Abstract
Supercomputer applications are usually implemented in the C, C++, and Fortran programming languages using different versions of the Message Passing Interface library. The "T-system" project (OpenTS) studies the issues of automatic dynamic parallelization of programs. In practical terms, the implementation of applications in a mixed (hybrid) style is relevant, when one part of the application is written in the paradigm of automatic dynamic parallelization of programs and does not use any primitives of the MPI library, and the other part of it is written using the Message Passing Interface library. In this case, the library is used, which is a part of the T-system and is called DMPI (Dynamic Message Passing Interface). In this way, it is necessary to evaluate the effectiveness of the MPI implementation available in the T-system. The purpose of this work is to examine the effectiveness of DMPI implementation in the T-system. In a classic MPI application, 0% of the code is implemented using automatic dynamic parallelization of programs and 100% of the code is implemented in the form of a regular Message Passing Interface program. For comparative analysis, at the beginning the code is executed on the standard Message Passing Interface, for which it was originally written, and then it is executed using the DMPI library taken from the developed T-system. Сomparing the effectiveness of the approaches, the performance losses and the prospects for using a hybrid programming style are evaluated. As a result of the conducted experimental studies for different types of computational problems, it was possible to make sure that the efficiency losses are negligible. This allowed to formulate the direction of further work on the T-system and the most promising options for building hybrid applications. Thus, this article presents the results of the comparative tests of LAMMPS application using OpenMPI and using OpenTS DMPI. The test results confirm the effectiveness of the DMPI implementation in the OpenTS parallel programming environment
Highlights
Supercomputer applications are usually implemented in the C, C++, and Fortran programming languages using different versions of the Message Passing Interface library
The implementation of applications in a mixed style is relevant, when one part of the application is written in the paradigm of automatic dynamic parallelization of programs and does not use any primitives of the MPI library, and the other part of it is written using the Message Passing Interface library
In a classic MPI application, 0% of the code is implemented using automatic dynamic parallelization of programs and 100% of the code is implemented in the form of a regular Message Passing Interface program
Summary
Первое слагаемое соответствует потенциалу Бреннера [28] второго поколения (REBO), который часто используется для моделирования взаимодействия между атомами углерода и водорода. Второе слагаемое отвечает за потенциал Леннарда-Джонса [22], который действует на расстояниях от 2 ангстрем до величины радиуса экранирования. 4. Диффузия при использовании метода стохастической вращательной динамики (SRD) для жестких прямоугольных частиц. При использовании метода стохастической вращательной динамики [29] частицы растворителя не взаимодействуют друг с другом, а взаимодействуют с частицами растворенного вещества, которые могут иметь разную форму, например, эллипсоиды, димеры, прямоугольники и т.д. Запускается команда fix srd, которая отрабатывает взаимодействие между наночастицами и частицами растворителя. 1. Демонстрация метода стохастической вращательной динамики (SRD) для жестких прямоугольных частиц в растворителе. Если во входном файле нет команд балансировки, то область симуляции распределяется между узлами с помощью грида (сетки) с равными ячейками С помощью команды balance [35] область симуляции можно перераспределить один раз, например, в начале программы – энергия i-го атома, включая энергию ионизации атома и энергию сродства к электрону, Eijshort – BO-потенциал (Bond order potential) [39],
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