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89 results on '"Moskovsky, Alexander"'

1. Evaluation of Intel Memory Drive Technology Performance for Scientific Applications

Author

Mironov, Vladimir, Kudryavtsev, Andrey, Alexeev, Yuri, Moskovsky, Alexander, Kulikov, Igor, and Chernykh, Igor

Subjects
Computer Science - Performance
Abstract

In this paper, we present benchmark data for Intel Memory Drive Technology (IMDT), which is a new generation of Software-defined Memory (SDM) based on Intel ScaleMP collaboration and using 3D XPointTM based Intel Solid-State Drives (SSDs) called Optane. We studied IMDT performance for synthetic benchmarks, scientific kernels, and applications. We chose these benchmarks to represent different patterns for computation and accessing data on disks and memory. To put performance of IMDT in comparison, we used two memory configurations: hybrid IMDT DDR4/Optane and DDR4 only systems. The performance was measured as a percentage of used memory and analyzed in detail. We found that for some applications DDR4/Optane hybrid configuration outperforms DDR4 setup by up to 20%.

Published
2018
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2. Studies on the energy and deep memory behaviour of a cache-oblivious, task-based hyperbolic PDE solver

Author

Charrier, Dominic E., Hazelwood, Benjamin, Tutlyaeva, Ekaterina, Bader, Michael, Dumbser, Michael, Kudryavtsev, Andrey, Moskovsky, Alexander, and Weinzierl, Tobias

Subjects
Computer Science - Mathematical Software
Abstract

We study the performance behaviour of a seismic simulation using the ExaHyPE engine with a specific focus on memory characteristics and energy needs. ExaHyPE combines dynamically adaptive mesh refinement (AMR) with ADER-DG. It is parallelized using tasks, and it is cache efficient. AMR plus ADER-DG yields a task graph which is highly dynamic in nature and comprises both arithmetically expensive tasks and tasks which challenge the memory's latency. The expensive tasks and thus the whole code benefit from AVX vectorization, though we suffer from memory access bursts. A frequency reduction of the chip improves the code's energy-to-solution. Yet, it does not mitigate burst effects. The bursts' latency penalty becomes worse once we add Intel Optane technology, increase the core count significantly, or make individual, computationally heavy tasks fall out of close caches. Thread overbooking to hide away these latency penalties contra-productive with non-inclusive caches as it destroys the cache and vectorization character. In cases where memory-intense and computationally expensive tasks overlap, ExaHyPE's cache-oblivious implementation can exploit deep, non-inclusive, heterogeneous memory effectively, as main memory misses arise infrequently and slow down only few cores. We thus propose that upcoming supercomputing simulation codes with dynamic, inhomogeneous task graphs are actively supported by thread runtimes in intermixing tasks of different compute character, and we propose that future hardware actively allows codes to downclock the cores running particular task types.

Published
2018
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3. An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Author

Mironov, Vladimir, Alexeev, Yuri, Keipert, Kristopher, D'mello, Michael, Moskovsky, Alexander, and Gordon, Mark S.

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, D.1.3, J.2
Abstract

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes., Comment: SC17 conference paper, 12 pages, 7 figures

Published
2017
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4. The Elbrus-4C Based Node as Part of Heterogeneous Cluster for Oil and Gas Processing Researches

Author

Tyutlyaeva, Ekaterina, Odintsov, Igor, Moskovsky, Alexander, Konyukhov, Sergey, Kalyakin, Alexander, Neiman-zade, Murad I., Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Ghosh, Ashish, Series Editor, Voevodin, Vladimir, editor, and Sobolev, Sergey, editor

Published
2019
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5. Performance and Energy Analysis of Nighttime Satellite Image Archive Processing Module

Author

Tyutlyaeva, Ekaterina, Konyukhov, Sergey, Odintsov, Igor, Moskovsky, Alexander, Zhizhin, Mikhail, Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Sokolinsky, Leonid, editor, and Zymbler, Mikhail, editor

Published
2018
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7. The Energy Consumption Analysis for the Multispectral Infrared Satellite Images Processing Algorithm

Author

Tyutlyaeva, Ekaterina, Konyukhov, Sergey, Odintsov, Igor, Moskovsky, Alexander, Barbosa, Simone Diniz Junqueira, Series editor, Chen, Phoebe, Series editor, Filipe, Joaquim, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Yuan, Junsong, Series editor, Zhou, Lizhu, Series editor, Voevodin, Vladimir, editor, and Sobolev, Sergey, editor

Published
2017
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8. The Hardware Configuration Analysis for HPC Processing and Interpretation of the Geological and Geophysical Data

Author

Tyutlyaeva, Ekaterina, Konyukhov, Sergey, Odintsov, Igor, Moskovsky, Alexander, Barbosa, Simone Diniz Junqueira, Series editor, Chen, Phoebe, Series editor, Filipe, Joaquim, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Yuan, Junsong, Series editor, Zhou, Lizhu, Series editor, Sokolinsky, Leonid, editor, and Zymbler, Mikhail, editor

Published
2017
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9. The Elbrus Platform Feasibility Assessment for High-Performance Computations

Author

Tyutlyaeva, Ekaterina, Konyukhov, Sergey, Odintsov, Igor, Moskovsky, Alexander, Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Kotenko, Igor, Series editor, Liu, Ting, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Voevodin, Vladimir, editor, and Sobolev, Sergey, editor

Published
2016
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10. On Quantum Chemistry Code Adaptation for RSC PetaStream Architecture

Author

Mironov, Vladimir, Khrenova, Maria, Moskovsky, Alexander, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Kunkel, Julian M., editor, and Ludwig, Thomas, editor

Published
2015
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12. The Performance Characterization of the RSC PetaStream Module

Author

Semin, Andrey, Druzhinin, Egor, Mironov, Vladimir, Shmelev, Alexey, Moskovsky, Alexander, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Kobsa, Alfred, editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Weikum, Gerhard, editor, Kunkel, Julian Martin, editor, Ludwig, Thomas, editor, and Meuer, Hans Werner, editor

Published
2014
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13. An Initial Approximation to the Resource-Optimal Checkpoint Interval

Author

Tyutlyaeva, Ekaterina, Moskovsky, Alexander, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, and Malyshkin, Victor, editor

Published
2011
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14. Dynamic Resources Management of Virtual Appliances on a Computational Cluster

Author

Moskovsky, Alexander A., Pervin, Artem Y., Walker, Bruce J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, César, Eduardo, editor, Alexander, Michael, editor, Streit, Achim, editor, Träff, Jesper Larsson, editor, Cérin, Christophe, editor, Knüpfer, Andreas, editor, Kranzlmüller, Dieter, editor, and Jha, Shantenu, editor

Published
2009
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15. Variable Reassignment in the T++ Parallel Programming Language

Author

Moskovsky, Alexander, Roganov, Vladimir, Abramov, Sergei, Kuznetsov, Anton, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Malyshkin, Victor, editor

Published
2007
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16. Parallelism Granules Aggregation with the T-System

Author

Moskovsky, Alexander, Roganov, Vladimir, Abramov, Sergei, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Malyshkin, Victor, editor

Published
2007
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17. OpenTS: An Outline of Dynamic Parallelization Approach

Author

Abramov, Sergey, Adamovich, Alexei, Inyukhin, Alexander, Moskovsky, Alexander, Roganov, Vladimir, Shevchuk, Elena, Shevchuk, Yuri, Vodomerov, Alexander, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Malyshkin, Victor, editor

Published
2005
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20. Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers

Author

Mironov, Vladimir, primary, Shchugoreva, Irina A., additional, Artyushenko, Polina V., additional, Morozov, Dmitry, additional, Borbone, Nicola, additional, Oliviero, Giorgia, additional, Zamay, Tatiana N., additional, Moryachkov, Roman V., additional, Kolovskaya, Olga S., additional, Lukyanenko, Kirill A., additional, Song, Yanling, additional, Merkuleva, Iuliia A., additional, Zabluda, Vladimir N., additional, Peters, Georgy, additional, Koroleva, Lyudmila S., additional, Veprintsev, Dmitry V., additional, Glazyrin, Yury E., additional, Volosnikova, Ekaterina A., additional, Belenkaya, Svetlana V., additional, Esina, Tatiana I., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Shanshin, Daniil V., additional, Berlina, Anna N., additional, Komova, Nadezhda S., additional, Svetlichnyi, Valery A., additional, Silnikov, Vladimir N., additional, Shcherbakov, Dmitriy N., additional, Zamay, Galina S., additional, Zamay, Sergey S., additional, Smolyarova, Tatyana, additional, Tikhonova, Elena P., additional, Chen, Kelvin H.‐C., additional, Jeng, U‐Ser, additional, Condorelli, Gerolama, additional, Franciscis, Vittorio, additional, Groenhof, Gerrit, additional, Yang, Chaoyong, additional, Moskovsky, Alexander A., additional, Fedorov, Dmitri G., additional, Tomilin, Felix N., additional, Tan, Weihong, additional, Alexeev, Yuri, additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional

Published
2022
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25. PROFESSİONAL EDUCATİON İN A PANDEMİC

Author

Lezhenina, Svetlana V., primary, Shuvalova, Nadezhda V., additional, Lammert, Ansell, additional, Viktorov, Oleg N., additional, Moscovskaya, Olesya I., additional, Moskovsky, Alexander V., additional, and Yastrebova, Svetlana A., additional

Published
2021
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33. Diatomics-in-ionic-systems and ab initio predictions for the stationary points on potential...

Author

Grigorenko, Bella L., Moskovsky, Alexander A., and Nemukhin, Alexander V.

Subjects
*POTENTIAL energy surfaces, *MICROCLUSTERS, *HYDROGEN fluoride
Abstract

Focuses on the diatomics-in-ionic systems and ab initio predictions for the stationary points on the potential energy surfaces of the hydrogen fluoride clusters. Reliance of the diatomics-in-ionic systems on the balanced treatment of neutral and ionic contributions to the electronic properties of polyatomic species.

Published
1999
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35. An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture.

Author

Mironov, Vladimir, Moskovsky, Alexander, D'Mello, Michael, and Alexeev, Yuri

Subjects
*MOLECULAR structure, *QUANTUM chemistry, *MESSAGE passing (Computer science), *SUPERCOMPUTERS, *HIGH performance processors
Abstract

The Hartree–Fock method in the General Atomic and Molecular Structure System (GAMESS) quantum chemistry package represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals and the building of the Fock matrix. These are the central components of the main self consistent field (SCF) loop, the key hot spot in electronic structure codes. By threading the Message Passing Interface (MPI) ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4× to 6× for large systems) but also achieve a significant ( > 2 ×) reduction in the overall memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel® Xeon Phi™ supercomputer. Scaling numbers are reported on up to 7680 cores on Intel Xeon Phi coprocessors. [ABSTRACT FROM AUTHOR]

Published
2019
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44. Variable Reassignment in the T++ Parallel Programming Language.

Author

Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Malyshkin, Victor, Moskovsky, Alexander, Roganov, Vladimir, Abramov, Sergei, and Kuznetsov, Anton

Abstract

The paper describes the OpenTS parallel programming system that provides the runtime environment for T++ language. T++ is an extension for C++ that adds a set of keywords to C++, allowing smooth transition from sequential to parallel applications. In this context the support of repeated assignments to a variable is an important feature. The paper focused on semantics and implementation of such variables in T++. Applications written in T++ can be run on computational clusters, SMPs and GRIDs, either in Linux or Windows OS. [ABSTRACT FROM AUTHOR]

Published
2007
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45. Parallelism Granules Aggregation with the T-System.

Author

Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Malyshkin, Victor, Moskovsky, Alexander, Roganov, Vladimir, and Abramov, Sergei

Abstract

T-system is a tool for parallel computing developed at the PSI RAS. The most recent implementation is available on both Linux and Windows platforms. The paper is dedicated to one of important T-system aspects — ability to change parallelism granule size at runtime. The technique is available, primarily, for recursive programs, but it's possible to extent it to non-recursive ones as well. In the latter case, we employ C++ template"traits"for program transformation. The technique is shown to reduce overhead incurred by runtime support library dramatically. [ABSTRACT FROM AUTHOR]

Published
2007
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46. OpenTS: An Outline of Dynamic Parallelization Approach.

Author

Malyshkin, Victor, Abramov, Sergey, Adamovich, Alexei, Inyukhin, Alexander, Moskovsky, Alexander, Roganov, Vladimir, Shevchuk, Elena, Shevchuk, Yuri, and Vodomerov, Alexander

Abstract

The paper is dedicated to an open T-system (OpenTS) — a programming system that supports automatic parallelization of computations for high-performance and distributed applications. In this paper, we describe the system architecture and input programming language as well as system's distinctive features. The paper focuses on the achievements of the last two years of development, including support of distributed, meta-cluster computations. [ABSTRACT FROM AUTHOR]

Published
2005
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48. Towards accurate machine learning predictions of properties of the P–O bond cleaving in ATP upon enzymatic hydrolysis.

Author

Polyakov, Igor V., Miroshnichenko, Kirill D., Mulashkina, Tatiana I., Moskovsky, Alexander A., Marchenko, Ekaterina I., and Khrenova, Maria G.

Subjects
*MACHINE learning, *ELECTRON density, *ADENOSINE triphosphate, *MACHINE dynamics, *MOLECULAR dynamics
Abstract

[Display omitted] Molecular dynamic simulations using QM/MM potentials are performed for the enzyme–substrate complex of adenosine triphosphate (ATP) with the motor protein myosin. Machine learning methods are applied to a dataset consisting of the geometry parameters of the active site in the enzyme–substrate complex to predict the Laplacian of electron density at the bond critical point of the P G –O 3B bond being broken in ATP. Using a gradient boosting machine learning model, a mean absolute error of 0.01 a.u. and an R 2 score of 0.99 are achieved, and it is found that the P G –O 3B bond length is the most important feature, contributing 2/3, while other geometry features contribute 1/3. [ABSTRACT FROM AUTHOR]

Published
2024
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49. On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface

Author

Kupchenko, Ilya V., Moskovsky, Alexander A., Nemukhin, Alexander V., and Kolomeisky, Anatoly B.

Abstract

Studies of motion of carborane wheel-like molecules on glassy surfaces provide an important contribution to the practical goal of designing molecular nanoscale transporters called nanocars. In these vehicles, carborane wheels are chemically coupled to chassis allowing these devices to participate in translations over the surface. As a preliminary step toward modeling dynamics of these species, we have investigated interactions of the p-carborane molecule with the hydrated (1010) surface of α-quartz. Quantum calculations with the CP2K package (cp2k.berlioz.de) have been performed for a series of model systems in order to explicitly estimate interaction energies between the carborane wheel and the surface. It was found that 8 kJ/mol for absorption of carborane on the surface provides a reasonable estimate for this interaction. Correspondingly, the four-wheeled vehicle would require at least 32 kJ/mol to activate its diffusion on the glassy surface. The latter value is consistent with experimental estimates of 42 kJ/mol for the activation energy as follows from single-molecule measurements of temperature dependence of the diffusion coefficient. It is argued that the translation of the four-wheeled carborane nanocars might be consistent with both rolling and hopping mechanisms of motion.

Published
2011
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50. Molecular Dynamics of Surface-Moving Thermally Driven Nanocars

Author

V. Akimov, Alexei, V. Nemukhin, Alexander, A. Moskovsky, Alexander, M. Tour, James, and B. Kolomeisky, Anatoly

Abstract

We developed molecular models describing the thermally initiated motion of nanocars, nanosized vehicles composed of two to four spherical fullerene wheels chemically coupled to a planar chassis, on a metal surface. The simulations were aimed at reproducing qualitative features of the experimentally observed migration of nanocars over gold crystals as determined by scanning tunneling microscopy. Coarse-grained-type molecular dynamics simulations were carried out for the species “Trimer” and “Nanotruck”, the simplified versions of the experimentally studied nanomachines. Toward this goal, we developed a version of the rigid body molecular dynamics based on the symplectic quaternion scheme in conjunction with the Nose−Poincare thermostat approach. Interactions between rigid fragments were described by using the corrected CHARMM force field parameters, while several empirical models were introduced for interactions of nanocars with gold crystals. With the single adjusted potential parameter, the computed trajectories are consistent with the qualitative features of the thermally activated migration of the nanocars: the primary pivoting motion of Trimer and the two-dimensional combination of translations and pivoting of Nanotruck. This work presents a first attempt at a theoretical analysis of nanocarsʼ dynamics on a surface by providing a computationally minimalist approach.

Published
2008
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