharmaceuticals in the body (transport constants, half-life periods, maximum activity in the organ and the time of its achievement) were determined. It is shown that the pharmacokinetic characteristics for each patient are strictly individual and cannot be described by averaged kinetic parameters. Within the framework of three pharmacokinetic models, “Activity–time” relationships were obtained and analyzed for different organs and tissues, including for tissues in which the activity of a radiopharmaceutical is impossible or difficult to measure by clinical methods. Also discussed are the features and the results of simulation and dosimetric planning of radioiodine therapy of the thyroid gland. It is shown that the values of absorbed radiation doses are very sensitive to the kinetic parameters of the compartment model. Therefore, special attention should be paid to obtaining accurate quantitative data from ultrasound and thyroid radiometry and identifying simulation parameters based on them. The work is based on the principles and methods of pharmacokinetics. For the numerical solution of systems of differential equations of the pharmacokinetic models we used Runge–Kutta methods and Rosenbrock method. The Hooke–Jeeves method was used to find the minimum of a function of several variables when identifying modeling parameters.

This work is devoted to molecular dynamic modeling of the thermal impact processes on the metal sample consisting of nickel atoms. For the solution of this problem, a continuous mathematical model on the basis of the classical Newton mechanics equations has been used; a numerical method based on the Verlet scheme has been chosen; a parallel algorithm has been offered, and its realization within the MPI and OpenMP technologies has been executed. By means of the developed parallel program, the investigation of thermodynamic equilibrium of nickel atoms’ system under the conditions of heating a sample to desired temperature has been executed. In numerical experiments both optimum parameters of calculation procedure and physical parameters of analyzed process have been defined. The obtained numerical results are well corresponding to known theoretical and experimental data.

The paper presents a software system aimed at finding best (in some sense) parameters of an algorithm. The system handles both discrete and continuous parameters and employs massive parallelism offered by public clouds. The paper presents an overview of the system, a method to measure algorithm's performance in the cloud and numerical results of system's use on several problem sets.